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

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. Feb 6. doi: 10.1038/nchembio.2296. [Epub ahead of print] PMID: 28166210

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

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 fron 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.

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

S. Brooks

Pagovich OE, Wang B, Chiuchiolo MJ, Kaminsky SM, Sondhi D, Jose CL, Price CC, Brooks SF, Mezey JG, Crystal RG, 2016, “Anti-hIgE gene therapy of peanut-induced anaphylaxis in a humanized murine model of peanut allergy,” J Allergy Clin Immunol. 138(6):1652-1662.e7. doi: 10.1016/j.jaci.2016.03.053. PMID: 27372563

M. Carty

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

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 U S A. pii: 201609287. [Epub ahead of print] 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

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

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.

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.

L. DeVargas Roditi

Deng P, de Vargas Roditi L, van Ditmarsch D, Xavier JB, 2014, “The ecological basis of morphogenesis: branching patterns in swarming colonies of bacteria.” New J Phys. 16:015006-15006. PMID: 24587694 PMCID: PMC3935381

De Vargas Roditi L, Boyle KE, Xavier JB., 2013, “Multilevel selection analysis of a microbial social trait,” Mol Syst Biol. 9:684. doi:10.1038/msb.2013.42. PMCID:PMC3779802. **

De Vargas Roditi L, Michor F., 2011, Evolutionary dynamics of BRCA1 alterations in breast tumorigenesis. J Theor Biol. Mar 21;273(1):207-15. Epub 2010 Dec 29. PMID: 21194536

Hooker G, Ellner SP, Roditi Lde V, Earn DJ., 2011, Parameterizing state-space models for infectious disease dynamics by generalized profiling: measles in Ontario. J R Soc Interface.  Jul 6;8(60):961-74. Epub 2010 Nov 17. PMID: 21084339

A. Doane

Doane AS, Elemento O, 2017, “Regulatory elements in molecular networks,” Wiley Interdiscip Rev Syst Biol Med. doi: 10.1002/wsbm.1374. [Epub ahead of print] PMID: 28093886

Jiang Y, Ortega-Molina A, Geng H, Ying HY, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre X, Teater M, Meydan C, Li Z, Poloway D, Wang S, Ennishi D, Scott DW, Stengel KR, Kranz JE, Holson E, Sharma S, Young JW, Chu CS, Roeder RG, Shaknovich R, Hiebert SW, Gascoyne RD, Tam W, Elemento O, Wendel HG, Melnick AM, 2017, “CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas,” Cancer Discov. 7(1): 38-53. doi: 10.1158/2159-8290.CD-16-0975. PMID: 27733359

M. Doktorova

Heberle FA, Marquardt D, Doktorova M, Geier B, Standaert RF, Heftberger P, Kollmitzer B, Nickels JD, Dick RA, Feigenson GW, Katsaras J, London E, Pabst G, 2016, “Subnanometer structure of an asymmetric model membrane: Interleaflet coupling influences domain properties,” Langmuir. 32(20):5195-200. doi: 10.1021/acs.langmuir.5b04562. Epub 2016 May 16. PMID: 27128636 PMCID: PMC4910133

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

Heberle FA, Doktorova M, Goh SL, Standaert RF, Katsaras J, Feigenson GW., 2013, “Hybrid and nonhybrid lipids exert common effects on membrane raft size and morphology,”J Am Chem Soc., 135(40):14932-5.

N. Dukler

Dukler N, Gulko B, Huang YF, Siepel A, 2016, “Is a super-enhancer greater than the sum of its parts?”, Nat Genet. 2016 Dec 28;49(1):2-3. doi: 10.1038/ng.3759. PMID: 28029159

L. Fairchild

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

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

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. Oct 10 [Epub ahead of print].

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

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 resoves 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 assciated with LDL-cholesterol levels affect alternative splicing of exon 13” Arterioscler Thromb Vasc Biol., 28(11):2078-84. Epub Sep 18. PMID: 18802019

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
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

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
AB. McIntyre

Gokhale NS, McIntyre AB, McFadden MJ, Roder AE, Kennedy EM, Gandara JA, Hopcraft SE, Quicke KM, Vazquez C, Willer J, Ilkayeva OR, Law BA, Holley CL, Garcia-Blanco MA, Evans MJ, Suthar MS, Bradrick SS, Mason CE, Horner SM, 2016, “N6-methyladenosine in flaviviridae viral RNA genomes regulates infection,” Cell Host Microbe. 20(5):654-665. doi: 10.1016/j.chom.2016.09.015. PMID: 27773535 PMCID: PMC5123813

Vijay P, McIntyre AB, Mason CE, Greenfield JP, Li S, 2016, “Clinical genomics: Challenges and opportunities,” Crit Rev Eukaryot Gene Expr. 26(2):97-113. doi: 10.1615/Crit Rev Eukaryot Gene Expr.2016015724. PMID: 27480773

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

McIntyre AB, Cleland TA, 2016, “Biophysical constraints on lateral inhibition in the olfactory bulb,” J Neurophysiol. 115(6):2937-49. doi: 10.1152/jn.00671.2015. PMID: 27009162

T. Melman

Melman, T, Victor, JD, 2016, Robust power spectral estimation for EEG data,” J Neurosci Methods. 268:14-22. doi: 10.1016/j.jneumeth.2016.04.015. Epub 2016 Apr 19.

MJ. Meyer

Das J, Meyer MJ, Yu H, 2015, “Studying autism in context,” Cell Syst. 1(5):312-3. doi: 10.1016/j.cels.2015.11.004. Epub 2015 Nov 25. PMID: 27136240

Meyer MJ, Lapcevic R, Romero AE, Yoon M, Das J, Beltrán JF, Mort M, Stenson PD, Cooper DN, Paccanaro A, Yu H, 2016, “Mutation3D: cancer gene prediction through atomic clustering of coding variants in the structural proteome,” Hum. Mutat. 37(5): 447-56, doi: 10.1002/humu.22963. Epub 2016 Feb 18. PMID: 26841357 PMCID: PMC4833594

Meyer MJ, Geske P, Yu H, 2016, “BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers,” Bioinformatics. 15;32(10):1598-600. doi: 10.1093/bioinformatics/btw043. PMID: 26803163 DOI: 10.1093/bioinformatics/btw043

Das J, Fragoza R, Lee HR, Cordero NA, Guo Y, Meyer, MJ, VoTV, Wang X, YuH., 2014, “Exploring mechanisms of human disease through structurally resolved protein interactome networks,” Mol. Biosyst., 10(1):9-17. PMID: 24096645

Meyer MJ, Das J, Wang X, Yu H, 2013, “INstruct: a database of high quality three-dimensional structurally resolved protein interactome networks,” Bioinformatics, 29(12):1577-9. PMCID: PMC3673217

J. Mohammed

Chak LL, Mohammed J, Lai EC, Tucker-Kellogg G, Okamura K., 2015, “A deeply conserved, noncanonical miRNA hosted by ribosomal DNA”, RNA, Mar; 21(3):375-84. PMCID: PMC4338334

Grenier JK, Arguello JR, Moreira MC, Gottipati S, Mohammed J, Hackett SR, Boughton R, Greenberg AJ, Clark AG., 2015, “Global diversity lines – a five-continent reference panel of sequenced Drosophila melanogaster strains,” G3 (Bethesda), Feb 11;5(4):593-603. PMCID: PMC4390575

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

Mohammed J, Siepel A, Lai EC., 2014, “Diverse modes of evolutionary emergence and flux of conserved microRNA clusters,” RNA, Dec;20(12):1850-63. PMCID: PMC4238352

Mohammed J, Bortolamiol-Becet D, Flynt AS, Gronau I, Siepel A, Lai EC., 2014, “Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila,” RNA, Aug;20(8):1195-209. PMCID: PMC4105746

Mohammed J, Flynt AS, Siepel A, Lai EC., 2013, “The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution,” RNA, 19: 1295-308. PMCID: PMC3753935

Wen J, Mohammed J, Tsai H, Robine N, et al., 2013, “Diversity of miRNAs, siRNAs and piRNAs surveyed across 25 Drosophila cell lines,” Genome Research. PMCID: PMC4079977

Gronau I, Arbiza L, Mohammed J, Siepel A., 2012, “Inference of natural selection from interspersed genomic elements based on polymorphism and divergence,” Mol Biol Evol.,(5):1159-71. PMCID: PMC3697874

Das J, Mohammed J, Yu H., 2012, “Genome-scale analysis of interaction dynamics reveals organization of biological networks,” Bioinformatics. 28(14):1873-8. PMCID: PMC3492000

E. Molinelli

Okada T, Lee AY, Qin LX, Agaram N, Mimae T, Shen Y, O’Connor R, López-Lago MA, Craig A, Miller ML, Agius P, Molinelli E, Socci ND, Crago AM, Shima F, Sander C, Singer S, 2016, “Integrin-α10 dependency identifies RAC and RICTOR as therapeutic targets in high-grade myxofibrosarcoma.” Cancer Discov. 6(10):1148-1165. PMID: 27577794

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. 4. doi: 10.7554/eLife.04640. PMID: 26284497 PMCID: PMC4539601

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. PMID: 25501559 PMCID: PMC4264691

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

Molinelli EJ, 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

Miller ML, Molinelli EJ, Nair JS, Sheikh T, Samy R, Jing X, He Q, Korkut A, Crago AM, Singer S, Schwartz GK, Sander C., 2013, “Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma Identifies CDK4 and IGF1R as Synergistic Drug Targets,” Sci Signal., 6(294):ra85. doi: 10.1126/scisignal.2004014.

Wang Q, Navarro MVAS, Peng G, Molinelli E, Goh SL, Judson BL, Rajashankar KR, Sodermann H., 2009, Molecular mechanism of membrane constriction and tubulation mediated by the F-BAR protein Pacsin/Syndapin. Proc Natl Acad Sci U S A., 106(31):12700-5. Epub 2009 Jun 19. PMID: 19549836

H. Monaco

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JL. Moore

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Pohl C, Tiongson M, Moore JL, Santella A, Bao Z., 2012, “Actomyosin-based self-organization of cell internalization during C. elegans gastrulation,” BMC Biol., 10:94. PMCID: PMC3583717

T. Nauvel

Adams ZM, Forgacs PB, Conte MM, Nauvel TJ, Drover JD, Schiff ND, 2016, “Late and progressive alterations of sleep dynamics following central thalamic deep brain stimulation (CT-DBS) in chronic minimally conscious state.” Clin Neurophysiol. 127(9):3086-92. doi: 10.1016/j.clinph.2016.06.028. PMID:27472544

Schiff ND, Nauvel T, Victor JD., 2014, “Large-scale brain dynamics in disorders of consciousness,” Curr Opin Neurobiol., 25:7-14. PMID: 24709594

Schiff ND, Shah SA, Hudson AE, Nauvel, T, Kalik SF, Purpura KP., 2013, “Gating of attentional effort through the central thalamus,” J Neurophysiol. 109(4):1152-63. PMCID: PMC3569130.

P. Ng

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Ng P and Keich U., 2008, GIMSAN: A Gibbs motif finder with significance analysis. Bioinformatics., 24(19):2256-7. Epub 2008 Aug 14. PMID: 18703586

Keich U, Ng P., 2007, A conservative parametric approach to motif significance analysis. Genome Inform., 19:61-72. PMID: 18546505

Ng P, Keich U., 2008, Factoring local sequence composition in motif significance analysis. Genome Inform. 21:15-26. PMID: 19425144

Ng, P., Nagarajan, N., Jones, N., and Keich, U., 2006, Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone Bioinformatics. Bioinformatics. 22(14):e393-401. PMID: 16873498

Z. Nichols

Nichols Z, Nirenberg S, Victor J., 2013, “Interacting Linear and Nonlinear Characteristics Produce Population Coding Asymmetries between ON and OFF Cells in the Retina,” J Neurosci., 33(37):14958-73. PMCID: PMC3771031

Meytlis M, Nichols Z, Nirenberg S., 2012, “Determining the role of correlated firing in large populations of neurons using white noise and natural scene stimuli,” Vision Res., 70:44-53. NIHMS399482

E. Nitzany

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Shamble PS, Menda G, Golden JR, Nitzany EI, Walden K, Beatus T, Elias DO, Cohen I, Miles RN, Hoy RR, 2016, “Airborne acoustic perception by a jumping spider,” Curr Biol. 26(21):2913-2920. doi: 10.1016/j.cub.2016.08.041. PMID: 27746028

Menda, G., Shamble, P. S., Nitzany, E. I., Golden, J. R., and Hoy, R. R., 2014, Visual Perception in the Brain of a Jumping Spider. Curr. Biol. 24, 2580–2585. PMID: 25308077

Gao Y, Nitzany E, Edelman S., 2012 “Online learning of causal structure in a dynamic game situation,” Proc. 34th Cognitive Science Society Conference, Sapporo, Japan, pages 372-377.

Nitzany EI,Victor JD., 2014, “The statistics of local motion signals in naturalistic movies,” J Vis., 14(4). PMCID: PMC3987513

L. Pipes

Lipovich L, Hou ZC, Jia H, Sinkler C, McGowen M, Sterner KN, Weckle A, Sugalski AB, Pipes L, Gatti DL, Mason CE, Sherwood CC, Hof PR, Kuzawa CW, Grossman LI, Goodman M, Wildman DE., 2016, “High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans,” J Comp Neurol. 2016 Feb 1;524(2):288-308. doi: 10.1002/cne.23843. Epub 2015 Aug 20. PMID: 26132897 PMCID:PMC4685035

Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE., 2015, “Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR),” Nucleic Acids Res., Jan;43 (Database issue):D737-42. PMID: 25392405; PMCID: PMC4383927

Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD., 2014, “Enabling large-scale next-generation sequence assembly with Blacklight”, Concurr Comput. Sep 10;26(13):2157-2166. PMID: 25294974; PMCID: PMC4185199

Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG, 2013, “The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics,” Nucleic Acids Research 41(Database issue):D906-14. PMCID: PMC3531109

D. Redmond

Page DB, Yuan J, Redmond D, Wen YH, Durack JC, Emerson R, Solomon S, Dong Z, Wong P, Comstock C, Diab A, Sung J, Maybody M, Morris E, Brogi E, Morrow M, Sacchini V, Elemento O, Robins H, Patil S, Allison JP, Wolchok JD, Hudis C, Norton L, McArthur HL, 2016, “Deep sequencing of T-cell receptor DNA as a biomarker of clonally expanded TILs in breast cancer after immunotherapy.” Cancer Immunol Res. 4(10):835-844. PMID: 27587469 PMCID: PMC5064839

Redmond D, Poran A, Elemento O, 2016, “Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq,” Genome Med. 8(1):80. doi: 10.1186/s13073-016-0335-7. PMID: 27460926 PMCID: PMC4962388
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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

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

Y. Saletore

Lichinchi 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

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

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.

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

Zhao Y, Terry DS, Shi L, Quick M, Weinstein H, Blanchard SC, Javitch JA., 2011, Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homologue. Nature., 474(7349):109-13. Epub 2011 Apr 24. PMID: 21516104

Zhao Y, Terry D, Shi L, Weinstein H, Blanchard SC, Javitch JA., 2010, “Single-molecule dynamics of gating in a neurotransmitter transporter homologue,” Nature, 465(7295):188-93. PMCID: PMC294011

Geggier P, Dave R, Feldman MB, Terry DS, Altman RB, Munro JB, Blanchard SC., 2010, Conformational Sampling of Aminoacyl-tRNA during Selection on the Bacterial Ribosome. J Mol Biol. PMID: 20434456

Feldman MB, Terry DS, Altman RB, Blanchard SC., 2010, Aminoglycoside activity observed on single pre-translocation ribosome complexes. Nat Chem Biol., 6(3):244. PMID: 20154669

Feldman, M.B., Terry, D.S., Altman, R.B., and Blanchard, S.C., 2010, Aminoglycoside activity observed on single pre-translocation ribosome complexes. Nature Chemical Biology 6: 54-62. PMID: 19946275

Dave, R., Terry, D. S., Munro, J. B., and Blanchard, S. C., 2009, Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging. Biophys J 96, 2371-2381. PMID: 19289062

N. Tippens

Liang S, Tippens ND, Zhou Y, Mort M, Stenson PD, Cooper DN, Yu H, 2017, “iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations”, Genome Biol. 18(1):10. doi: 10.1186/s13059-016-1138-2.
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Ang YS, Rivas RN, Ribeiro AJ, Srivas R, Rivera J, Stone NR, Pratt K, Mohamed TM, Fu JD, Spencer CI, Tippens ND, Li M, Narasimha A, Radzinsky E, Moon-Grady AJ, Yu H, Pruitt BL, Snyder MP, Srivastava D, 2016, “Disease model of GATA4 mutation reveals transcription factor cooperativity in human cardiogenesis,” Cell 167(7): 1734-1749.e22. doi: 10.1016/j.cell.2016.11.033. PMID: 27984724
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S. Tischfield

Lange J, Yamada S, Tischfield SE, Pan J, Kim S, Zhu X, Socci ND, Jasin M, Keeney S, 2016, “The landscape of mouse meiotic double-strand break formation, processing, and repair,” Cell
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Sasaki M, Tischfield, S, van Overbeek M, Keeney S., 2013, “Meiotic recombination initiation in and around retrotransposable elements in Saccharomyces cerevisiae,” PLoS Genet. Epub Aug 29. PMCID: PMC3757047.

Asselbergs FW,…Tischfield SE,…, 2012, “Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci,” Am J Hum Genet., 91(5):823-38. PMCID: PMC3487124

Guo Y,…Tischfield S,…, 2012, “Gene-centric meta-analyses of 108 912 individuals confirm known body mass index loci and reveal three novel signals,” Hum Mol Genet., 22(1):184-201. PMCID: PMC3522401

Tischfield SE, Keeney S., 2012, “Scale matters: the spatial correlation of yeast meiotic DNA breaks with histone H3 trimethylation is driven largely by independent colocalization at promoters,” Cell Cycle, 11(8):1496-503. PMCID: PMC3341227

Pan J, Sasaki M, Kniewel R, Murakami H, Blitzblau HG, Tischfield SE, Zhu X, Neale MJ, Jasin M, Socci ND, Hochwagen A, Keeney S., 2011, “A hierarchical combination of factors shapes the genome-wide topography of yeast meiotic recombination initiation,” Cell, 144(5):719-31. PMCID: PMC3063416

Lanktree MB,…Tischfield S,…, 2011, “Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height,” Am J Hum Genet., 88(1):6-18. PMCID: PMC3014369

P. Vijay

Vijay P, McIntyre AB, Mason CE, Greenfield JP, Li S, 2016, “Clinical genomics: Challenges and opportunities,” Crit Rev Eukaryot Gene Expr. 26(2):97-113. doi: 10.1615/CritRevEukaryotGeneExpr.2016015724. PMID: 27480773

Li S, Garrett-Bakelman FE, Chung SS, Sanders MA, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Cannon J, Bullinger L, Luger S, Becker M, Lewis ID, To LB, Delwel R, Löwenberg B, Döhner H, Döhner K, Guzman ML, Hassane DC, Roboz GJ, Grimwade D, Valk PJ, D’Andrea RJ, Carroll M, Park CY, Neuberg D, Levine R, Melnick AM, Mason CE, 2016, “Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia,” Nat Med. 22(7):792-9. doi: 10.1038/nm.4125. PMID: 27322744 PMCID: PMC4938719

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

Chiron D, Di Liberto M, Martin P, Huang X, Sharman J, Blecua P, Mathew S, Vijay P, Eng K, Ali S, Johnson A, Chang B, Ely S, Elemento O, Mason CE, Leonard JP, Chen-Kiang S., 2014, “Cell-cycle reprogramming for PI3K inhibition overrides a relapse-specific C481S BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma,” Cancer Discov. Sep;4(9):1022-35. PMCID: PMC4155003

C. Wellock Wellock CD, Reeke GN., 2012, Quantitative tools for examining the vocalizations of juvenile songbirds. Comput Intell Neurosci. 2012;2012:261010. doi: 10.1155/2012/261010. Epub. Jun 4. PMID: 22701474
JL. Yang

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

Lianoglou S, Garg V, Yang, JL, Leslie CS, Mayr C., 2013, “Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression,” Genes Dev. 27(21):2380-96. PMCID: PMC3828523

A. Yu

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 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 pii: S1934-5909(17)30031-0. doi: 10.1016/j.stem.2017.01.009. [Epub ahead of print] 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

Updated 3/2017