Student Publications

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

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

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.

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

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

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

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

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

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

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

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

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

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

Li YR, Li J, Zhao SD, Bradfield JP, Mentch FD, Maggadottir SM, Hou C, Abrams DJ, Chang D, Gao F, Guo Y, Wei Z, Connolly JJ, Cardinale CJ, Bakay M, Glessner JT, Li D, Kao C, Thomas KA, Qiu H, Chiavacci RM, Kim CE, Wang F, Snyder J, Richie MD, Flatø B, Førre Ø, Denson LA, Thompson SD, Becker ML, Guthery SL, Latiano A, Perez E, Resnick E, Russell RK, Wilson DC, Silverberg MS, Annese V, Lie BA, Punaro M, Dubinsky MC, Monos DS, Strisciuglio C, Staiano A, Miele E, Kugathasan S, Ellis JA, Munro JE, Sullivan KE, Wise CA, Chapel H, Cunningham-Rundles C, Grant SF, Orange JS, Sleiman PM, Behrens EM, Griffiths AM, Satsangi J, Finkel TH, Keinan A, Prak ET, Polychronakos C, Baldassano RN, Li H, Keating BJ, Hakonarson H, 2015, “Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases.” Nat Med. 21(9):1018-27. doi: 10.1038/nm.3933. PMID: 26301688 PMCID: PMC4863040

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

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

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