Student Publications

Name Publications
BA. Aksoy

Miller ML, Reznik E, Gauthier NP, Aksoy BA, Korkut A, Gao J, Ciriello G, Schultz N, Sander C, 2015, “Pan-Cancer analysis of mutation hotspots in protein domains,” Cell Syst. 1(3):197-209. doi: 10.1016/j.cels.2015.08.014. Epub 2015 Sep 23. PMID: 27135912 PMCID: PMC4982675

Luna A, Babur Ö, Aksoy BA, Demir E, Sander C, 2016, PaxtoolsR: pathway analysis in R using Pathway Commons,” Bioinformatics 32(8):1262-4. doi:10.1093/bioinformatics/btv733.
PMID: 26685306 PMCID: PMC4824129

Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli EJ, Babur Ö, Bemis DL, Onur Sumer S, Solit DB, Pratilas CA, Sander C, 2015, “Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells,” Elife. Aug 18;4. doi: 10.7554/eLife.04640.PMID: 26284497 PMCID: PMC4539601

Babur Ö, Dogrusoz U, Çakır M, Aksoy BA, Schultz N, Sander C, Demir E. 2014. “Integrating biological pathways and genomic profiles with ChiBE 2.” BMC Genomics. 2014 Aug 3;15:642. doi: 10.1186/1471-2164-15-642. PMCID:PMC4131037

Aksoy BA, Demir E, Babur O, Wang W, Jing X, Schultz N, Sander C., 2014, “Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles,” Bioinformatics 30(14): 2051-2059 doi: 10.1093/bioinformatics/btu164. Epub 2014 Mar 24. PMCID:PMC4080742

Cancer Genome Atlast Research Network (Weinstein JN,…Aksoy BA,…Sander C…,) 2014, “Comprehensive molecular characterization of urothelial bladder carcinoma,” Nature, 507(7492):315-22. PMCID: PMC3962515

Babur Ö, Aksoy BA, Rodchenkov I, Sümer SO, Sander C, Demir E., 2014, “Pattern search in BioPAX models,”Bioinformatics, 30(1):139-40. PMCID: PMC3866551

Cancer Genome Atlas Research Network. (Creighton CJ,…Aksoy BA,…Sander C…,) 2013, “Comprehensive molecular characterization of clear cell renal cell carcinoma,” Nature, 499(7456):43-9. PMCID: PMC3771322

Arbiza L, Gronau I, Aksoy, BA, Hubisz MJ, Gulko B, Keinan A, Siepel A., 2013, “Genome-wide inference of natural selection on human transcription factor binding sites,” Nature Genetics, 45(7):723-9. PMCID: PMC3932982

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N., 2013, “Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal,” Sci Signal, 6(269):pl1.

Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N., 2013, “Using MEMo to discover mutual exclusivity modules in cancer,” Curr Protoc Bioinformatics, Chapter 8:Unit 8.17.

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N., 2012, “The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data,” Cancer Discov., 2(5):401-4. NIHMS384915

Cancer Genome Atlas Research Network (Getz G,…Aksoy B…Sander C…,) 2013, “Integrated genomic characterization of endometrial carcinoma,” Nature, 497(7447):67-73.

Aksoy BA, Gao J, Dresdner G, Wang W, Root A, Jing X, Cerami E, Sander C., 2013, “PiHelper: an open source framework for drug-target and antibody-target data,” Bioinformatics.  15;29(16):2071-2. doi: 10.1093/bioinformatics/btt345. PMCID:PMC3722529

Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sumer OS, Bader GD, Sander C. “Using biological pathway data with paxtools,” PLoS Comput Biol. 2013; 9(9):e1003194. doi: 10.1371/journal.pcbi.1003194. PMCID: PMC3777916.

Cancer Genome Atlas Research Network (Brennan CW,…Aksoy, B…Sander, C.)., 2013, “The somatic genomic landscape of glioblastoma,” Cell. 10;155(2):462-77.

Cancer Genome Atlas Research Network; Genome Characterization Center (Chang, K. …Aksoy, A., …Sander C.) (2013). “The Cancer Genome Atlas Pan-Cancer analysis project,” Nat Genet. 45(10):1113-20. PMID: 24071849.

Cancer Genome Atlas Research Network (Koboldt DC,…Aksoy B…Sander C,…,) 2012, “Comprehensive molecular portraits of human breast tumours,” Nature., 490(7418):61-70. PMCID: PMC3465532

Cancer Genome Atlas Research Network (Hammerman,PS,…Aksoy B,…Sander C,…,) 2012, “Comprehensive genomic characterization of squamous cell lung cancer,” Nature, 489(7417):519-25. PMCID: PMC3466113

Cancer Genome Atlas Research Network (Muzny DM, …Aksoy B…Sander C,…) 2012, “Comprehensive molecular characterization of human colon and rectal cancer,” Nature, 487(7407):330-7. PMCID: PMC3401966

B. Barker

Barker BE, Sadagopan N, Wang Y, Smallbone K, Myers CR, Xi H, Locasale JW, Gu Z., 2015, “A robust and efficient method of estimating enzyme complex abundance and metabolic flux from expression data,” Comput Biol. Chem, Sep 1:15:30107-09.

Barker B, Xu L,, Gu Z., 2015, “Dynamic Epistasis Under Varying Environmental Perturbations,” PLoS One., Jan 27:10(1):e114911.doi: 10.1371/journal.pone.0414911 PMCID: PMC4308068

Shestov AA, Barker B, Gu Z, Locasale JW., 2013, “Computational approaches for understanding energy metabolism,” Wiley Interdiscip Rev Syst Biol Med., 5(6):733-50. PMCID: PMC3906216

Xu L, Barker B, Gu Z., 2012, “Dynamic epistasis for different alleles of the same gene,” Proc Natl Acad Sci U S A.,109(26):10420-5. PMCID: PMC3387062

Zanders S, Ma X, Roychoudhury A, Hernandez RD, Demogines A, Barker B, Gu Z, Bustamante CD, Alani E., 2010, “Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach,” Genetics, 186(2):493-503. PMCID: PMC2954485

Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP., 2012, “Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network,” BMC Syst Biol., 6:55. PMCID: PMC3413506

A. Basu

Basu A, Rose KL, Zhang J, Beavis RC, Ueberheide B, Garcia BA, Chait B, Zhao Y, Hunt DF, Segal E, Allis CD, Hake SB., 2009, “Proteome-wide prediction of acetylation substrates,”. Proc Natl Acad Sci U S A., 106(33):13785-90. PMCID: PMC2728972

Whitcomb SJ, Basu A, Allis CD, Bernstein E., 2007, “Polycomb Group proteins: an evolutionary perspective,” Trends Genet, (10):494-502.

J. Behr

Hadi K, Yao X, Behr JM, Deshpande A, …Imielinski M. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell. 2020 Oct 1;183(1):197-210.e32. doi: 10.1016/j.cell.2020.08.006. PMID: 33007263; PMCID: PMC7912537

Dewhurst SM, Yao X, Rosiene J, Tian H, Behr J, Bosco N, Takai KK, de Lange T, Imieliński M. Structural variant evolution after telomere crisis. Nat Commun. 2021 Apr 7;12(1):2093. doi: 10.1038/s41467-021-21933-7. PMID: 33828097; PMCID: PMC8027843

Albanese SK, Parton DL, Işık M, Rodríguez-Laureano L, Hanson SM, Behr JM, Gradia S, Jeans C, Levinson NM, Seeliger MA, Chodera JD. An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression. Biochemistry. 2018 Aug 7;57(31):4675-4689. doi: 10.1021/acs.biochem.7b01081. Epub 2018 Jul 26. PubMed PMID: 30004690; PubMed Central PMCID: PMC6081246

Ruff EF, Muretta JM, Thompson AR, Lake EW, Cyphers S, Albanese SK, Hanson SM, Behr JM, Thomas DD, Chodera JD, Levinson NM. A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation. Elife. 2018 Feb 21;7. pii: e32766. doi: 10.7554/eLife.32766. PubMed PMID: 29465396; PubMed Central PMCID: PMC5849412

Kahles A, Behr J, Rätsch G., 2016, “MMR: a tool for read multi-mapper resolution,” Bioinformatics, Mar 1;32(5):770-2. doi: 10.1093/bioinformatics/btv624. Epub 2015 Oct 30. PubMed PMID: 26519503; PubMed Central PMCID: PMC4795617

Cyphers S, Ruff EF, Behr JM, Chodera JD, Levinson NM, 2017, “A water-mediated allosteric network governs activation of Aurora kinase A.” Nat Chem Biol. 2017 Apr;13(4):402-408. doi: 10.1038/nchembio.2296. Epub 2017 Feb 6. PMID: 28166210

Hartmann L, Drewe-Boß P, Wießner T, Wagner G, Geue S, Lee HC, Obermüller DM, Kahles A, Behr J, Sinz FH, Rätsch G, Wachter A, 2016, “Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis.” Plant Cell. 2016 Nov;28(11):2715-2734. Epub 2016 Nov 1. PMID: 27803310

Beauchamp KA, Behr JM, Rustenburg AS, Bayly CI, Kroenlein K, Chodera JD, 2015, “Toward automated benchmarking of atomistic force fields: Neat liquid densities and static dielectric constants from the thermoML data archive,” J Phys Chem B., Oct 8; 119(40):12912-20. PMID: 26339862

C. Bhattacharya

Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., … & Black, C. (2021). A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell, 184(13), 3376-3393

Butler, D., Mozsary, C., Meydan, C., Foox, J., Rosiene, J., Shaiber, A.,Bhattacharya, C., … & Mason, C. E. (2021). Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nature communications, 12(1), 1660.

Afshinnekoo, E., Bhattacharya, C., Burguete-García, A., Castro-Nallar, E., Deng, Y., Desnues, C., … & Bhattacharyya, M. (2021). COVID-19 drug practices risk antimicrobial resistance evolution. The Lancet Microbe, 2(4), e135-e136.

Danko, D. C., Sierra, M. A., Benardini, J. N., Guan, L., Wood, J. M., Singh, N.,Bhattacharya, C., … & Mason, C. E. (2021). A comprehensive metagenomics framework to characterize organisms relevant for planetary protection. Microbiome, 9, 1-15

Sierra, M. A., Ryon, K. A., Tierney, B. T., Foox, J., Bhattacharya, C., Afshin, E., … & Tighe, S. W. (2022). Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations. Environmental Microbiome, 17(1), 1-20.

C. Bielski

Gorelick AN, Sánchez-Rivera F, Cai Y, Bielski CM, Biederstedt E, Jonsson P, Richards AL, Vasan N, Penson AV, Friedman ND, Ho Y, Baslan T, Bandlamudi C, Scaltriti M, Schultz N, Lowe SW, Reznik E, Taylor BS. “Phase and context shape the function of composite oncogenic mutations.” Nature. 2020. In press.

Sakamoto H, Attiyeh MA, Gerold JM, Makohon-Moore AP, Hayashi A, Hong J, Kappagantula R, Zhang L, Melchor JP, Reiter JG, Heyde A, Bielski CM, Penson AV, Gonen M, Chakravarty D, O’Reilly EM, Wood LD, Hruban RH, Nowak MA, Socci ND, Taylor BS, Iacobuzio-Donahue CA. The Evolutionary Origins of Recurrent Pancreatic Cancer. Cancer Discov. 2020 Mar 19. pii: CD-19-1508. doi:10.1158/2159-8290.CD-19-1508. [Epub ahead of print] PubMed PMID: 32193223

Jonsson P, Bandlamudi C, Cheng ML, Srinivasan P, Chavan SS, Friedman ND, Rosen EY, Richards AL, Bouvier N, Selcuklu SD, Bielski CM, Abida W, Mandelker D, Birsoy O, Zhang L, Zehir A, Donoghue MTA, Baselga J, Offit K, Scher HI, O’Reilly EM, Stadler ZK, Schultz N, Socci ND, Viale A, Ladanyi M, Robson ME, Hyman DM, Berger MF, Solit DB, Taylor BS. Tumour lineage shapes BRCA-mediated phenotypes. Nature. 2019 Jul;571(7766):576-579. doi: 10.1038/s41586-019-1382-1. Epub 2019 Jul 10. Erratum in: Nature. 2019 Dec 11;:. PubMed PMID: 31292550; PubMed Central PMCID:PMC7048239

Bielski CM, Donoghue MTA, Gadiya M, Hanrahan AJ, Won HH, Chang MT, Jonsson P, Penson AV, Gorelick A, Harris C, Schram AM, Syed A, Zehir A, Chapman PB, Hyman DM, Solit DB, Shannon K, Chandarlapaty S, Berger MF, Taylor BS. Widespread
Selection for Oncogenic Mutant Allele Imbalance in Cancer. Cancer Cell. 2018 Nov 12;34(5):852-862.e4. doi: 10.1016/j.ccell.2018.10.003. Epub 2018 Nov 1. PubMed PMID: 30393068; PubMed Central PMCID: PMC6234065

I. Bomash

Bomash I, Roudi Y, Nirenberg S., 2013, “A virtual retina for studying population coding,” PLoS One., 8(1):e53363. PMCID: PMC3544815

Pandarinath C, Bomash I, Victor J, Prusky G, Tschetter W, and Nirenberg S. 2010, A novel mechanism for switching a neural system from one state to another. Frontiers in Computational Neuroscience, Mar 31;4:2. PMID: 20407612

Nirenberg S, Bomash I, Pillow J, and Victor J., 2010, Heterogeneous response dynamics in retinal ganglion cells: the interplay of predictive coding and adaptation. J Neurophysiol.  Jun;103(6):3184-94. Epub 2010 Mar 31. PMID: 20357061

C. Braiman

Reichenbach CS, Braiman C, Schiff ND, Hudspeth AJ, Reichenbach T, 2016, “The auditory-brainstem response to continuous, non-repetitive speech is modulated by the speech envelope and reflects speech processing,” 2016, Front Comput Neurosci. 10:47. doi: 10.3389/fncom.2016.00047. eCollection 2016. PMID:27303286 PMCID: PMC 4880572

Meltzer B, Reichenbach CS, Braiman C, Schiff ND, Hudspeth AJ, Reichenbach T., 2015, “The steady-state response of the cerebral cortex to the beat of music reflects both the comprehension of music and attention,” Front Hum Neurosci., Aug 6;9:436. doi: 10.3389/fnhum.2015.00436. eCollection 2015. PMID: 26300760 PMCID: PMC4526810

C. Burdziak

van Dijk D, Sharma R, Nainys J, Yim K, Kathail P, Carr AJ, Burdziak C, Moon KR, Chaffer CL, Pattabiraman D, Bierie B, Mazutis L, Wolf G, Krishnaswamy S, Pe’er D, 2018, “Recovering gene interactions from single-cell data using data diffusion. Cell. Jul 26;174(3):716-729.e27. doi: 10.1016/j.cell.2018.05.061. Epub 2018 Jun 28. PMID: 29961576

Alonso-Curbelo, D., Ho, YJ., Burdziak, C. et al. A gene–environment-induced epigenetic program initiates tumorigenesis. Nature 590, 642–648 (2021). https://doi.org/10.1038/s41586-020-03147-x

M. Carty

Carty M, Zamparo L, Sahin M, González A, Pelossof R, Elemento O, Leslie CS., 2017, “An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data,” Nat Commun., May 17;8:15454. doi: 10.1038/ncomms15454. PubMed PMID: 28513628; PMCID: PMC5442359

Carty MA, Elemento O, 2016, “Practical analysis of genome contact interaction experiments,”, Methods Mol Biol. 1418:177-89. doi: 10.1007/978-1-4939-3578-9_9. PMID: 27008015

Sanghvi VR, Mavrakis KJ, Van der Meulen J., Boice M, Wolfe AL, Carty M, Mohan P, Rondou P, Socci ND, Benoit Y, Taghon T, Van Vlierberghe P, Leslie CS, Speleman F, Wendel HG., 2014, “Characterization of a set of tumor suppressor microRNAs in T cell acute lymphoblastic leukemia,” Sci Signal, Nov 18: 7:352. PubMed PMID: 25406379

White P, Carty M., 2010, Reducing bias through process inventory dataset normalization. Int J Life Cycle Assess. 15(1):1-20. doi: 10.1007/s11367-010-0215-0

E. Cerami

Aksoy BA, Gao J, Dresdner G, Wang W, Root A, Jing X, Cerami E, Sander C., 2013, “PiHelper: an open source framework for drug-target and antibody-target data,” Bioinformatics. 15;29(16):2071-2. doi: 10.1093/bioinformatics/btt345. PMCID:PMC3722529

Cancer Genome Atlas Research Network (Getz G,…Cerami E…Sander C…,) 2013, “Integrated genomic characterization of endometrial carcinoma,” Nature, 497(7447):67-73.

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N., 2013, “Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal,” Sci Signal., 6(269):pl1.

Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N., 2013, “Using MEMo to discover mutual exclusivity modules in cancer,” Curr Protoc Bioinformatics, Chapter 8:Unit 8.17.

Cancer Genome Atlas Network (Koboldt DC,…Cerami E,…Sander C,…,) 2012, “Comprehensive molecular portraits of human breast tumours,” Nature, 490(7418):61-70. PMCID: PMC3465532

Cancer Genome Atlas Research Network (Hammerman, PS,…Cerami E,…Sander C,…,) 2012, “Comprehensive genomic characterization of squamous cell lung cancer,” Nature, 489(7417):519-25. PMCID: PMC3466113

Cancer Genome Atlas Network (Muzny DM, …Cerami E…Sander C,…) 2012, “Comprehensive molecular characterization of human colon and rectal cancer,” Nature, 487(7407):330-7. PMCID: PMC3401966

Ciriello G, Cerami E, Sander C, Schultz N., 2012, “Mutual exclusivity analysis identifies oncogenic network modules,” Genome Res, 22(2):398-406. PMCID: PMC3266046

Cancer Genome Atlas Research Network (Bell D, … Cerami E,…Sander C,…) 2011, “Integrated genomic analyses of ovarian carcinoma,” Nature, 474(7353):609-15. PMCID: PMC3163504

Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C., 2011, “Pathway Commons, a web resource for biological pathway data,” Nucleic Acids Res., 39(Database issue):D685-90. PMCID: PMC3013659

Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL., 2010, Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010 Jul 13;18(1):11-22. Epub Jun 24.PMID: 20579941 PMCID: PMC3198787

Cerami E, Demir E, Schultz N, Taylor BS, Sander C., 2010, Automated network analysis identifies core pathways in glioblastoma. PLoS One. Feb 12; 5 (2): e8918. PMID: 20169195

Cancer Genome Atlas Research Network (…Cerami E,…)., 2008 Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. Oct 23;455(7216):1061-8. Epub Sep 4. PubMed PMID: 18772890

MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD., 2007, Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2(10):2366-82.PMID: 17947979

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H., 2007, Broadening the horizon–level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. Oct 9;5:44. PMID: 17925023

J. Chacon-Barahona

Sun, S, Hong, J, You, E, Tsanov, KM, Chacon-Barahona, J, De Gioacchina, A, Hoyos, D, Li, H, Jiang, H, Ly, H, Marhon, S, Murali, R, Chanda, P, Karacay, A, Vabret, N, De Carvalho, DD, LaCava, J, Lowe, SW, Ting, DT, Iacobuzio-Donahue, CA, Solovyov, A, Greenbaum, BD. (2023). Cancer Cells Co-evolve with Retrotransposons to Mitigate Viral Mimicry.
bioRxiv [Preprint]. 20:2023.05.19.541456. doi: 10.1101/2023.05.19.541456.
PMID: 37292765 PMCID: 10245669

N. Chambwe

Dominguez PM, Teater M, Chambwe N, Kormaksson M, Redmond D, Ishii J, Vuong B, Chaudhuri J, Melnick A, Vasanthakumar A, Godley LA, Papavasiliou FN, Elemento O, Shaknovich R, 2015, “DNA methylation dynamics of germinal center B cells are mediated by AID,” Cell Rep. 12(12):2086-98. doi: 10.1016/j.celrep.2015.08.036. Epub 2015 Sep 10. PMID: 26365193 PMCID: PMC4591215

Chambwe N, Kormaksson M, Geng H, De S, Michor F, Johnson NA, Morin RD, Scott DW, Godley LA, Gascoyne RD, Melnick A, Campagne F, Shaknovich R., 2014, “Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes,” Blood, 123(11):1699-708. PMID: 24385541

Campagne F, Dorff KC, Chambwe N, Robinson JT, Mesirov JP., 2013, “Compression of structured high-throughput sequencing data,” PLoS One, 8(11). PMCID: PMC3832420

Dorff KC1, Chambwe N, Zeno Z, Simi M, Shaknovich R, Campagne F., 2013, “GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data,”PLoS One, 8(7):e69666. PMCID: PMC3720652

Oh JE, Chambwe N, Klein S, Gal J, Andrews S, Gleason G, Shaknovich R, Melnick A, Campagne F, Toth M., 2013, “Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment,” Transl Psychiatry, 3:e218. PMCID: PMC3566713

Dorff KC, Chambwe N, Srdanovic M, Campagne F., 2010, “BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets,” Bioinformatics, 26(19):2472-3. PMCID: PMC2944207

D. Chandramohan

Nandi S, Chandramohan D, Fioriti L, Melnick AM, Hébert JM, Mason CE, Rajasethupathy P, Kandel ER, 2016 “Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain” Proc Natl Acad Sci USA. Proc Natl Acad Sci U S A. 2016 Nov 8; 113(45): 12697–12702. Published online 2016 Oct 24. doi: 10.1073/pnas.1609287113. PMID: 27791114 PMCID: PMC5111663

Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M, 2016, “Extensive sequencing of seven human genomes to characterize benchmark reference materials,” Sci Data. 3:160025. doi: 10.1038/sdata.2016.25. PMID: 27271295 PMCID: PMC4896128

Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium (45 member collaboration that includes D. Chandramohan)., Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P, 2015, “Summary of the DREAM8 parameter estimation challenge: Toward parameter identification for whole-cell models, PLoS Comput Biol. 11(5):e1004096. doi: 10.1371/journal.pcbi.1004096. PMID: 26020786 PMCID: PMC4447414

Hu W, Dooley J, Chung SS, Chandramohan D, Cimmino L, Mukherjee S, Mason CE, de Strooper B, Liston A, Park CY., 2015, “miR-29a maintains mouse hematopoietic stem cell self-renewal by regulating Dnmt3a,” Blood, Apr 2;125(14):2206-16. doi: 10.1182/blood-2014-06-585273. Epub 2015 Jan 29. PMID: 25634742 PMCID: PMC4383797

D. Chang

Chang D, Gao F, Slavney A, Ma L, Waldman YY, Sams AJ, Billing-Ross P, Madar A, Spritz R, Keinan A, 2014, “Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases.” PLoS One. 9(12):e113684. doi: 10.1371/journal.pone.0113684. PMID: 25479423 PMCID: PMC4257614

Gao F, Chang D, Biddanda A, Ma L, Guo Y, Zhou Z, Keinan A, 2015, “XWAS: A Software Toolset for Genetic Data Analysis and Association Studies of the X Chromosome.” J Hered. 106(5):666-71. doi: 10.1093/jhered/esv059. PMID:26268243 PMCID: PMC4567842

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Chang D, Keinan A, 2014, “Principal component analysis characterizes shared pathogenetics from genome-wide association studies.” PLoS Comput Biol. 10(9):e1003820. doi: 10.1371/journal.pcbi.1003820.PMID: 25211452 PMCID:PMC4161298

Yu F, Lu J, Liu X, Gazave E, Chang D, Raj S, Hunter-Zinck H, Blekhman R, Arbiza L, Van Hout C, Morrison A, Johnson AD, Bis J, Cupples LA, Psaty BM, Muzny D, Yu J, Gibbs RA, Keinan A, Clark AG, Boerwinkle E., 2015, “Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions,” PLoS One., Mar 25; 10(3):e0121644. PMID: 25807536; PMCID: PMC4373932

Gazave E*, Ma L*, Chang D*, et al., 2013, “Neutral genomic regions refine models of recent rapid human population growth,” Proc Natl Acad Sci U S A. 111(2):757-62. PMCID: PMC3896169 *These authors contributed equally to this work

Gazave E, Chang D, Clark AG, Keinan A., 2013,”Population Growth Inflates the Per-Individual Number of Deleterious Mutations and Reduces Their Mean Effect,” Genetics.195(3):969-78. PMCID: PMC3813877

Chang D, Keinan A., 2012, “Predicting signatures of “synthetic associations” and “natural associations” from empirical patterns of human genetic variation,” PLoS Comput Biol. 8(7):e1002600. PMCID: PMC3390358

E. Char

Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. (2024). 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. Nat Struct Mol Biol. 31(1):125-140. PMID: 38053013 PMCID: 10897904

Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. “Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression.” bioRxiv [Preprint]. 2023 Jul 19:2023.07.19.549714. doi: 10.1101/2023.07.19.549714. PMID: 37577543 PMID 3757543 PMCID: 10432694

W. Chatila

Adileh M, Yuval JB, Walch HS, Chatila WK, Yaeger R, Garcia-Aguilar J, Schultz N, Paty PB, Cercek A, Nash GM.Primary Tumor Location and Outcomes After Cytoreductive Surgery and Intraperitoneal Chemotherapy for Peritoneal Metastases of Colorectal Origin. Ann Surg Oncol. 2020 Aug 25. doi: 10.1245/s10434-020-08993-7. Online ahead of print. PMID: 32844293

Mondaca S, Walch H, Nandakumar S, Chatila WK, Schultz N, Yaeger R. Specific Mutations in APC, but Not Alterations in DNA Damage Response, Associate With Outcomes of Patients With Metastatic Colorectal Cancer. 2020 Jul 27;S0016-5085(20)35004-6. doi: 10.1053/j.gastro.2020.07.041. Online ahead of print. PMID: 32730818

Janjigian YY, Maron SB, Chatila WK, …Schultz N, Hechtman JF. First-line pembrolizumab and trastuzumab in HER2-positive oesophageal, gastric, or gastro-oesophageal junction cancer: an open-label, single-arm, phase 2 trial. Lancet Oncol. 2020 Jun;21(6):821-831. doi: 10.1016/S1470-2045(20)30169-8. Epub 2020 May 18. PMID: 32437664

Yaeger R, Paroder V, Bates DDB, Capanu M, Chou J, Tang L, Chatila W, Schultz N, Hersch J, Kelsen D. 2020. Systemic Chemotherapy for Metastatic Colitis-Associated Cancer has a Worse Outcome than for Sporadic Colorectal Cancer: a Matched Case Cohort Analysis. Clinical Colorectal Cancer. https://doi.org/10.1016/j.clcc.2020.02.008. PMID: 32798155

Zhou J, Sanchez-Vega F, Caso R, Tan KS, Brandt WS, Jones GD, Yan S, Adusumilli PS, Bott M, Huang J, Isbell JM, Sihag S, Molena D, Rusch VW, Chatila WK,…Schultz N, Jones DR. Analysis of Tumor Genomic Pathway Alterations Using Broad-Panel Next-Generation Sequencing in Surgically Resected Lung Adenocarcinoma. Clin Cancer Res. 2019 Dec 15;25(24):7475-7484. doi: 10.1158/1078-0432.CCR-19-1651. Epub 2019 Aug 27. PMID: 31455678 PMCID: PMC6911636

Won E, Basunia A, Chatila WK, …Schultz N, Janjigian YY. Efficacy of Combined VEGFR1-3, PDGFα/β, and FGFR1-3 Blockade Using Nintedanib for Esophagogastric Cancer. Clin Cancer Res. 2019 Jul 1;25(13):3811-3817. doi: 10.1158/1078-0432.CCR-18-3789. Epub 2019 Apr 5. PMID: 30952642 PMCID: PMC6606369

Datta, J., Smith, J. J., Chatila, W. K., McAuliffe, J. C., Kandoth, C., Vakiani, E., … D’Angelica, M. I. 2019. Co-Altered Ras/B-raf and TP53 is Associated with Extremes of Survivorship and Distinct Patterns of Metastasis in Metastatic Colorectal Cancer Patients. Clinical Cancer Research, clincanres.2390.2019. https://doi.org/10.1158/1078-0432.CCR-19-2390. PMID: 31719050; PMCID: PMC7056517

Smith, J. J., Chatila, W. K., Sanchez-Vega, F., Datta, J., Connell, L. C., Szeglin, B. C., … Kemeny, N. E. 2019. Genomic stratification beyond Ras/B-Raf in colorectal liver metastasis patients treated with hepatic arterial infusion. Cancer Medicine, 8(15), 6538–6548. https://doi.org/10.1002/cam4.2415. PMID: 31503397; PMCID: PMC6825986

Greally, M., Chou, J. F., Chatila, W. K., Margolis, M., Capanu, M., Hechtman, J. F., … Ku, G. Y. 2019. Clinical and Molecular Predictors of Response to Immune Checkpoint Inhibitors in Patients with Advanced Esophagogastric Cancer. Clinical Cancer Research, 25(20), 6160 LP –6169. https://doi.org/10.1158/1078-0432.CCR-18-3603. PMID: 31337644; PMCID: PMC6905384

Vedanayagam, J., Chatila, W. K., Aksoy, B. A., Majumdar, S., Skanderup, A. J., Demir, E., … Lai, E. C. 2019. Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis. Nature Communications, 10(1), 3682. https://doi.org/10.1038/s41467-019-11610-1. PMID: 31417090; PMCID: PMC6695490

Mondaca S, Chatila WK, Bates D, Hechtman JF, Cercek A, Segal NH, Stadler ZK, Varghese AM, Kundra R, Capanu M, Shia J, Schultz N, Saltz L, Yaeger R. FOLFCIS Treatment and Genomic Correlates of Response in Advanced Anal Squamous Cell Cancer. Clin Colorectal Cancer. 2019 Mar;18(1):e39-e52. doi: 10.1016/j.clcc.2018.09.005. Epub 2018 Sep 21. PMID: 30316684 PMCID: PMC6428631

F. Chaudhry

Kim TW, Koo SY, Riessland M, Cho H, Chaudhry F, Kolisnyk B, Russo MV, Saurat N, Mehta S, Garippa R, Betel D, Studer L. (2024). TNF-NFkb-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron. Cell 87: 3671-3689. PMID: 37034664

Y. Cheng

Choudhury S…,Cheng YK…, 2013, “Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics,” Cell Stem Cell, 13(1):117-30. PMCID: PMC3703476

Cheng YK, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, Michor F., 2012, A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS Comput Biol. Jan;8(1):e1002337. Epub 2012 Jan 5. PMID: 22241976

Hambardzumyan D, Cheng YK, Haeno H, Holland EC, Michor F., 2011, The probable cell of origin of NF1- and PDGF-driven glioblastomas. PLoS One. 6(9):e24454. Epub Sep 9. PMID: 21931722

Attolini CS, Cheng YK, Beroukhim R, Getz G, Abdel-Wahab O, Levine RL, Mellinghoff IK, Michor F., 2010, A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc Natl Acad Sci U S A. Oct 12;107(41):17604-9. Epub Sep 23. PMID: 20864632

SW. Chi

Chi SW, Hannon GJ, Darnell RB, 2012, “An alternative mode of microRNA target recognition,” Nat Struct Mol Biol. 19(3):321-7. PMCID: PMC3541676

Darnell JC, Van Driesche SJ, Zhang C, Hung KY, Mele A, Fraser CE, Stone EF, Chen C, Fak JJ, Chi SW, Licatalosi DD, Richter JD, Darnell RB., 2011, “FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism,” Cell, 146(2):247-61. PMCID: PMC3232425

Chi SW, Zang JB, Mele A, Darnell RB., 2009, “Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps,” Nature, 460(7254):479-86. PMCID: PMC2733940

Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB., 2008, “HITS-CLIP yields genome-wide insights into brain alternative RNA processing,” Nature, 456(7221):464-9. PMCID: PMC2597294

Chi SW, Zang JB, Mele A, Darnell RB., 2009, Argonaute HITS-CLIP decodes miRNA-mRNA interaction maps. Nature. Jul 23;460(7254):479-86. Epub Jun 17. PMID: 19536157

Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB., 2008, HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. Nov 27;456(7221):464-9. Epub 2008 Nov 2. PMID: 18978773

Chang, J. H., Chi, S. W., and Zhang, B. T., 2003, Gene Expression Pattern Analysis via Latent Variable Models Coupled with Topographic Clustering. Genomics & Informatics, vol. 1, no. 1, pp. 32-39. PMID: not available.

C. Chin

Ferraro GB, Ali A, Luengo A, Kodack DP, Deik A, Abbott KL, Bezwada D, Blanc L, Prideaux B, Jin X, Possada JM, Chen J, Chin CR, …Vander Heiden MG. Fatty acid synthesis is required for breast cancer brain metastasis. Nat Cancer 2, 414–428 (2021). https://doi.org/10.1038/s43018-021-00183-y

Gong B, Li D, Kusko R, Novoradovskaya N, Zhang Y, Wang S, Pabón-Peña C, Zhang Z, Lai K, Cai W, LoCoco JS, Lader E, Richmond TA, Mittal VK, Liu LC, Johann DJ Jr, Willey JC, Bushel PR, Yu Y, Xu C, Chen G, Burgess D, Cawley S, Giorda K, Haseley N, Qiu F, Wilkins K, Arib H, Attwooll C, Babson K, Bao L, Bao W, Lucas AB, Best H, Bhandari A, Bisgin H, Blackburn J, Blomquist TM, Boardman L, Burgher B, Butler DJ, Chang CJ, Chaubey A, Chen T, Chierici M, Chin CR, …Xu J. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biol. 2021 Apr 16;22(1):109. doi: 10.1186/s13059-021-02315-0. PMID: 33863344; PMCID: PMC8051090

Duy C, Li M, Teater M, Meydan C, Garrett-Bakelman FE, Lee TC, Chin CR, Durmaz C, Kawabata KC, Dhimolea E, Mitsiades CS, Doehner H, D’Andrea RJ, Becker MW, Paietta EM, Mason CE, Carroll M, Melnick AM. Chemotherapy induces senescence-like resilient cells capable of initiating AML recurrence. Cancer Discov. 2021 Jan 26:candisc.1375.2020. doi: 10.1158/2159-8290.CD-20-1375. Epub ahead of print. PMID: 33500244

Rivas MA, Meydan C, Chin CR, Challman MF, Kim D, Bhinder B, Kloetgen A, Viny AD, Teater MR, McNally DR, Doane AS, Béguelin W, Fernández MTC, Shen H, Wang X, Levine RL, Chen Z, Tsirigos A, Elemento O, Mason CE, Melnick AM. Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation. Nat Immunol. 2021 Feb;22(2):240-253. doi: 10.1038/s41590-020-00827-8. Epub 2021 Jan 11. PMID: 33432228; PMCID: PMC7855695

Yusufova N, Kloetgen A, Teater M, Osunsade A, Camarillo JM, Chin CR, … Melnick AM. Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture. Nature. 2020 Dec 9. doi: 10.1038/s41586-020-3017-y. Epub ahead of print. PMID: 33299181.

Malkani S*, Chin CR*, Cekanaviciute E*, Mortreux M, Okinula H, Tarbier M, Schreurs AS, Shirazi-Fard Y, Tahimic CGT, Rodriguez DN, Sexton BS, Butler D, Verma A, Bezdan D, Durmaz C, MacKay M, Melnick A, Meydan C, Li S, Garrett-Bakelman F, Fromm B, Afshinnekoo E, Langhorst BW, Dimalanta ET, Cheng-Campbell M, Blaber E, Schisler JC, Vanderburg C, Friedländer MR, McDonald JT, Costes SV, Rutkove S, Grabham P, Mason CE, Beheshti A. Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development. Cell Rep. 2020 Nov 21:108448. doi: 10.1016/j.celrep.2020.108448. Epub ahead of print. PMID: 33242410.

Gertz ML*, Chin CR*, Tomoiaga D, MacKay M, Chang C, Butler D, Afshinnekoo E, Bezdan D, Schmidt MA, Mozsary C, Melnick A, Garrett-Bakelman F, Crucian B, Lee SMC, Zwart SR, Smith SM, Meydan C, Mason CE. Multi-omic, Single-Cell, and Biochemical Profiles of Astronauts Guide Pharmacological Strategies for Returning to Gravity. Cell Rep. 2020 Nov 20:108429. doi: 10.1016/j.celrep.2020.108429. Epub ahead of print. PMID: 33242408.

Trinchant NM, MacKay MJ, Chin C, Afshinnekoo E, Foox J, Meydan C, Butler D, Mozsary C, Vernice NA, Darby C, Schatz MC, Bailey SM, Melnick AM, Guzman M, Bolton K, Braunstein LZ, Garrett-Bakelman F, Levine RL, Hassane D, Mason CE. Clonal Hematopoiesis Before, During, and After Human Spaceflight. Cell Rep. 2020 Nov 20:108458. doi: 10.1016/j.celrep.2020.108458. Epub ahead of print. PMID: 33242405.

Lau AN, Li Z, Danai LV, Westermark AM, Darnell AM, Ferreira R, Gocheva V, Sivanand S, Lien EC, Sapp KM, Mayers JR, Biffi G, Chin CR, Davidson SM, Tuveson DA, Jacks T, Matheson NJ, Yilmaz O, Vander Heiden MG. Dissecting cell type-specific metabolism in pancreatic ductal adenocarcinoma. Elife. 2020 Jul 10;9:e56782. doi: 10.7554/eLife.56782. Epub ahead of print. PMID: 32648540.

Venturutti L, Teater M, Zhai A, Chadburn A, Babiker L, Kim D, Béguelin W, Lee TC, Kim Y, Chin CR, Yewdell WT, Raught B, Phillip JM, Jiang Y, Staudt LM, Green MR, Chaudhuri J, Elemento O, Farinha P, Weng AP, Nissen MD, Steidl C, Morin RD, Scott DW, Privé GG, Melnick AM. TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate. Cell. 2020 Jul 23;182(2):297-316.e27. doi: 10.1016/j.cell.2020.05.049. Epub 2020 Jul 2. PMID: 32619424 PMCID: PMC7384961

Nguyen DTT, Lu Y, Chu KL, Yang X, Park SM, Choo ZN, Chin CR, Prieto C, Schurer A, Barin E, Savino AM, Gourkanti S, Patel P, Vu LP, Leslie CS, Kharas MG. HyperTRIBE uncovers increased MUSASHI-2 RNA binding activity and differential regulation in leukemic stem cells. Nat Commun. 2020 Apr 24;11(1):2026. doi: 10.1038/s41467-020-15814-8. PMID: 32332729 PMCID: PMC7181745

Hamza B, Ng SR, Prakadan SM, Delgado FF, Chin CR, et al. Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer. Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2232-2236. doi: 10.1073/pnas.1814102116. Epub 2019 Jan 23. PMID: 30674677; PMCID: PMC6369805

C. Chun

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Niemeyer JE, Gadamsetty P, Chun C, Sylvester S, Lucas JP, Ma H, Schwartz TH, Aksay ER, 2022. “Seizures initiate in zones of relative hyperexcitation in a zebrafish epilepsy model.” Brain, 145(7), 2347-2360.

D. Cizin

Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin TY, Liberatore K, Cizin DM, Cohen BM, Vasan N, Ma Y, Krismer K, Robles JT, van de Kooij B, van Vlimmeren AE, Andrée-Busch N, Käufer NF, Dorovkov MV, Ryazanov AG, Takagi Y, Kastenhuber ER, Goncalves MD, Hopkins BD, Elemento O, Taatjes DJ, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry SD, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck PV, Turk BE, Yaffe MB, Cantley LC. (2023) An atlas of substrate specificities for the human serine/threonine kinome. Nature 613: 759-766. PMID: 36631611 PMCID: 9876800

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TW. Cornforth

Cornforth TW, Lipson H, 2013, “Inference of hidden variables in systems of differential equations with genetic programming,” Genetic Programming and Evolvable Machines, , Volume 14, Issue 2, pp 155-190. PMID: not available.

Cornforth TW, Lipson H, 2012, “Symbolic regression of multiple‐time‐scale dynamical systems,” Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), pp. 735-742.

Gardner D, Banfelder J, Chan E, Cornforth TW, Jagdale AB, Repucci M, 2011, “Towards massively-parallel analytic capabilities for multielectrode recordings,” Biophysical Journal, Vol. 100, p. 95a.

Cornforth TW, Torresen J, Lipson H, 2011, “Ion channel modeling with analog circuit evolution,” Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), pp. 33-34.

Cornforth TW, Kim KJ, Lipson H, 2010, “Evolution of analog circuit models of ion channels,” Lecture Notes in Computer Science, Vol. 6274, pp. 157‐168.

D. Danko

Danko DC, Sierra MA, Benardini JN, Guan L, Wood JM, Singh N, Seuylemezian A, Butler DJ, Ryon K, Kuchin K, Meleshko D, Bhattacharya C, Venkateswaran KJ, Mason CE. A comprehensive metagenomics framework to characterize organisms relevant for planetary protection. Microbiome. 2021 Apr 1;9(1):82. doi: 10.1186/s40168-021-01020-1. PMID: 33795001; PMCID: PMC8016160

Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D,…Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun. 2021 Mar 12;12(1):1660. doi: 10.1038/s41467-021-21361-7. PMID: 33712587; PMCID: PMC7954844

Danko DC, Meleshko D, Bezdan D, Mason C, Hajirasouliha I., 2019, “Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics”, Genome Res. Jan;29(1):116-124. doi: 10.1101/gr.235499.118. Epub 2018 Dec 6. PMID:30523036

M. Darmofal

Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczyński KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M. (2020). Distinct classes of complex structural variation uncovered across thousands of cancer genome graphs. Cell 183(1):197-210. PMID: 33007263 PMCID:7912537

Darmofal M, Suman S, Atwal G, Toomey M, Chen JF, Chang JC, Vakiani E,Varghese AM, Balakrishnan Rema A, Syed A, Schultz N, Berger MF, Morris Q.(2024). Deep learning model for tumor type prediction using targeted clinicalgenomic sequencing data. Cancer Discovery 14:1064-1081.PMID: 38416134 PMCID: 11145170

N. Davidson Krishnamoorthy GP, Davidson NR,…Rätsch G, Fagin JA., 2019, “EIF1AX and RAS Mutations Cooperate to Drive Thyroid Tumorigenesis through ATF4 and c-MYC”, Cancer Discov. Feb;9(2):264-281. doi: 10.1158/2159-8290.CD-18-0606. Epub 2018 Oct 10. PubMed PMID: 30305285; PubMed Central PMCID: PMC6373451
A. Deshpande

Hadi K, Yao X, Behr JM, Deshpande A,…, Imielinski M. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell. 2020 Oct 1;183(1):197-210.e32. doi: 10.1016/j.cell.2020.08.006. PMID: 33007263; PMCID: PMC7912537

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L. DeVargas Roditi

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A. Doane

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M. Doktorova

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Khelashvili G, Doktorova M, Sahai MA, Johner N, Shi L, Weinstein H, 2015, “Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes,” Proteins. 83(5):952-69. doi: 10.1002/prot.24792. PMID: 25739722 PMCID: PMC4400265

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N. Dukler

Danko CG, Choate LA, Marks BA, Rice EJ, Wang Z, Chu T, Martins AL, Dukler N, Coonrod SA, Tait Wojno ED, Lis JT, Kraus WL, Siepel A, 2018, “Dynamic evolution of regulatory element ensembles in primate CD4+ T cells.” Nat Ecol Evol. 2018 Mar;2(3):537-548. doi: 10.1038/s41559-017-0447-5. Epub 2018 Jan 29. PMID: 29379187

Dukler N, Booth GT, Huang YF, Tippens N, Waters CT, Danko CG, Lis JT, Siepel A, 2017, “Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol.” Genome Res. 2017 Nov;27(11):1816-1829. doi: 10.1101/gr.222935.117. Epub 2017 Oct 12. PMID: 29025894

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E. Earlie

Li J, Hubisz MJ, Earlie EM, Duran MA, Hong C, Varela AA, Lettera E, Deyell M, Tavora B, Havel JJ, Phyu SM, Amin AD, Budre K, Kamiya E, Cavallo JA, Garris C, Powell S, Reis-Filho JS, Wen H, Bettigole S, Khan AJ, Izar B, Parkes EE, Laughney AM, Bakhoum SF. (2023). Non-cell autonomous cancer progression from chromosomal instability. Nature 620:1080-1088. PMID: 37612508 PMCID: 10468402

Rogava M, Aprati TJ, Chi WY, Melms JC, Hug C, Davis SH, Earlie EM, Chung C, Deshmukh SK, Wu S, Sledge G, Tang S, Ho P, Amin AD, Caprio L, Gurjao C, Tagore S, Ngo B, Lee MJ, Zanetti G, Wang Y, Chen S, Ge W, Melo LMN, Allies G, Rösler J, Gibney GT, Schmitz OJ, Sykes M, Creusot RJ, Tüting T, Schadendorf D, Röcken M, Eigentler TK, Molotkov A, Mintz A, Bakhoum SF, Beyaz S, Cantley LC, Sorger PK, Meckelmann SW, Tasdogan A, Liu D, Laughney AM, Izar B. (2024) Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3KAKT pathway activation. Nat Cancer 5:433-447. PMID: 38286827 PMCID: 11175596

Gardner EE, Earlie EM, Li K, Thomas J, Hubisz MJ, Stein BD, Zhang C, Cantley LC, Laughney AM, Varmus H. (2024) Lineage-specific intolerance to oncogenic drivers restricts histological transformation. Science 383 (6683) PMID:38330136 PMCID: 11155264

J. Elkhader Gilvary C, Madhukar N, Elkhader J, Elemento O., 2019, “The missing pieces of artificial intelligence in medicine”, Trends Pharmacol Sci., Aug;40(8):555-564. doi: 10.1016/j.tips.2019.06.001. Epub 2019 Jul 2. Review. PMID: 31277839
L. Fairchild

Philip M, Fairchild L, Sun L, Horste EL, Camara S, Shakiba M, Scott AC, Viale A, Lauer P, Merghoub T, Hellmann MD, Wolchok JD, Leslie CS, Schietinger A., 2017, “Chromatin states define tumour-specific T cell dysfunction and reprogramming,” Nature. May 25;545(7655):452-456. doi: 10.1038/nature22367. Epub 2017 May 17. PubMed PMID: 28514453.

Pelossof R, Fairchild L, Huang CH, Widmer C, Sreedharan VT, Sinha N, Lai DY, Guan Y, Premsrirut PK, Tschaharganeh DF, Hoffmann T, Thapar V, Xiang Q, Garippa RJ, Rätsch G, Zuber J, Lowe SW, Leslie CS, Fellmann C., 2017, “Prediction of potent shRNAs with a sequential classification algorithm,” Nat Biotechnol. Apr;35(4):350-353. doi: 10.1038/nbt.3807. Epub 2017 Mar 6.PMID: 28263295

Pelossof R, Chow OS, Fairchild L, Smith JJ, Setty M, Chen CT, Chen Z, Egawa F, Avila K, Leslie CS, Garcia-Aguilar J, 2016, “Integrated genomic profiling identified microRNA-92a regulation of IQGAP2 in locally advanced rectal cancer,” Genes Chromosomes Cancer 55(4):311-21. doi: 10.1002/gcc.22329.PMID:26865277

Verma A, Jiang Y, Du W, Fairchild L, Melnick A, Elemento O, 2015, “Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma,” Genome Med. 7:110. doi: 10.1186/s13073-015-0230-7. PMID: 26521025 PMCID: PMC4628784

M. Fansler McMaster, M. L., Berndt, S. I., Zhang, J., Slager, S. L., Li, S. A., Vajdic, C. M., Smedby, K. E., Yan, H., Birmann, B. M., Brown, E. E., Smith, A., Kleinstern, G., Fansler, M. M., Mayr, C., Zhu, B., Chung, C. C., Park, J. H., Burdette, L., Hicks, B. D., Hutchinson, A., … Caporaso, N. E. (2018). Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia. Nat Commun. 2018 Oct 10;9(1):4182. doi:10.1038/s41467-018-06541-2. PubMed PMID: 30305637; PubMed Central PMCID: PMC6180091
J. Fass

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Ross GA, Rustenburg AS, Grinaway PB, Fass J, Chodera JD, 2018, “Biomolecular simulations under realistic macroscopic salt conditions.” J Phys Chem B. May 31;122(21):5466-5486. doi: 10.1021/acs.jpcb.7b11734. PMID: 29649876

Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL, 2018, “Binding modes of ligands using enhanced sampling (BLUES): Rapid decorrelation of ligand binding modes via nonequilibrium candidate Monte Carlo.” J Phys Chem B. May 31;122(21):5579-5598. doi: 10.1021/acs.jpcb.7b11820. Epub 2018 Mar 12. PMID: 29486559; PMCID: PMC5980761

T. Funnell Funnell T, Zhang AW, Grewal D, McKinney S, Bashashati A, Wang YK, Shah SP. Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models. PLoS Comput Biol. 2019 Feb 22;15(2):e1006799. doi: 10.1371/journal.pcbi.1006799. eCollection 2019 Feb. PubMed PMID: 30794536; PubMed Central PMCID: PMC6402697.
K. Gayvert

Gayvert KM, Aly O, Platt J, Bosenberg MW, Stern DF, Elemento O, 2017, “A computational approach for identifying synergistic drug combinations,” PLoS Comput Biol. 13(1):e1005308. doi: 10.1371/journal.pcbi.1005308. PMID: 28085880 PMCID: PMC5234777

Gayvert KM, Madhukar NS, Elemento O, 2016, “A data-driven approach to predicting successes and failures of clinical trials,” Cell Chem Biol. 23(10):1294-1301. doi: 10.1016/j.chembiol.2016.07.023. PMID:27642066

Dardenne E, Beltran H, Benelli M, Gayvert KM, Berger A, Puca L, Cyrta J, Sboner A, Noorzad Z, MacDonald T, Cheung C, Yuen KS, Gao D, Chen Y, Eilers M, Mosquera JM, Robinson BD, Elemento O, Rubin MA, Demichelis F, Rickman DS, 2016, “N-myc induces an EZH2-mediated transcriptional program driving neuroendocrine prostate cancer,” Cancer Cell.30(4):563-577. doi: 10.1016/j.ccell.2016.09.005. PMID: 27728805

Gayvert KM, Dardenne E, Cheung C, Boland MR, Lorberbaum T, Wanjala J, Chen Y, Rubin MA, Tatonetti NP, Rickman DS, Elemento O, 2016, “A computational drug repositioning approach for targeting oncogenic transcription factors.” Cell Rep. 15(11):2348-56. doi: 10.1016/j.celrep.2016.05.037. PMID: 27264179PMCID: PMC4912004

Das J, Gayvert KM, Yu H, 2014, “Predicting cancer prognosis using functional genomics data sets,” Cancer Inform. 13(Suppl 5):85-8. doi: 10.4137/CIN.S14064. Review. PMID: 25392695 PMCID: PMC4218897

Das J, Gayvert KM, Bunea F, Weghamp MH, Yu H., 2015, “ENCAPP: elastic-net-based prognosis prediction and biomarker discovery for human cancers,” BMC Genomics, Apr 3; 16: 1465-69. PMCID: PMC4392808

C. Gilvary Gilvary C, Madhukar N, Elkhader J, Elemento O., 2019, “The missing pieces of artificial intelligence in medicine”, Trends Pharmacol Sci., Aug;40(8):555-564. doi: 10.1016/j.tips.2019.06.001. Epub 2019 Jul 2. Review. PMID:31277839
A. Gorelick

Cocco E, Lee JE, Kannan S, Schram AM, Won HH, Shifman S, Kulick A, Baldino L, Toska E, Arruabarrena-Aristorena A, Kittane S, Wu F, Cai Y, Arena S, Mussolin B, Kannan R, Vasan N, Gorelick AN, …, Scaltriti M. 2020. TRK xDFG mutations trigger a sensitivity switch from type I to II kinase inhibitors. Cancer Discov. 2020 Oct 1: CD-20-0571. doi: 10.1158/2159-8290.CD-20-0571. PMID: 33004339

Hanrahan AJ, Sylvester BE, Chang MT, Elzein A, Gao J, Han W, Liu Y, Xu D, Gao SP, Gorelick AN, …, Solit DB. 2020. Leveraging Systematic Functional Analysis to Benchmark an In Silico Framework Distinguishes Driver from Passenger MEK Mutants in Cancer. Cancer Res. 2020 Oct 1;80(19):4233-4243. doi: 10.1158/0008-5472.CAN-20-0865. PMID: 32641410

Gorelick AN, Sánchez-Rivera F, Cai Y, Bielski CM, Biederstedt E, Jonsson P, Richards AL, Vasan N, Penson AV, Friedman ND, Ho Y, Baslan T, Bandlamudi C, Scaltriti M, Schultz N, Lowe SW, Reznik E, Taylor BS. 2020. Phase and context shape the function of composite oncogenic mutations. Nature. 2020 Jun;582(7810):100-103. doi: 10.1038/s41586-020-2315-8. Epub 2020 May 27. PMID: 32461694

DiNatale RG, Gorelick AN,…Hakimi AA. 2019. Putative Drivers of Aggressiveness in TCEB1-mutant Renal Cell Carcinoma: An Emerging Entity with Variable Clinical Course. Eur Urol Focus. 2019 Dec 6. pii: S2405-4569(19)30354-2. doi: 10.1016/j.euf.2019.11.013. PMID: 31813809

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Vasan N, Razavi P, Johnson JL, Shao H, Shah H, Antoine A, Ladewig E, Gorelick A,…Baselga J. 2019. “Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors.” Science. 2019 Nov 8;366(6466):714-723. doi: 10.1126/science.aaw9032. PMID: 31699932

Taylor J, Sendino M, Gorelick A, et al., 2019, “Altered nuclear export signal recognition as a driver of oncogenesis.” Cancer Discov. July 2019:CD-19-0298. doi:10.1158/2159-8290.CD-19-0298. PMID: 31285298

Gao Y, Maria A, Na N, Da Cruz P, Gorelick A, Hechtman, Jaclyn F, Carson J, Lefkowitz R, Weigelt B, Taylor B, Zhao H, Reis-Filho J, de Stanchina E, Rosen N, Yao Z, Yaeger R., 2019, “211D mutation in MEK1 causes resistance to MEK inhibitors in colon cancer.” Cancer Discov. 2019;(September):CD-19-0356. doi:10.1158/2159-8290.cd-19-0356. PMID: 31227518

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D. Hoyos

Baldwin, E.T., van Eeuwen, T., Hoyos, D. et al. Structures, functions and adaptations of the human LINE-1 ORF2 protein. Nature 626, 194–206 (2024).

Q. Hu

Mechler F, Victor JD, Ohiorhenuan I, Schmid AM, Hu Q., 2011, Three-dimensional localization of neurons in cortical tetrode recordings. J Neurophysiol. Aug;106(2):828-48. Epub May 25. PMID: 21613581

Ohiorhenuan, I.E., Mechler, F., Purpura, K.P., Schmid, A.M., Hu, Q., and Victor, J.D., 2010, Sparse coding and high-order correlations in fine-scale cortical networks. Nature. 466(7306):617-21. Epub 2010 Jul 4. PMID: 20601940

Hu, Q., and Victor, J.D., 2010, A set of high-order spatiotemporal stimuli that elicit motion and reverse-phi percepts. J Vis. 2010 Mar 25;10(3):9.1-16. PMID: 20377286

H. Hunter-Zinck

Hunter-Zinck H, Clark AG., 2015, “Aberrant time to most recent common ancestor as a signature of natural selection”, Mol Biol Evol., Oct; 32(10):2784-97. PubMed PMID: 26093129

Yu F, Lu J, Liu X, Gazave E, Chang D, Raj S, Hunter-Zinck H, Blekhman R, Arbiza L, Van Hout C, Morrison A, Johnson AD, Bis J, Cupples LA, Psaty BM, Muzny D, Yu J, Gibbs RA, Keinan A, Clark AG, Boerwinkle E., 2015, “Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions,” PLoS One., Mar 25; 10(3):e0121644. PMID: 25807536; PMCID: PMC4373932

Rodriguez-Flores JL, Fakhro K, Hackett NR, Salit J, Fuller J, Agosto-Perez F, Gharbiah M, Malek JA, Zirie M, Jayyousi A, Badii R, Al-Marri AA, Chouchane L, Stadler DJ, Hunter-Zinck H, Mezey JG, Crystal RG., 2013, “Exome Sequencing Identifies Potential Risk Variants for Mendelian Disorders at High Prevalence in Qatar,” Human Mutation 2014 Jan;35(1):105-16. doi: 10.1002/humu.22460. Epub 2013 Nov 10. PMID: 24123366

Hunter-Zinck H, Musharoff S, Salit J, Al-Ali KA, Chouchane L, Gohar A, Matthews R, Butler MW, Fuller J, Hackett NR, Crystal RG, Clark AG., 2010, Population genetic structure of the people of Qatar. Am J Hum Genet. 87(1):17-25. Epub 2010 Jun 24.

S. Hyland Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A. 2015, Identification of active transcriptional regulatory elements from GRO-seq data, Nat Methods 12(5):433-8. doi: 10.1038/nmeth.3329. Epub 2015 Mar 23. PMID:25799441 PMCID: PMC4507281
H. Ingólfsson

Herold KF, Sanford RL, Lee W, Schultz MF, Ingólfsson HI, Andersen OS, Hemmings HC Jr, 2014, “Volatile anesthetics inhibit sodium channels without altering bulk lipid bilayer properties.” J Gen Physiol 144(6):545-60. doi: 10.1085/jgp.201411172. Epub 2014 Nov 10. PMID:25385786 PMCID: PMC4242807

Ingólfsson HI, Thakur P, Herold KF, Hobart EA, Ramsey NB, Periole X, de Jong DH, Zwama M, Yilmaz D, Hall K, Maretzky T, Hemmings HC Jr, Blobel C, Marrink SJ, Koçer A, Sack JT, Andersen OS, 2014, “Phytochemicals perturb membranes and promiscuously alter protein function,”, ACS Chem. Biol. 9(8): 1788-98 doi: 10.1021/cb500086e. Epub 2014 Jun 17. PMID: 24901212 PMCID: PMC4136704

Darby CM, Ingólfsson HI, Jiang X, Shen C, Sun M, Zhao N, Burns K, Liu G, Ehrt S, Warren JD, Anderson OS, Brickner SJ, Nathan C., 2013, “Whole cell screen for inhibitors of pH homeostasis in Mycobacterium tuberculosis,” PLoS One. 8(7):e68942. doi: 10.1371/journal.pone.0068942. PMCID: PMC3728290. *

Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ., 2013, “The Power of Coarse-Graining in Biomolecular Simulations,” WIREs CMS. (in review).

Wassenaar TA, Ingólfsson HI, Prie M, Marrink SJ, Schäfer LV., 2013, “Mixing MARTINI: electrostatic coupling in hybrid atomistic–coarse-grained biomolecular simulations,” Journal of Physical Chemistry B, 117:3516–3530.

Ingólfsson HI, Koeppe RE 2nd, Andersen OS., 2011, “Effects of green tea catechins on gramicidin channel function and inferred changes in bilayer properties,” FEBS Lett., 585(19):3101-5. PMCID: PMC3188397

Ingólfsson HI, Andersen OS., 2011, “Alcohol’s effects on lipid bilayer properties,” Biophys J., 101(4):847-55. PMCID: PMC3175087

Ingólfsson HI, Li Y, Vostrikov VV, Gu H, Hinton JF, Koeppe RE 2nd, Roux B, Andersen OS., 2011, “Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations,” J Phys Chem B., 115(22):7417-26. PMCID: PMC3107394

Vostrikov VV, Gu H, Ingólfsson HI, Hinton JF, Andersen OS, Roux B, Koeppe RE 2nd., 2011, “Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments,” J Phys Chem B., 115(22):7427-32. PMCID: PMC3114435

Ingólfsson HI, Sanford RL, Kapoor R, Andersen OS., 2010, Gramicidin-based fluorescence assay; for determining small molecules potential for modifying lipid bilayer properties. J Vis Exp., (44). pii: 2131. doi: 10.3791/2131. PMID: 20972414

Ingólfsson HI, Andersen OS., 2010, Screening for small molecules’ bilayer-modifying potential using a gramicidin-based fluorescence assay. Assay Drug Dev Technol. 8(4):427-36. PMID: 20233091

Lundbaek JA, Collingwood SA, Ingólfsson HI, Kapoor R, Andersen OS., 2010, Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes. J R Soc Interface. 7(44):373-95. Epub 2009 Nov 25. PMID: 19940001. PMCID: PMC2842803.

Andersen OS, Ingólfsson HI, Lundbæk JA., 2009, “Ion channels. In Handbook of Molecular Biophysics,” Methods and Applications, edited by H.G. Bohr. WILEY-VCH Verlag GmbH & Co. KGaA

Ingolfsson H.I., R. Kapoor, S.A. Collingwood and O.S. Andersen., 2008, Single Molecule Methods for Monitoring Changes in Bilayer Elastic Properties. Journal of Visualized Experiments. PMID: not available.

Kapoor R., J.H. Kim, H.I. Ingolfsson and O.S. Andersen., 2008, Preparation of Artificial Bilayers for Electrophysiology Experiments. Journal of Visualized Experiments. PMID: not available.

Olaf S. Andersen, Helgi I. Ingolfsson and Jens A. Lundbaek., 2008, Ion Channels. In Wiley Encyclopedia of Chemical Biology. John Wiley & Sons, Inc. (book chapter).

Ingolfsson, H. and Yona, G., 2008, Protein domain prediction. In Structural Proteomics – High-throughput Methods, edited by Guss, M., Huber, T., and Kobe, B. Humana Press (book chapter).

Ingolfsson HI, Koeppe RE 2nd, Andersen OS., 2007, Curcumin is a modulator of bilayer material properties. Biochemistry. 46(36):10384-91. Epub 2007 Aug 17. PMID: 17705403

Adachi, S., Nagao, T., Ingolfsson, H.I., Maxfield, F.R., Andersen, O.S., Kopelovich, L., and Weinstein, I.B., 2007, The Inhibitory Effect of (-)-Epigallocatechin Gallate (EGCG) on Activation of the Epidermal Growth Factor Receptor is Associated With Altered Lipid Order in HT29 Colon Cancer Cells. Cancer Res. 67(13):6493-501. PMID: 17616711

A. Joglekar

Mikheenko A, Prjibelski AD, Joglekar A, Tilgner HU. Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns. Genome Res. 2022 Mar 17:gr.276405.121. doi: 10.1101/gr.276405.121. Epub ahead of print. PMID: 35301264.

Hardwick SA*, Hu W*, Joglekar A*, Fan L, …, Gan L, Tilgner HU. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nat Biotechnol. 2022 Mar 7. doi: 10.1038/s41587-022-01231-3. Epub ahead of print. PMID: 35256815.

Joglekar A, Prjibelski A, …, Ross ME, Tilgner HU. A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. Nat Commun. 2021 Jan 19;12(1):463. doi: 10.1038/s41467-020-20343-5. PMID: 33469025; PMCID: PMC7815907.

Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. Getting the Entire Message: Progress in Isoform Sequencing. Front Genet. 2019 Aug 16;10:709. doi:10.3389/fgene.2019.00709. eCollection 2019. Review. PubMed PMID: 31475029; PubMed Central PMCID: PMC6706457

Koopmans F, van Nierop P,…Joglekar A,…Verhage M. SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron. 2019 Jul 17;103(2):217-234.e4. doi: 10.1016/j.neuron.2019.05.002. Epub 2019 Jun 3. PubMed PMID: 31171447; PubMed Central PMCID: PMC6764089

Gupta I, Collier PG, Haase B, Mahfouz A, Joglekar A, Floyd T, Koopmans F, Barres B, Smit AB, Sloan SA, Luo W, Fedrigo O, Ross ME, Tilgner HU. Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nat Biotechnol. 2018 Oct 15. doi: 10.1038/nbt.4259. [Epub ahead of print] PubMed PMID: 30320766

K. Johnson

Hoshino A*, Kim HS*, Bojmar L*, Gyan KE*, Cioffi M, Hernandez J, Zambirinis CP, Rodrigues G, Molina H, Heissel S, Harris A… Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers. Cell. 2020 Aug 20;182(4):1044-1061.e18. doi: 10.1016/j.cell.2020.07.009. Epub 2020 Aug 13. PMID: 32795414; PMCID: PMC7522766

Bojmar L, Kim HS, Tobias GC, Pelissier Vatter FA, Lucotti S, Gyan KE, Kenific CM, Wan Z, Kim KA, Kim D, Hernandez J, Pascual V, Heaton TE, La Quaglia MP, Kelsen D, Trippett TM, Jones DR, Jarnagin WR, Matei IR, Zhang H, Hoshino A, Lyden D. Extracellular vesicle and particle isolation from human and murine cell lines, tissues, and bodily fluids. STAR Protoc. 2020 Dec 22;2(1):100225. doi: 10.1016/j.xpro.2020.100225. PMID: 33786456; PMCID: PMC7988237

B. Kaminow

Kaminow, B, Ballouz, S, Gillis, J, Dobin, A (2022). Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses. Genome Res. 32: 738-749. PMID: 35256454 PMCID: 8997357

Wang, Y, Fass, J, Kaminow, B, Herr, JE, Rufa, D, Zhang, I, Pulido, I, Henry, M, Macdonald, B, Hannah, E, Takaba, K, Chodera, JD. (2022). End-to-end differentiable construction of molecular mechanics force fields”, Chemical Science 13: 12016-12033. PMID: 36349096 PMCID: 9600499

Boby, ML, Fearon, D, Ferla, M, Mihajlo, F, Koekemoer, L, Robinson, MC. The COVID Moonshot Consortium (multiple authors), Chodera, JD, Lee, A, London, N, von Delft, A, von Delft, F. …. Kaminow, B…. (2023). Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science, 382: 663-678. PMID: 37943932 PMCID: 7615835

Saar, KL, McCorkindale, W, Fearon, D, Boby, M, Barr, H, Ben-Shmuel, A, COVID Moonshot Consortium (multiple authors…. Kaminow, B,…), London, N, von Delft, F, Chodera, JD, Lee, Lee, AA. (2023). Turning high-throughput structural biology into predictive inhibitor design. Proc. Natl. Acad. Sci USA 120(11):e2214168120. doi:10.1073/pnas,22141668120. Epub 2023 Mar 6.
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Wang, Y, Pulidao, I, Tabaka, K, Kaminow, B, Sheen, J, Wang, L, Chodera, JD. (2024). Espaloma charge: Machine-learning-enabled ultrafast partial charge assignment. J. Phys. Chem. 128: 4160-4067. PMID: 38717302 PMCID: 11129294

P. Kaushik

Kaushik P, Molinelli EJ, Miller ML, Wang W, Korkut A, Liu W, Ju Z, Lu Y, Mills G, Sander C, 2014, Spatial normalization of reverse phase protein array data,” PLoS One. 9(12):e97213. doi: 10.1371/journal.pone.0097213. eCollection 2014 PMID: 25501559 PMCID: PMC4264691

Molinelli E, Korkut A, Wang W, Miller M, Gauthier N, Jing X, Kaushik P, He Q, Weigt M, Braunstein A, Pagnani A, Zecchina R, Sander S, 2013, “Perturbation Biology: inferring signaling networks in cellular systems,” PLOS Computational Biology, 9(12). PMCID: PMC3868523

Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL., 2010, “Integrative genomic profiling of human prostate cancer,” Cancer Cell, 18(1):11-22. PMCID: PMC3198787

Tasseff R, Nayak S, Salim S, Kaushik P, Rizvi N, Varner JD., 2010, “Analysis of the molecular networks in androgen dependent and independent prostate cancer revealed fragile and robust subsystems,” PLoS One., 5(1):e8864. PMCID: PMC2812491

E. Kenny

Vacic V, Ozelius LJ, Clark LN, Bar-Shira A, Gana-Weisz M, Gurevich T, Gusev A, Kedmi M, Kenny EE, Liu X, Mejia-Santana H, Mirelman A, Raymond D, Saunders-Pullman R, Desnick RJ, Atzmon G, Burns ER, Ostrer H, Hakonarson H, Bergman A, Barzilai N, Darvasi A, Peter I, Guha S, Lencz T, Giladi N, Marder K, Pe’er I, Bressman SB, Orr-Urtreger A., 2014, Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes. Hum Mol Genet. Sep 1;23(17):4693-702. doi: 10.1093/hmg/ddu158. Epub May 19. PubMed PMID: 24842889; PubMed Central PMCID: PMC4119402

Kenny EE, Atzmon G, Bergman A, Chowders J, Darvasi A, Desnick JR, Eliakim R, Erazo M, Gregersen P, Hakonarson H, Karban A, Mayer L, McGovern D, Mitchell A, Mulle J, Ostrer H, Ozelius L, Pulver A, Ullman T, Waterman M, Pe’er I, Peters I and Cho J., 2012, “Genome-wide scan of Ashkenazi Jewish Crohn’s Disease suggest novel susceptibility loci unique to this population,” PLoS Genet, 8(3)

Gusev A, Shah MJ, Kenny EE, Ramachandran A, Lowe JK, Salit J, Lee CC, Levandowsky EC, Weaver TN, Doan QC, Peckham HE, McLaughlin SF, Lyons MR, Sheth VN, Stoffel M, De La Vega FM, Friedman JM, Breslow JL, Pe’er I., 2012, “Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population,” Genetics., 190(2):679-89. PMCID: PMC3276614

Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, Smith JG, Kovvali S, Min Kang H, Newton-Cheh C, Daly M, Stoffel M, Altshuler DM, Friedman JM, Eskin E, Breslow JL and Pe’er I. Increased power of mixed-models facilitates association mapping of 10 loci for metabolic traits in an isolated population. Hum Mol Genet. 2011 Feb 15;20(4):827-39. Epub 2010 Nov 30. PMID: 21118897

Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler DM, Friedman JM, Breslow JL, Pe’er I., 2011, “DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation,” Am J Hum Genet., 88(6):706-17. PMCID: PMC3113343

Kenny EE, Gusev A, Riegel K, Lutjohann D, Lowe JK, Salit J, Maller JB, Stoffel M, Daly MJ, Altshuler DM, Friedman JM, Breslow JL, Pe’er I and Sehayek E., 2009, Systematic haplotype analysis resolves a complex locus affecting plasma plant sterol levels in a Micronesian Island population. Proc Natl Acad Sci U S A. Aug 18;106(33):13886-91. Epub Aug 10. PMID: 19667188

Lowe JK, Maller JB, Pe’er I, Neale BM, Salit J, Kenny EE, Shea JL, Burkhardt R, Ji W, Noel M, Nee Foo J, Blundell ML, Garcia L, Sullivan ML, Lee HE, Utterman A, Ferdowsian H, Lifton RP, Breslow JL, Stoffel M, Daly MJ, Altshuler DM, Friedman JM., 2009, “Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae” PLoS Genet. Feb;5(2):e1000365. Epub Feb 6. PMID: 19197348

Burkhardt R, Kenny EE and Breslow JL., 2009, “Genome-wide associations and lipid risk factors” Current Cardiovascular Lipid Reports 3(1):12-17

Burkhardt R, Kenny EE, Lowe JK, Birkeland A, Josowitz R, Noel M, Salit J, Maller JB, Pe’er I, Daly MJ, Altshuler D, Stoffel M, Friedman JM and Breslow JL., 2008, “Common SNPs in HMGCR in Micronesians and Caucasians associated with LDL-cholesterol levels affect alternative splicing of exon 13” Arterioscler Thromb Vasc Biol., 28(11):2078-84. Epub Sep 18. PMID: 18802019

M. Kim

Tang C, Xie AX, Liu EM, Kuo F, Kim M, et al. Immunometabolic coevolution defines unique microenvironmental niches in ccRCC. Cell Metabolism. 2023. doi: 10.1016/j.cmet.2023.06.005

Mahmood M, Liu EM, Shergold AL, et al. Tumour mitochondrial DNA mutations drive aerobic glycolysis to enhance checkpoint blockade. bioRxiv. 2023. doi: 10.1101/2023.03.21.533091

Kim M*, Mahmood M*, Reznik, E., et al. Mitochondrial DNA is a major source of driver mutations in cancer. Trends Cancer. 2022. doi: 10.1016/j.trecan.2022.08.001 *These authors contributed equally.

Tourigny DS., Zucker M, Kim M, et al. Molecular Characterization of the Tumor Microenvironment in Renal Medullary Carcinoma. Frontiers in Oncology. 2022. doi: 10.3389/fonc.2022.910147

Gorelick AN, Kim M, Chatila WK, et al. Respiratory complex and tissue lineage drive recurrent mutations in tumour mtDNA. Nat Metab. 2021. doi: 10.1038/s42255-021-00378-8

Seidman DN, Shenoy SA, Kim M, et al. Rapid, Phase-free Detection of Long Identity-by-Descent Segments Enables Effective Relationship Classification. AJHG. 2020. doi: 10.1016/j.ajhg.2020.02.012

C. Krishna

Chowell D*, Krishna C*, Pierini F*, Makarov V, Rizvi NA, Kuo F, Morris LGT, Riaz N, Lenz TL, Chan TA. “Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy.” Nat Med. 2019 Nov;25(11):1715-1720. doi:10.1038/s41591-019-0639-4. Epub 2019 Nov 7. PubMed PMID: 31700181

Weizman OE, Song E, Adams NM, Hildreth AD, Riggan L, Krishna C, Aguilar OA, Leslie CS, Carlyle JR, Sun JC, O’Sullivan TE. “Mouse cytomegalovirus-experienced ILC1s acquire a memory response dependent on the viral glycoprotein m12.” Nat Immunol. 2019 Aug;20(8):1004-1011. doi: 10.1038/s41590-019-0430-1. Epub 2019 Jul 1. PubMed PMID: 31263280; PubMed Central PMCID: PMC6697419

Khalil DN, Suek N, Campesato LF, Budhu S, Redmond D, Samstein RM, Krishna C,…Merghoub T. “In situ vaccination with defined factors overcomes T cell exhaustion in distant tumors.” J Clin Invest. 2019 Jul 22;129(8):3435-3447. doi: 10.1172/JCI128562. eCollection 2019 Jul 22. PubMed PMID: 31329159; PubMed Central PMCID: PMC6668692

Weizman O, Adams NM, Schuster I, Krishna C,.Leslie, CS. “ILC1 Confer Early Host Protection at Initial Sites of Viral Infection.” Cell. 2017 Nov 2;171(4):795-808.e12. Epub 2017 Oct 19. PMID: 29056343 PMCID: PMC5687850

Geary CD, Krishna C, Lau CM, Adams NM, Gearty SV, Pritykin Y, Thomsen AR, Leslie CS, Sun JC. “Non-redundant ISGF3 components promote NK cell survival in an auto-regulatory manner during viral infection.” Cell Rep. 2018 Aug 21;24(8):1949-1957.e6. PMID: 30134157 PMCID: PMC6153266

Mandal R, Samstein RM, Lee KW, Havel JJ, Wang H, Krishna C, Sabio EY, Makarov V, Kuo F, Blecua P, Ramaswamy AT, Durham JN, Bartlett B, Ma X, Srivastava R, Middha S, Zehir A, Hechtman JF, Morris LG, Weinhold N, Riaz N, Le DT, Diaz LA Jr, Chan TA. “Genetic diversity of tumors with mismatch repair deficiency influences anti-PD-1 immunotherapy response.” 2019 Science. 2019 May 3;364(6439):485-491. doi: 10.1126/science.aau0447. PMID:31048490 [PMC in process]

Yang W, Lee KW, Srivastava RM, Kuo F, Krishna C, Chowell D, Makarov V, Hoen D, Dalin MG, Wexler L, Ghossein R, Katabi N, Nadeem Z, Cohen MA, Tian SK, Robine N, Arora K, Geiger H, Agius P, Bouvier N, Huberman K, Vanness K, Havel JJ, Sims JS, Samstein RM, Mandal R, Tepe J, Ganly I, Ho AL, Riaz N, Wong RJ, Shukla N, Chan TA, Morris LGT. ” Immunogenic neoantigens derived from gene fusions stimulate T cell responses.” 2019 Nat Med. 2019 May;25(5):767-775. doi: 10.1038/s41591-019-0434-2. Epub 2019 Apr 22. PMID:31011208 [PMC in process]

K. La

Weber RA, Yen FS, Nicholson SPV, Alwaseem H, Bayraktar EC, Alam M, Timson RC, La K, Abu-Remaileh M, Molina H, Birsoy K. Maintaining Iron Homeostasis Is the Key Role of Lysosomal Acidity for Cell Proliferation. Mol Cell. 2020 Feb 6;77(3):645-655.e7. doi: 10.1016/j.molcel.2020.01.003. Epub 2020 Jan 23. PubMed PMID: 31983508

Zhu XG, Nicholson Puthenveedu S, Shen Y, La K, Ozlu C, Wang T, Klompstra D, Gultekin Y, Chi J, Fidelin J, Peng T, Molina H, Hang HC, Min W, Birsoy K. CHP1 Regulates Compartmentalized Glycerolipid Synthesis by Activating GPAT4. Mol Cell. 2019 Apr 4;74(1):45-58.e7. doi: 10.1016/j.molcel.2019.01.037. Epub 2019 Mar 4. PubMed PMID: 30846317; PubMed Central PMCID: PMC6450717

Williams RT, Guarecuco R, Gates LA, Barrows D, Passarelli MC, Carey B, Baudrier L, Jeewajee S, La K, Prizer B, Malik S, Garcia-Bermudez J, Zhu XG, Cantor J, Molina H, Carroll T, Roeder RG, Abdel-Wahab O, Allis CD, Birsoy K. ZBTB1 Regulates Asparagine Synthesis and Leukemia Cell Response to L-Asparaginase. Cell Metab. 2020 Apr 7;31(4):852-861.e6. doi:
10.1016/j.cmet.2020.03.008. PubMed PMID: 32268116

Garcia-Bermudez J, Baudrier L, Bayraktar EC, Shen Y, La K, Guarecuco R, Yucel B, Fiore D, Tavora B, Freinkman E, Chan SH, Lewis C, Min W, Inghirami G, Sabatini DM, Birsoy K., 2019, “Squalene accumulation in cholesterol auxotrophic lymphomas prevents oxidative cell death,” Nature., Mar;567(7746):118-122. doi:10.1038/s41586-019-0945-5. Epub 2019 Feb 13. PubMed PMID: 30760928; PubMed Central PMCID: PMC6405297

Garcia-Bermudez J, Baudrier L, La K, Zhu XG, Fidelin J, Sviderskiy VO, Papagiannakopoulos T, Molina H, Snuderl M, Lewis CA, Possemato RL, Birsoy K., 2018, “Aspartate is a limiting metabolite for cancer cell proliferation under hypoxia and in tumours, “ Nat Cell Biol., Jul;20(7):775-781. doi:10.1038/s41556-018-0118-z. Epub 2018 Jun 25. Erratum in: Nat Cell Biol. 2018 Oct;20(10):1228. PubMed PMID: 29941933; PubMed Central PMCID: PMC6030478

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, et al., “Oncogenic Signaling Pathways in The Cancer Genome Atlas,” Cell., Apr 5;173(2):321-337.e10. doi:10.1016/j.cell.2018.03.035. PubMed PMID: 29625050; PubMed Central PMCID: PMC6070353

Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C,Cherniack AD, Mina M, Ciriello G, Schultz N; Cancer Genome Atlas Research Network, Sanchez Y, Greene CS., 2018, “Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas,” Cell Rep., Apr 3;23(1):172-180.e3. doi: 10.1016/j.celrep.2018.03.046. PubMed PMID: 29617658; PubMed Central PMCID: PMC5918694

Reznik E, Luna A, Aksoy BA, Liu EM, La K, Ostrovnaya I, Creighton CJ, Hakimi AA, Sander C, 2018, “A Landscape of Metabolic Variation across Tumor Types.” Cell Syst. 2018 Mar 28;6(3):301-313.e3. doi: 10.1016/j.cels.2017.12.014. Epub 2018 Jan 27. PMID: 29396322

Rizvi H, Sanchez-Vega F, La K, Chatila W, Jonsson P, Halpenny D, Plodkowski A, Long N, Sauter JL, Rekhtman N, Hollmann T, Schalper KA, Gainor JF, Shen R, Ni A, Arbour KC, Merghoub T, Wolchok J, Snyder A, Chaft JE, Kris MG, Rudin CM, Socci ND, Berger MF, Taylor BS, Zehir A, Solit DB, Arcila ME, Ladanyi M, Riely GJ, Schultz N, Hellmann MD, 2018, “Molecular Determinants of Response to Anti-Programmed Cell Death (PD)-1 and Anti-Programmed Death-Ligand 1 (PD-L1) Blockade in Patients With Non-Small-Cell Lung Cancer Profiled With Targeted Next-Generation Sequencing.” J Clin Oncol. 2018 Mar 1;36(7):633-641. doi: 10.1200/JCO.2017.75.3384. Epub 2018 Jan 16. PMID: 29337640

Montero-Conde C, Leandro-Garcia LJ, Chen X, Oler G, Ruiz-Llorente S, Ryder M, Landa I, Sanchez-Vega F, La K, Ghossein RA, Bajorin DF, Knauf JA, Riordan JD, Dupuy AJ, Fagin JA., 2017, “Transposon mutagenesis identifies chromatin modifiers cooperating with Ras in thyroid tumorigenesis and detects ATXN7 as a cancer gene,” Proc Natl Acad Sci U S A., Jun 20;114(25):E4951-E4960. doi: 10.1073/pnas.1702723114. Epub 2017 Jun 5. PubMed PMID: 28584132; PMCID: PMC5488945

Bahceci I, Dogrusoz U, La KC, Babur Ö, Gao J, Schultz N., 2017, “PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data,” Bioinformatics, Jul 15;33(14):2238-2240. doi: 10.1093/bioinformatics/btx149. PubMed PMID: 28334343

Reznik E, Wang Q, La K, Schultz N, Sander C., 2017, “Mitochondrial respiratory gene expression is suppressed in many cancers,” Elife., Jan 18;6. pii: e21592. doi: 10.7554/eLife.21592. PubMed PMID: 28099114; PubMed Central PMCID: PMC5243113

Serano JM, Martin A, Liubicich DM, Jarvis E, Bruce HS, La K, Browne WE, Grimwood J, Patel NH., 2016, “Comprehensive analysis of Hox gene expression in the amphipod crustacean Parhyale hawaiensis,” Dev Biol., Jan 1;409(1):297-309. doi: 10.1016/j.ydbio.2015.10.029. Epub 2015 Nov 10. PubMed PMID: 26569556

M. Lee Lee MM, Arrenberg AB, Aksay ER3., 2015, “A structural and genotypic scaffold underlying temporal integration”, J Neurosci. 2015 May 20;35(20):7903-20. doi: 10.1523/JNEUROSCI.3045-14.2015. PMCID: PMC4438132
O. Lyudovyk

Lyudovyk, O., Kim, J.Y., Qualls, D., Hwee, M.A., Lin, Y.H., Boutemine, S.R., Elhanati, Y., Solovyov, A., Douglas, M., Chen, E., Babady, N.E., Ramanathan, L., Vedantam, P., Bandlamudi, C., Gouma, S., Wong, P., Hensley, S.E., Greenbaum, B., Huang, A.C., Vardhana, S.A. Impaired humoral immunity is associated with prolonged COVID-19 despite robust CD8 T cell responses. Cancer Cell. 2022 Jul 11;40(7):738-753.e5. doi: 10.1016/j.ccell.2022.05.013. Epub 2022 May 30. PMID: 35679859; PMCID: PMC9149241

DeWolf, S., Elhanati, Y., Nichols, K., Waters, N.R., Nguyen, C.L., Slingerland, J.B., Rodriguez, N., Lyudovyk, O., Giardina, P.A., Kousa, A.I., Andrlová, H., Ceglia, N., Fei, T., Kappagantula, R., Li, Y., Aleynick, N., Baez, P., Murali, R., Hayashi, A., Lee, N., Gipson, B., Rangesa, M., Katsamakis, Z., Dai, A., Blouin, A.G., Arcila, M., Masilionis, I., Chaligne, R., Ponce, D.M., Landau, H.J., Politikos, I., Tamari,R., Hanash, A.M., Jenq, R.R., Giralt, S.A., Markey, K.A., Zhang, Y., Perales, M.A., Socci, N.D., Greenbaum, B.D., et al. Tissue-specific features of the T cell repertoire after allogeneic hematopoietic cell transplantation in human and mouse. Sci Transl Med. 2023 Jul 26;15(706):eabq0476. doi: 10.1126/scitranslmed.abq0476. Epub 2023 Jul 26. PMID: 37494469; PMCID: PMC10758167

Wang, G., Lyudovyk, O., Kim, J.Y., Lin, Y.H., Elhanati, Y., Mathew, D., Wherry, E.J/, Herati, R.S., Greenplate, A.R., Greenbaum, B., Vardhana, S.A., Huang, A.C. High-throughput interrogation of immune responses using the Human Immune Profiling Pipeline. STAR Protoc. 2023 May 8;4(2):102289. doi: 10.1016/j.xpro.2023.102289. Epub ahead of print. PMID: 37159385; PMCID: PMC10193120.

M. MacKay

MacKay, M., Afshinnekoo, E., Rub, J. et al. The therapeutic landscape for cells engineered with chimeric antigen receptors. Nat Biotechnol (2020) doi:10.1038/s41587-019-0329-2

Vu LP, Pickering BF, Cheng Y, Zaccara S, Nguyen D, Minuesa G, Chou T, Chow A, Saletore Y, MacKay M, Schulman J, Famulare C, Patel M, Klimek VM, Garrett-Bakelman FE, Melnick A, Carroll M, Mason CE, Jaffrey SR, Kharas MG, 2018, “The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells.” Nat Med. Nov;23(11):1369-1376. doi: 10.1038/nm.4416. Epub 2017 Sep 18. PMID: 28920958 PMCID: PMC5677536 DOI: 10.1038/nm.4416

N. Madhukar

Gayvert KM, Madhukar NS, Elemento O, 2016, “A data-driven approach to predicting successes and failures of clinical trials,” Chem. Cell Biol. 23(10):1294-1301. doi: 10.1016/j.chembiol.2016.07.023. PMID: 27642066 PMCID: 5074862

Allen JE, Kline CL, Prabhu VV, Wagner J, Ishizawa J, Madhukar N, Lev A, Baumeister M, Zhou L, Lulla A, Stogniew M, Schalop L, Benes C, Kaufman HL, Pottorf RS, Nallaganchu BR, Olson GL, Al-Mulla F, Duvic M, Wu GS, Dicker DT, Talekar MK, Lim B, Elemento O, Oster W, Bertino J, Flaherty K, Wang ML, Borthakur G, Andreeff M, Stein M, El-Deiry WS, 2016, “Discovery and clinical introduction of first-in-class imipridone ONC201,”, Oncotarget. 7(45):74380-74392. doi: 10.18632/oncotarget.11814. Review. PMID: 27602582 PMCID: in process.

Madhukar NS, Elemento O, Pandey G. 2015, “Prediction of genetic interactions using machine learning and network properties,” Front. Bioeng. Biotechnol. 3:172. doi: 10.3389/fbioe.2015.00172. (Review) PMID: 26579514; PMCID 46200407

Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Chen Z, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson BD, Nanus DM, Tagawa ST, Xiang JZ, Smogorzewska A, Demichelis F, Rickman DS, Sboner A, Elemento O, Rubin MA, 2015, “Whole-exome sequencing of metastatic cancer and biomarkers of treatment response,” B JAMA Oncol. 1(4):466-74. doi: 10.1001/jamaoncol.2015.1313. PMID:26181256; PMCID: 4505739

Madhukar, N. S., Warmoes, M. O., & Locasale, J. W., 2015, “Organization of Enzyme Concentration across the Metabolic Network in Cancer Cells”, PLoS ONE, 10(1), e0117131. PMCID: PMC4306493

L. Mak

Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., … Mak,L.Others. (2021). A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell, 184(13), 3376–3393.

Mak, L., Meleshko, D., Danko, D. C., Barakzai, W. N., Maharjan, S., Belchikov, N., & Hajirasouliha, I. (2023). Ariadne: synthetic long read deconvolution using assembly graphs. Genome Biology, 24(1), 197.

Mak, L., Tierney, B., Ronkowski, C., Toomey, M., Martinez, J. S. A., Zimmerman, S., … Others. (2023). A modular metagenomics analysis system for integrated multi-step data exploration. bioRxiv, 2023–2004.

A. Maoz Maoz, A., Krogh-Madsen, T., and Christini, D., 2009, Instability in action potential morphology underlies phase-2 reentry-a mathematical modeling study. Heart Rhythm. 2009 Jun;6(6):813-22. Epub 2009 Mar 13. Erratum in: Heart Rhythm. 6(8):1255. PMID: 19467510
A. Marderstein

Marderstein AR, Uppal M, Verma A, Bhinder B, Tayyebi Z, Mezey J, Clark* AG, Elemento* O., (2020). Demographic and Genetic Factors Influence the Abundance of Infiltrating Immune Cells in Human Tissues. Nat Commun. 2020 May 5;11(1):2213. doi: 10.1038/s41467-020-16097-9 PMID: 32371927 PMCID: PMC7200670

Castellanos JG, Woo V, Viladomiu M, Putzel G, Lima S, Diehl GE, Marderstein AR, Gandara J, Perez AR, Withers DR, Targan SR, Shih DQ, Scherl EJ, Longman RS (2018). Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis. Immunity. 49(6):1077-1089.e5. doi: 10.1016/j.immuni.2018.10.014

AB. McIntyre

Imam H, Khan M, Gokhale NS, McIntyre ABR, Kim GW, Jang JY, Kim SJ, Mason CE, Horner SM, Siddiqui A, 2018, N6-methyladenosine modification of hepatitis B virus RNA differentially regulates the viral life cycle. Proc Natl Acad Sci U S A. Aug 28;115(35):8829-8834. doi: 10.1073/pnas.1808319115. Epub 2018 Aug 13. PMID: 30104368

Castro-Wallace SL, Chiu CY, John KK, Stahl SE, Rubins KH, McIntyre ABR ,…Mason CE, and Burton AS, 2017, “Nanopore DNA Sequencing and Genome Assembly on the International Space Station.” Sci Rep. 2017; 7: 18022. Published online 2017 Dec 21. doi: 10.1038/s41598-017-18364-0. PMCID: PMC5740133

McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE., 2017, “Comprehensive benchmarking and ensemble approaches for metagenomic classifiers,” Genome Biol., Sep 21;18(1):182. doi: 10.1186/s13059-017-1299-7. PubMed PMID: 28934964; PMCID: PMC5609029McIntyre ABR, Rizzardi L, Yu AM, Alexander N, Rosen GL, Botkin DJ, Stahl SE, John KK, Castro-Wallace SL, McGrath K, Burton AS, Feinberg AP, Mason CE., 2016, “Nanopore sequencing in microgravity,” NPJ Microgravity, Oct 20;2:16035. doi:10.1038/npjmgrav.2016.35. eCollection 2016. PubMed PMID: 28725742; PMCID: PMC5515536

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Jiang Y, Nie K, Redmond D, Melnick AM, Tam W, Elemento O, 2015, “VDJ-Seq: deep sequencing analysis of rearranged immunoglobulin heavy chain gene to reveal clonal evolution patterns of b cell lymphoma.” J Vis Exp. (106):e53215. doi: 10.3791/53215. PMID: 26780364

Ma J, Nie K, Redmond D, Liu Y, Elemento O, Knowles DM, Tam W., 2015, “EBV-miR-BHRF1-2 targets PRDM1/Blimp1: potential role in EBV lymphomagenesis,” Leukemia, Nov 4. doi: 10.1038/leu.2015.285. PMID: 26530011

Dominguez PM, Teater M, Chambwe N, Kormaksson M, Redmond D, Ishii J, Vuong B, Chaudhuri J, Melnick A, Vasanthakumar A, Godley LA, Papavasiliou FN, Elemento O, Shaknovich R., 2015, “DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID,” Cell Rep. Sep 29;12(12):2086-98. doi: 10.1016/j.celrep.2015.08.036. Epub 2015 Sep 10. PMID: 26365193 PMCID: PMC4591215

Pan H, Jiang Y, Boi M, Tabbò F, Redmond D, Nie K, Ladetto M, Chiappella A, Cerchietti L, Shaknovich R, Melnick AM, Inghirami GG, Tam W, Elemento O., 2015, “Epigenomic evolution in diffuse large B-cell lymphomas,” Nat Commun. 2015 Apr 20;6:6921. doi: 10.1038/ncomms7921. PMID: 25891015 PMCID: PMC4411286

Jiang Y, Redmond D, Nie K, Eng KW, Clozel T, Martin P, Tan LH, Melnick AM, Tam W, Elemento O., 2014, “Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas,” Genome Biol., Aug 15;15(8):432. doi: 10.1186/s13059-014-0432-0. PMID: 25123191 PMCID: PMC4158101

J. Reichel

Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M, 2015, “Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells,” Blood 125(7):1061-72. doi: 10.1182/blood-2014-11-610436. Epub 2014 Dec 8. PMID: 25488972

Vogel MJ, Xie L, Guan H, Tooze RM, Maier T, Kostezka U, Maier HJ, Holzmann K, Chan FC, Steidl C, Reichel JB, Weitzer CD, Gehringer F, Kick AB, Cesarman E, Roshal M, Gascoyne RD, Möller P, Wirth T, Ushmorov A, 2014, “FOXO1 repression contributes to block of plasma cell differentiation in classical Hodgkin lymphoma,” Blood 124(20):3118-29. doi: 10.1182/blood-2014-07-590570. Epub 2014 Sep 17. PMID: 25232062

Singh D, Chan JM, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EM, Reichel J, Porrati P, Pellegatta S, Qiu K, Gao Z, Ceccarelli M, Riccardi R, Brat DJ, Guha A, Aldape K, Golfinos JG, Zagzag D, Mikkelsen T, Finocchiaro G, Lasorella A, Rabadan R, Iavarone A., 2012, “Transforming fusions of FGFR and TACC genes in human glioblastoma,” Transforming fusions of FGFR and TACC genes in human glioblastoma,” Science, 337(6099):1231-5.

C. (Braiman) Reichenbach

Reichenbach CS, Braiman C, Schiff ND, Hudspeth AJ, Reichenbach T, 2016, “The auditory-brainstem response to continuous, non-repetitive speech is modulated by the speech envelope and reflects speech processing,” Front Comput Neurosci. 10:47. doi: 10.3389/fncom.2016.00047. eCollection 2016

Meltzer B, Reichenbach CS, Braiman C, Schiff ND, Hudspeth AJ, Reichenbach T., 2015, “The steady-state response of the cerebral cortex to the beat of music reflects both the comprehension of music and attention,” Front Hum Neurosci., Aug 6;9:436. doi: 10.3389/fnhum.2015.00436. eCollection 2015. PMID: 26300760 PMCID: PMC4526810

D. Reeves

Kolokotronis SO, Foox J, Rosenfeld JA, Brugler MR, Reeves D, Benoit JB, Booth W, Robison G, Steffen M, Sakas Z, Palli SR, Schal C, Richards S, Narechania A, Baker RH, Sorkin LN, Amato G, Mason CE, Siddall ME, DeSalle R, 2016, “The mitogenome of the bed bug Cimex lectularius (Hemiptera: Cimicidae),” Mitochondrial DNA B Resour. 1(1):425-427. PMID: 27617305

Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE. 2016, “Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius,” Nat Commun. 7:10164. doi: 10.1038/ncomms10164. PMID: 26836631

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE, 2015, “Geospatial resolution of human and bacterial diversity with city-scale metagenomics,” Cell Syst. 1(1):97-97.e3. doi: 10.1016/j.cels.2015.07.006. PMID: 27135689

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. 2015, “Modern methods for delineating metagenomic complexity,” Cell Syst. 1(1):6-7. doi: 10.1016/j.cels.2015.07.007. PMID: 27135684

Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE. 2016, “Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius,” Nat Commun. 7:10164. doi: 10.1038/ncomms10164. PMID: 26836631

Afshinnekoo E,…Reeves E,Salatore Y,Vijay P, et al., 2015, “Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics,” doi:10.1016/j.cels.2015.01.001

C. Ricketts

Ricketts C, Seidman D, Popic V, Hormozdiari F, Batzoglou S, Hajirasouliha I., 2019, “Meltos: Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants”, Bioinformatics., Oct 4. pii: btz737. doi: 10.1093/bioinformatics/btz737. [Epub ahead of print] PMID:31584621

Ricketts C, Popic V, Toosi H, Hajirasouliha I, 2018, “Using LICHeE and BAMSE for reconstructing cancer phylogenetic trees.” Curr Protoc Bioinformatics. Jun;62(1):e49. doi: 10.1002/cpbi.49. Epub 2018 May 16. PMID:29927069 PMCID: PMC6020047 DOI:10.1002/cpbi.49

A. Rizzi

Minuesa G, Albanese SK, Xie W, Kazansky Y, Worroll D, Chow A, Schurer A, Park SM, Rotsides CZ, Taggart J, Rizzi A, Naden LN, Chou T, Gourkanti S, Cappel D, Passarelli MC, Fairchild L, Adura C, Glickman JF, Schulman J, Famulare C, Patel M, Eibl JK, Ross GM, Bhattacharya S, Tan DS, Leslie CS, Beuming T, Patel DJ, Goldgur Y, Chodera JD, Kharas MG. Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia. Nat Commun. 2019 Jun 19;10(1):2691. doi:10.1038/s41467-019-10523-3. PubMed PMID: 31217428; PubMed Central PMCID:PMC6584500

Wade AD, Rizzi A, Wang Y, Huggins DJ. Computational Fluorine Scanning Using Free-Energy Perturbation. J Chem Inf Model. 2019 Jun 24;59(6):2776-2784. doi:10.1021/acs.jcim.9b00228. Epub 2019 May 9. PubMed PMID: 31046267

Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Overview of the SAMPL6 host-guest binding affinity prediction challenge. J Comput Aided Mol Des. 2018 Oct;32(10):937-963. doi: 10.1007/s10822-018-0170-6. Epub 2018 Nov 10. PubMed PMID: 30415285; PubMed Central PMCID: PMC6301044

Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK. Escaping Atom Types in Force Fields Using Direct Chemical Perception. J Chem Theory Comput. 2018 Nov
13;14(11):6076-6092. doi: 10.1021/acs.jctc.8b00640. Epub 2018 Oct 30. PubMed PMID: 30351006; PubMed Central PMCID: PMC6245550

B. Roberts

Roberts BN, Christini DJ., 2012, “The relative influences of phosphometabolites and pH on action potential morphology during myocardial reperfusion: a simulation study,” PLoS One., 7(11):e47117. PMCID: PMC3492384

Roberts BN, Christini DJ., 2011, NHE inhibition does not improve Na(+) or Ca(2+) overload during reperfusion: using modeling to illuminate the mechanisms underlying a therapeutic failure. PLoS Comput Biol., 7(10):e1002241. Epub 2011 Oct 20. PMID: 22028644

J. Rub

MacKay M, Afshinnekoo E, Rub J, Hassan C, Khunte M, Basharan N, Owens B, Liu L, Roboz GJ, Guzman ML, Melnick AM, Wu S, Mason CE (2020). The therapeutic landscape for cells engineered with chimeric antigen receptors. Nat. Biotechnol. 38: 233-244. PMID: 31907405

Singhal A, Styers HC, Rub J, Li Z, Torborg SR, Kim JY, Grbovic-Huezo O, Feng H, Tarcan ZC, Ozkan, HS, Hallin J, Basturk O, Yaeger R, Christensen JG, Betel D, Yan Y, Chio IIC, de Stanchina E, Tammela T. (2024). A classical epithelial state drives acute resistance to KRAS inhibition in pancreas cancer. Cancer Discov Jul 8. doi: 10.1158/2159-8290.CD-24-0740.PMID: 38975873

M. Sahin Carty M, Zamparo L, Sahin M, González A, Pelossof R, Elemento O, Leslie CS., 2017, “An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data,” Nat Commun., May 17;8:15454. doi: 10.1038/ncomms15454. PubMed PMID: 28513628; PMCID: PMC5442359
Y. Saletore

ichinchi G, Gao S, Saletore Y, Gonzalez GM, Bansal V, Wang Y, Mason CE, Rana TM, 2016, “Dynamics of the human and viral m(6)A RNA methylomes during HIV-1 infection of T cells,” Nat Microbiol. 1:16011. doi: 10.1038/nmicrobiol.2016.11.PMID: 275724

Afshinnekoo E,…Reeves E,Salatore Y,Vijay P, et al., 2015, “Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics,” doi:10.1016/j.cels.2015.01.001

Hess ME, Hess S, Meyer KD, Verhagen LA, Koch L, Bronneke HS, Dietrich MO, Jordan SD, Saletore Y, Elemento O, Belgardt BF, Franz T, Horvath TL, Ruther U, Jaffrey SR, Kloppenburg P, Bruning JC., 2013, “The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry,” Nature Neuroscience, 16(8):1042-8.

Saletore Y, Chen-Kiang S, Mason CE., 2013, “Novel RNA regulatory mechanisms revealed in the epitranscriptome,” RNA Biol.,10(3). PMC Journal – In Process

Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE., 2012, “The birth of the Epitranscriptome: deciphering the function of RNA modifications,” Genome Biol., 13(10):175. PMCID: PMC3491402

Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR., 2012, “Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons,” Cell, 149(7):1635-46. PMCID: PMC3383396

A. Schaumberg

Schaumberg AJ, Juarez-Nicanor WC, Choudhury SJ, Pastrián LG, Pritt BS, Prieto Pozuelo M, Sotillo Sánchez R, Ho K, Zahra N, Sener BD, Yip S, Xu B, Annavarapu SR, Morini A, Jones KA, Rosado-Orozco K, Mukhopadhyay S, Miguel C, Yang H, Rosen Y, Ali RH, Folaranmi OO, Gardner JM, Rusu C, Stayerman C, Gross J, Suleiman DE, Sirintrapun SJ, Aly M, Fuchs TJ., “Interpretable multimodal deep learning for real-time pan-tissue pan-disease pathology search on social media.” Mod Pathol. 2020 May 28. doi: 10.1038/s41379-020-0540-1. Online ahead of print. PMID: 32467650

Schaumberg AJ, Joseph Sirintrapun S., Al-Ahmadie H.A., Schüffler P.J., Fuchs T.J. (2017) DeepScope: Nonintrusive Whole Slide Saliency Annotation and Prediction from Pathologists at the Microscope. In: Bracciali A., Caravagna G., Gilbert D., Tagliaferri R. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2016. Lecture Notes in Computer Science, vol 10477. Springer, Cham. https://doi.org/10.1007/978-3-319-67834-4_4 PubMed PMID: 29601065 PMCID: PMC5870882

Spencer AK, Schaumberg AJ, Zallen JA, 2017, Scaling of cytoskeletal organization with cell size in Drosophila.” Mol Biol Cell. 2017 Jun 1;28(11):1519-1529. doi: 10.1091/mbc.E16-10-0691. Epub 2017 Apr 12. PMID: 28404752

A. Schweickart

Gomari D*, Schweickart A*, et al. “Variational autoencoders learn universal latent representations of metabolomics data.” Nat Commun Bio 5, 645 (2022) https://doi.org/10.1038/s42003-022-03579-3 * Co-first author

Chetnik K, Benedetti E, Gomari D, Schweickart A , et al. “maplet: An R toolbox for modular and reproducible omics pipelines.” Bioinformatics 38, 4 (2022) doi:10.1093/bioinformatics/btab741

Soni, V., Bartelo, N., Schweickart, A., Chawla, Y., Dutta, A., Jain, S. (2023). Future perspectives of metabolomics: Gaps, planning, and recommendations. In: Soni, V.,
Hartman, T.E. (eds) Metabolomics. Springer, Cham. https://doi.org/10.1007/978-3-031-39094-4_14

Ma W, Smirnov D, Forman J, Schweickart A, et al. “DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations.” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15, 2 (2018). doi:10.1109/TCBB.2016.2537319

Schweickart A, Batra R, Neth BJ, Martino C, Shenhave L, Zhang AR, Shi P, Karu N, HuyhnK. Meikle PJ, Schimmel L, Dilmore AH, Blennow K, Zetterberg H, Blach, C, Dorrestein PC, Knight R, Alzheimer’s gut microbome project consortium; Craft S, Kaddurah-Daouk R, Krumsiek J. (2024). Serum and CSF metabolomics analysisshows Mediterranean ketogenic diet mitigates risk factors of Alzheimer’s disease. NPJ Metab. Health Dis. 2(1):15. PMID: 38962750 PMCID: 10705656

Schweickart A , et al. “AutoFocus: A hierarchical framework to explore multi-omic disease associations spanning multiple scales of biomolecular interaction.” bioRxiv (2023)

Houerbi N. Kim J., Overbey EG, Batra R. Schweickart A, ……. Krumsiek J, ….Mason CE (multiple authors) (2024). Secretome profiling reveals acute changes in oxidative stress, brain homeostatis, and coagulation following short-duration spaceflight. Nat. Commun 15(1): 4862 PMID: 38862464.

Siew, K. Nestler, KA, Nelson, C, D’Ambrosio, V, Zhong C,…Schweickart, A. Mason, CE (multiple authors) (2024). Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction.Nat. Commun. 15(1): 4923.

S. Shenker

Wen J, Ladewig E, Shenker S, Mohammed J, Lai EC., 2015, “Analysis of nearly one thousand mammalian mirtrons reveals novel features of dicer substrates,” PLoS Comput. Biol., Sep 1: 11(9): E1004441. PMCID: PMC4556696

Shenker S, Miura P, Sanfilippo P, Lai EC., 2015, “IsoSCM: improved and alternative 3′ UTR annotation using multiple change-point inference,” RNA Jan; 21(1):14-27. PMCID: PMC4274634

Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker SE, Graveley BR, Lai EC., 2014, “Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation,” Cell Rep., Dec 11: 9(5): 1966-80. PMCID: PMC4279448

Miura P, Sanfilippo P, Shenker S, Lai EC., 2014, “Alternative polyadenylation in the nervous system: to what lengths will 3′ UTR extensions take us?”, Bioessays, Aug; 36(8):766-77. PMCID: PMC4503322

Brown JB,…Shenker S, et al. 2014, “Diversity and dynamics of the Drosophila transcriptome,” Nature, 512(7515):393-9. PMCID: PMC4152413

Miura P, Shenker S, Andreu-Agullo C, Westholm JO, Lai EC, 2013, “Widespread and extensive lengthening of 3′ UTRs in the mammalian brain,” Genome Research., 23(5):812-25. PMCID: PMC3638137

Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, Graveley BR, Lai EC, 2012, “Global patterns of tissue-specific alternative polyadenylation in Drosophila,” Cell Reports, 1(3):277-89. PMCID: PMC3368434

D. Seidman Ricketts C, Seidman D, Popic V, Hormozdiari F, Batzoglou S, Hajirasouliha I., 2019, “Meltos: Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants”, Bioinformatics., Oct 4. pii: btz737. doi: 10.1093/bioinformatics/btz737. [Epub ahead of print] PMID:31584621
M.A. Sierra

Bijlani, S., Parker, C., Singh, N. K., Sierra, M. A., Foox, J., Wang, C. C., … & Venkateswaran, K. (2022). Genomic characterization of the titan-like cell producing Naganishia tulchinskyi, the first novel eukaryote isolated from the International Space Station. Journal of Fungi.

Danko, D. C., Sierra, M. A., Benardini, J. N., Guan, L., Wood, J. M., Singh, N., … & Mason, C. E. (2021). A comprehensive metagenomics framework to characterize organisms relevant for planetary protection. Microbiome, 9, 1-15

Sierra, M. A., Ryon, K. A., Tierney, B. T., Foox, J., Bhattacharya, C., Afshin, E., … & Tighe, S. W. (2022). Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations. Environmental Microbiome, 17(1), 1-20.

Cifuentes, E. A., Sierra, M. A., Yepes, A. F., Baldión, A. M., Rojas, J. A., Álvarez-Moreno, C. A., … & Huertas, M. G. (2022). Endotracheal tube microbiome in hospitalized patients defined largely by hospital environment. Respiratory Research

Shiwa, Y., Baba, T., Sierra, M. A., Kim, J., Mason, C. E., & Suzuki, H. (2023). Evaluation of rRNA depletion methods for capturing the RNA virome from environmental surfaces. BMC Research Notes.

I. Singh

Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS., 2015, “Affinity regression predicts the recognition code of nucleic acid-binding proteins,” Nat Biotechnol. Dec;33(12):1242-1249. doi: 10.1038/nbt.3343. Epub 2015 Nov 16. PMID: 26571099

Han YC, Vidigal JA, Mu P, Yao E, Singh I, González AJ, Concepcion CP, Bonetti C, Ogrodowski P, Carver B, Selleri L, Betel D, Leslie C, Ventura A., 2015, “An allelic series of miR-17 ∼ 92-mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron,” Nat Genet. Jul;47(7):766-75. doi: 10.1038/ng.3321. Epub 2015 Jun 1. PMID: 26029871

Curanovic D, Cohen M, Singh, I, Slagle CD, Leslie CS, Jaffrey SR. “Global profiling of stimulus-induced polyadenylation in cells using a poly(A) trap,”Nat Chemical Biol. 2013; 9(11):671-3.

P. Srinivasan Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P,…Berger MF., 2017, “Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients,” Nat Med., Jun;23(6):703-713. doi: 10.1038/nm.4333. Epub 2017 May 8. PubMed PMID: 28481359; PMCID: PMC5461196
CL. Tam

Luo, H., Cortés-López M, Tam, C.L., Xiao, M., Wakiro, I., Chu, K.L., Pierson, A., Chan, M., Chang, K., Yang, X., Fecko, D., Han, G., Ahn, E.E., Morris, Q.D., Landau, D.A., Kharas, M.G.SON is an essential m6A target for hematopoietic stem cell fate. Cell Stem Cell. 2023 Dec 7;30(12):1658-1673.e10. doi: 10.1016/j.stem.2023.11.006.

Ray, D., Laverty, K.U., Jolma, A., Nie, K., Samson, R., Pour, S,E., Tam, C.L., von Krosigk, N., Nabeel-Shah, S., Albu, M., Zheng, H., Perron, G., Lee, H., Najafabadi, H., Blencowe, B., Greenblatt, J., Morris, Q., Hughes, T.R. RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Sci Rep. 2023 Mar 31;13(1):5238. doi: 10.1038/s41598-023-32245-9.

Y. Tazi

Tazi Y, Arango-Ossa JE, Zhou Y, Bernard E, Thomas I, Gilkes A, Freeman S , Pradat Y, Johnson SJ , Hills R, Dillon R, Levine MF, Leongamornlert D, Butler A, Ganser A, Bullinger L, Döhner K, Ottmann O, Adams R, Döhner H, Campbell PJ, Burnett AK, Dennis M, Russell NH, Devlin SM, Huntly B JP, Papaemmanuil E. Unified classification and risk-stratification in Acute Myeloid Leukemia. Nature Communications (2022)

Bolton KL, Chen D, Corona de la Fuente R, Fu Z, Murali R, Köbel M, Tazi Y, Cunningham JM, Chan I CC, Wiley BJ, Moukarzel LA, Winham SJ, Armasu SM, Lester J, Elishaev E, Laslavic A, Kennedy CJ, Piskorz A, Sekowska M, et al. Molecular subclasses of clear cell ovarian carcinoma and their impact on disease behavior and outcomes. Clinical Cancer Research Journal (2022)

Tazi Y, Arango JE, Zhou Y, Thomas I, Bernard E, Gilkes A. A unified classification and risk stratification algorithm to support clinical decisions in acute myeloid leukemia. Haematologica Journal (2021)

Lachowiez CA, Asimomitis G, Bernard E, Tang I, Tazi Y, Gilkes A, Thomas I, Bullinger L, Döhner K, Dohner H, Huntly B, Russell NH, Loghavi S, Papaemmanuil E. Influence of Bone Marrow Blast Enumeration and Co-Occurring Myelodysplasia Related Gene Mutations in NPM1-Mutated Myeloid Malignancies. Blood Journal (2023)

Othman J, Potter N, Ivey A, Tazi Y, Papaemmanuil E, Jovanovic J, Freeman SD, Gilkes A, Thomas I, Johnson S, Canham J, et al. Interaction between Presenting Features, Co-Occurring Mutations, MRD and Induction Treatment Influences Outcome in Adults with NPM1 Mutated AML-an Analysis of 1357 Patients in Adults with NPM1 Mutated AML – an Analysis of 1357 Patients in the UK NCRI AML17 and AML19 Studies. Blood Journal (2023)

Tazi Y, Berger M, Freiwald WA. Emergence of Interpretable Functional Specialization in Neural Networks Trained on Facial Expression and Identity Recognition
International Conference on Machine Learning (ICML). The 2023 ICML Workshop on Computational Issue. July 2023

Tazi Y, Berger M, Freiwald WA. Towards an objective characterization of an individual’s facial movements using Self-Supervised Person-Specific-Models. arXiv preprint arXiv:2211.08279. 2022/11/15

Khosravi P, Sutton EJ, Jee J, Dalfonso T, Fong CJ, Rose D, Da Silva EM, Kohli A, Ho DJ, Ahmed MS, Martinez D, Begum A, Zakszewski E, Aukerman A, Tazi Y, Pinker-Domenig K, Eskreis-Winkler S, Khan AJ, Brogi E, Morris E, Chandarlapaty S, Plitas G, et al. Prediction of neoadjuvant treatment outcomes with multimodal data integration in breast cancer. Cancer Research (2022)

D. Terry

Jenner L, Starosta AL, Terry DS, Mikolajka A, Filonava L, Yusupov M, Blanchard SC, Wilson DN, Yusupova G., 2013, “Structural basis for potent inhibitory activity of the antibiotic tigecycline during protein synthesis,” Proc Natl Acad Sci U S A., 110(10):3812-6. PMCID: PMC3593886

Altman RB, Zheng Q, Zhou Z, Terry DS, Warren JD, Blanchard SC., 2012, Enhanced photostability of cyanine fluorophores across the visible spectrum. Nat Methods., 9(5):428-9. doi: 10.1038/nmeth.1988. No abstract available. PMID: 22543373

Altman RB, Terry DS, Zhou Z, Zheng Q, Geggier P, Kolster RA, Zhao Y, Javitch JA, Warren JD, Blanchard SC., 2011, Cyanine fluorophore derivatives with enhanced photostability. Nat Methods., 9(1):68-71. doi: 10.1038/nmeth.1774. PMID: 22081126

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T. Yaron

Han Y*, Duan X*, Yang L*, Nilsson-Payant BE*, Wang P*, Duan F*, Tang X*, Yaron TM*, Zhang T, Uhl S, Bram Y, …, Cantley LC, …, Chen S. Identification of SARS-CoV-2 Inhibitors using Lung and Colonic Organoids. Nature. 2020 Oct 28:1-8. PMID: 33116299 PMCID: PMC8034380

Robert T, Johnson JL, Guichaoua R, Yaron TM, Bach S, Cantley LC, Colas P., “Development of a CDK10/CycM in vitro kinase screening assay and identification of first small-molecule inhibitors”. Frontiers in Chemistry. 2020 Feb 27;8:147.PMID: 32175313 PMCID: PMC7056863

Ferguson FM, Doctor ZM, Ficarro SB, Browne CM, Marto JA, Johnson JL, Yaron TM, Cantley LC, Kim ND, Sim T, Berberich MJ., “Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. Cell chemical biology”. 2019 Jun 20;26(6):804-17. PMID: 30930164 PMCID: PMC6588450

Liu C, Knudsen GM, Pedley AM, He J, Johnson JL, Yaron TM, Cantley LC, Benkovic SJ., “Mapping post-translational modifications of de novo purine biosynthetic enzymes: Implications for pathway regulation”. Journal of proteome research. 2019 Apr 9;18(5):2078-87. PMID: 30964683 PMCID: PMC6499638

Zheng Y, Ramsamooj S, Li Q, Johnson JL, Yaron TM, Sharra K, Cantley LC., “Regulation of folate and methionine metabolism by multisite phosphorylation of human methylenetetrahydrofolate reductase”. Scientific reports. 2019 Mar 12;9(1):1-1.
PMID: 30862944 PMCID: PMC6414673

Browne CM, Jiang B, Ficarro SB, Doctor ZM, Johnson JL, Card JD, Sivakumaren SC, Alexander WM, Yaron TM, Murphy CJ, Kwiatkowski NP., “A chemoproteomic strategy for direct and proteome-wide covalent inhibitor target-site identification”. Journal of the American Chemical Society. 2018 Dec 6;141(1):191-203. PMID: 30518210 PMCID: PMC6487859

A. Yu

Yu AM, Lucks JB. Tracking RNA structures as RNAs transit through the cell. Nat Struct Mol Biol. 2019 Apr;26(4):256-257. doi: 10.1038/s41594-019-0213-2. PubMed PMID: 30936529.

Carlson PD, Evans ME*, Yu AM*, Strobel EJ, Lucks JB. SnapShot: RNA Structure Probing Technologies. Cell. 2018 Oct 4;175(2):600-600.e1. doi:10.1016/j.cell.2018.09.024. PubMed PMID: 30290145; PubMed Central PMCID: PMC6582637

Xue AY, Yu AM, Lucks JB, Bagheri N. DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data. Bioinformatics. 2019 Dec 15;35(24):5103-5112. doi: 10.1093/bioinformatics/btz449.
PubMed PMID: 31389563; PubMed Central PMCID: PMC6954663

Strobel, EJ, Yu, AM, Lucks, JB, 2018, “High-throughput determination of RNA structures.” Nat Rev Genet. 2018 Jul 27. doi: 10.1038/s41576-018-0034-x. [Epub ahead of print] PMID: 30054568

McIntyre ABR, Rizzardi L, Yu AM, Alexander N, Rosen GL, Botkin DJ, Stahl SE, John KK, Castro-Wallace SL, McGrath K, Burton AS, Feinberg AP, Mason CE., 2016, “Nanopore sequencing in microgravity,” NPJ Microgravity, Oct 20;2:16035. doi:10.1038/npjmgrav.2016.35. eCollection 2016. PubMed PMID: 28725742; PMCID: PMC5515536

Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB, 2016, “Cotranscriptional folding of a riboswitch at nucleotide resolution,”, Nat Struct Mol Biol. 23(12):1124-1131. doi: 10.1038/nsmb.3316. PMID: 27798597

Watters KE, Yu AM, Strobel EJ, Settle AH, Lucks JB, 2016, “Characterizing RNA structures in vitro and in vivo with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq),”, Methods 1:103:34-48. doi: 10.1016/j.ymeth.2016.04.002. PMID: 27064082 PMCID: PMC4921265

H. Yuan

Yuan H, Paskov I, Paskov H, González AJ, Leslie CS. 2016, “Multitask learning improves prediction of cancer drug sensitivity.” Sci Rep. 2016 Aug 23;6:31619. doi: 10.1038/srep31619. PMID: 27550087 PMCID: PMC4994023

Kotini AG, Chang CJ, Chow A, Yuan H, Ho TC, Wang T, Vora S, Solovyov A, Husser C, Olszewska M, Teruya-Feldstein J, Perumal D, Klimek VM, Spyridonidis A, Rampal RK, Silverman L, Reddy EP, Papaemmanuil E, Parekh S, Greenbaum BD, Leslie CS, Kharas MG, Papapetrou EP, 2017, “Stage-specific human induced pluripotent stem cells map the progression of myeloid transformation to transplantable leukemia,” Cell Stem Cell. 2017 Mar 2;20(3):315-328.e7. doi: 10.1016/j.stem.2017.01.009. Epub 2017 Feb 16. PMID: 28215825

K. Zawack

Love WJ, Zawack KA, Booth JG, Grӧhn YT, Lanzas C 2016, “Markov networks of collateral resistance: national antimicrobial resistance monitoring system surveillance results from escherichia coli isolates, 2004-2012,” PLoS Comput Biol. 12(11):e1005160. doi: 10.1371/journal.pcbi.1005160. PMID: 27851767 PMCID: PMC5112851

Zawack K, Li M, Booth JG, Love W, Lanzas C, Gröhn YT, 2016, “Monitoring antimicrobial resistance in the food supply chain and its implications for FDA policy initiatives,” Antimicrob Agents Chemother. 60(9):5302-11. doi: 10.1128/AAC.00688-16. PMID: 27324772

Rhoads TW, Prasad A, Kwiecien NW, Merrill AE, Zawack K, Westphall MS, Schroeder FC, Kimble J, Coon JJ, 2015, “NeuCode labeling in nematodes: proteomic and phosphoproteomic impact of ascaroside treatment in caenorhabditis elegans,” Mol Cell Proteomics 14(11):2922-35. doi: 10.1074/mcp.M115.049684.PMID: 26392051 PMCID: PMC4638036