Metrics for Gerstein Lab Publications

Total papers: 702

(Last updated Mon Jul 22 17:44:25 2024)



Preprint (8)

Zhuosheng Zhang, Yao Yao, Aston Zhang, Xiangru Tang, Xinbei Ma, Zhiwei He, Yiming Wang, Mark Gerstein, Rui Wang, Gongshen Liu, Hai Zhao (2023). arXiv.
Yuliang Liu, Xiangru Tang, Zefan Cai, Junjie Lu, Yichi Zhang, Yanjun Shao, Zexuan Deng, Helan Hu, Zengxian Yang, Kaikai An, Ruijun Huang, Shuzheng Si, Sheng Chen, Haozhe Zhao, Zhengliang Li, Liang Chen, Yiming Zong, Yan Wang, Tianyu Liu, Zhiwei Jiang, Baobao Chang, Yujia Qin, Wangchunshu Zhou, Yilun Zhao, Arman Cohan, Mark Gerstein (2023). arXiv.
M Frank, P Ni, M Jensen, MB Gerstein (2023). bioRxiv.
B Borsari, M Frank, ES Wattenberg, K Xu, S Liu, X Yu, MB Gerstein (2023). bioRxiv.
F Reese, B Williams, G Balderrama-Gutierrez, D Wyman, MH Celik, E Rebboah, N Rezaie, D Trout, M Razavi-Mohseni, Y Jiang, B Borsari, S Morabito, HY Liang, CJ McGill, S Rahmanian, J Sakr, S Jiang, W Zeng, K Carvalho, AK Weimer, LA Dionne, A McShane, K Bedi, SI Elhajjajy, S Upchurch, J Jou, I Youngworth, I Gabdank, P Sud, O Jolanki, JS Strattan, MS Kagda, MP Snyder, BC Hitz, JE Moore, Z Weng, D Bennett, L Reinholdt, M Ljungman, MA Beer, MB Gerstein, L Pachter, R Guigo, BJ Wold, A Mortazavi (Preprint). bioRxiv.
CJF Cameron, SJH Seager, FJ Sigworth, HD Tagare, MB Gerstein (2023). bioRxiv.
J Warrell, H Mohsen, M Gerstein (2020). bioRxiv.
J Leng, CJF Cameron, S Oh, E Khurana, JP Noonan, MB Gerstein (2019). bioRxiv.



2024 (12)

X Tang, A Tran, J Tan, MB Gerstein (2024). Bioinformatics 40: i357-i368.
X Tang, A Zou, Z Zhang, Y Zhao, X Zhang, A Cohan, M Gerstein. 2024. MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning. In Findings of the Association for Computational Linguistics: ACL
X Tang, Y Zong, J Phang, Y Zhao, W Zhou, A Cohan, M Gerstein. 2024. Struc-Bench: Are Large Language Models Good at Generating Complex Structured Tabular Data?. In Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 2: Short Papers), pages 12–34, Mexico City, Mexico. Association for Computational Linguistics.
X Tang, B Qian, R Gao, J Chen, X Chen, MB Gerstein (2024). Bioinformatics 40: i266-i276.
SA Ament, RR Campbell, MK Lobo, JP Receveur, K Agrawal, A Borjabad, SN Byrareddy, L Chang, D Clarke, P Emani, D Gabuzda, KJ Gaulton, M Giglio, FM Giorgi, B Gok, C Guda, E Hadas, BR Herb, W Hu, A Huttner, MR Ishmam, MM Jacobs, J Kelschenbach, DW Kim, C Lee, S Liu, X Liu, BK Madras, AA Mahurkar, DC Mash, EA Mukamel, M Niu, RM O'Connor, CM Pagan, APS Pang, P Pillai, V Repunte-Canonigo, WB Ruzicka, J Stanley, T Tickle, SA Tsai, A Wang, L Wills, AM Wilson, SN Wright, S Xu, J Yang, M Zand, L Zhang, J Zhang, S Akbarian, S Buch, CS Cheng, MJ Corley, HS Fox, M Gerstein, S Gummuluru, M Heiman, YC Ho, M Kellis, PJ Kenny, Y Kluger, TA Milner, DJ Moore, S Morgello, LC Ndhlovu, TM Rana, PP Sanna, JS Satterlee, N Sestan, SA Spector, S Spudich, HU Tilgner, DJ Volsky, OR White, DW Williams, H Zeng (2024). Mol Psychiatry.
PS Emani, JJ Liu, D Clarke, M Jensen, J Warrell, C Gupta, R Meng, CY Lee, S Xu, C Dursun, S Lou, Y Chen, Z Chu, T Galeev, A Hwang, Y Li, P Ni, X Zhou, PsychENCODE Consortium, TE Bakken, J Bendl, L Bicks, T Chatterjee, L Cheng, Y Cheng, Y Dai, Z Duan, M Flaherty, JF Fullard, M Gancz, D Garrido-Martin, S Gaynor-Gillett, J Grundman, N Hawken, E Henry, GE Hoffman, A Huang, Y Jiang, T Jin, NL Jorstad, R Kawaguchi, S Khullar, J Liu, J Liu, S Liu, S Ma, M Margolis, S Mazariegos, J Moore, JR Moran, E Nguyen, N Phalke, M Pjanic, H Pratt, D Quintero, AS Rajagopalan, TR Riesenmy, N Shedd, M Shi, M Spector, R Terwilliger, KJ Travaglini, B Wamsley, G Wang, Y Xia, S Xiao, AC Yang, S Zheng, MJ Gandal, D Lee, ES Lein, P Roussos, N Sestan, Z Weng, KP White, H Won, MJ Girgenti, J Zhang, D Wang, D Geschwind, M Gerstein (2024). bioRxiv.
TN Aung, J Warrell, S Martinez-Morilla, N Gavrielatou, I Vathiotis, V Yaghoobi, HM Kluger, M Gerstein, DL Rimm (2024). Clin Cancer Res.
J Warrell, L Salichos, M Gancz, MB Gerstein (2024). J R Soc Interface 21: 20230647.
Z Duan, S Xu, S Sai Srinivasan, A Hwang, CY Lee, F Yue, M Gerstein, Y Luan, M Girgenti, J Zhang (2024). Brief Bioinform 25.
J Xu, J Gao, P Ni, M Gerstein (2024). Nucleic Acids Res 52: e20.
Yujia Qin, Shihao Liang, Yining Ye, Kunlun Zhu, Lan Yan, Yaxi Lu, Yankai Lin, Xin Cong, Xiangru Tang, Bill Qian, Sihan Zhao, Lauren Hong, Runchu Tian, Ruobing Xie, Jie Zhou, Mark Gerstein, Dahai Li, Zhiyuan Liu, Maosong Sun (2024). The Twelfth International Conference on Learning Representations (ICLR 2024).
C Deng, Y Zhao, X Tang, M Gerstein, A Cohan. 2024. Investigating Data Contamination in Modern Benchmarks for Large Language Models. In Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers), pages 8706–8719, Mexico City, Mexico. Association for Computational Linguistics.



2023 (20)

Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark Gerstein (2023). Proceedings of the 5th Clinical Natural Language Processing Workshop.
Xiangru Tang, Arman Cohan, Mark Gerstein (2023). Proceedings of the 5th Clinical Natural Language Processing Workshop.
PS Emani, MN Geradi, G Gursoy, MR Grasty, A Miranker, MB Gerstein (2023). Genome Res 33: 2156-73.
T Li, H Guo, F Grazioli, MB Gerstein, MR Min (2023). NeurIPS 2023.
D Greenbaum, M Gerstein (2023). Science 380: 589.
D Greenbaum, M Gerstein (2023). Science 381: 1162.
CJ Minteer, K Thrush, J Gonzalez, P Niimi, M Rozenblit, J Rozowsky, J Liu, M Frank, T McCabe, AT Higgins-Chen, E Hofstatter, L Pusztai, K Beckman, M Gerstein, ME Levine (2023). Sci Adv 9: eadf4163.
A Augspach, KD Drake, L Roma, E Qian, SR Lee, D Clarke, S Kumar, M Jaquet, J Gallon, M Bolis, J Triscott, JA Galvan, Y Chen, GN Thalmann, M Kruithof-de Julio, JP Theurillat, S Wuchty, M Gerstein, S Piscuoglio, RN Kanadia, MA Rubin (2023). Mol Cell 83: 1983-2002e11.
WU Meyerson, SK Fineberg, FC Andrade, P Corlett, MB Gerstein, RH Hoyle (2023). Sleep Med 107: 212-218.
L Salichos, J Warrell, H Cevasco, A Chung, M Gerstein (2023). Sci Rep 13: 8470.
EL LaPlante, A Sturchler, R Fullem, D Chen, AC Starner, E Esquivel, E Alsop, AR Jackson, I Ghiran, G Pereira, J Rozowsky, J Chang, MB Gerstein, RP Alexander, ME Roth, JL Franklin, RJ Coffey, RL Raffai, IM Mansuy, S Stavrakis, AJ deMello, LC Laurent, YT Wang, CF Tsai, T Liu, J Jones, K Van Keuren-Jensen, E Van Nostrand, B Mateescu, A Milosavljevic (2023). Cell Genom 3: 100303.
S Lou, M Yang, T Li, W Zhao, H Cevasco, YT Yang, M Gerstein (2023). PLoS Comput Biol 19: e1011222.
S Kumar, M Gerstein (2023). Trends Genet 39: 442-450.
J Rozowsky, J Gao, B Borsari, YT Yang, T Galeev, G Gursoy, CB Epstein, K Xiong, J Xu, T Li, J Liu, K Yu, A Berthel, Z Chen, F Navarro, MS Sun, J Wright, J Chang, CJF Cameron, N Shoresh, E Gaskell, J Drenkow, J Adrian, S Aganezov, F Aguet, G Balderrama-Gutierrez, S Banskota, GB Corona, S Chee, SB Chhetri, GC Cortez Martins, C Danyko, CA Davis, D Farid, NP Farrell, I Gabdank, Y Gofin, DU Gorkin, M Gu, V Hecht, BC Hitz, R Issner, Y Jiang, M Kirsche, X Kong, BR Lam, S Li, B Li, X Li, KZ Lin, R Luo, M Mackiewicz, R Meng, JE Moore, J Mudge, N Nelson, C Nusbaum, I Popov, HE Pratt, Y Qiu, S Ramakrishnan, J Raymond, L Salichos, A Scavelli, JM Schreiber, FJ Sedlazeck, LH See, RM Sherman, X Shi, M Shi, CA Sloan, JS Strattan, Z Tan, FY Tanaka, A Vlasova, J Wang, J Werner, B Williams, M Xu, C Yan, L Yu, C Zaleski, J Zhang, K Ardlie, JM Cherry, EM Mendenhall, WS Noble, Z Weng, ME Levine, A Dobin, B Wold, A Mortazavi, B Ren, J Gillis, RM Myers, MP Snyder, J Choudhary, A Milosavljevic, MC Schatz, BE Bernstein, R Guigo, TR Gingeras, M Gerstein (2023). Cell 186: 1493-1511e40.
WU Meyerson, SK Fineberg, YK Song, A Faber, G Ash, FC Andrade, P Corlett, MB Gerstein, RH Hoyle (2023). JMIR Form Res 7: e38112.
E Sarkar, E Chielle, G Gursoy, L Chen, M Gerstein, M Maniatakos (2023). Sci Rep 13: 1661.
Z Chen, B Zhang, H Guo, P Emani, T Clancy, C Jiang, M Gerstein, X Ning, C Cheng, MR Min (2023). Bioinformatics 39.
G Shi, C Song, J Torres Robles, L Salichos, HJ Lou, TT Lam, M Gerstein, BE Turk (2023). Sci Signal 16: eabm5518.
GS Erwin, G Gursoy, R Al-Abri, A Suriyaprakash, E Dolzhenko, K Zhu, CR Hoerner, SM White, L Ramirez, A Vadlakonda, A Vadlakonda, K von Kraut, J Park, CM Brannon, DA Sumano, RA Kirtikar, AA Erwin, TJ Metzner, RKC Yuen, AC Fan, JT Leppert, MA Eberle, M Gerstein, MP Snyder (2023). Nature 613: 96-102.
B Lau, PS Emani, J Chapman, L Yao, T Lam, P Merrill, J Warrell, MB Gerstein, HYK Lam (2023). Bioinformatics 39.



2022 (20)

IA Vathiotis, L Salichos, S Martinez-Morilla, N Gavrielatou, TN Aung, S Shafi, PF Wong, S Jessel, HM Kluger, KN Syrigos, S Warren, M Gerstein, DL Rimm (2022). NPJ Precis Oncol 6: 92.
D Greenbaum, M Gerstein (2022). Science 377: 826-827.
J Xu, HE Pratt, JE Moore, MB Gerstein, Z Weng (2022). Hum Mol Genet 31: R114-R122.
D Greenbaum, M Gerstein (2022). Nat Genet 54: 1758-1760.
IA Vathiotis, L Salichos, S Martinez-Morilla, N Gavrielatou, TN Aung, S Shafi, PF Wong, S Jessel, HM Kluger, KN Syrigos, S Warren, M Gerstein, DL Rimm (2022). NPJ Precis Oncol 6: 92.
S Liu, H Won, D Clarke, N Matoba, S Khullar, Y Mu, D Wang, M Gerstein (2022). Genome Med 14: 133.
C Kockan, D Greenbaum, D Lee, M Gerstein (2022). Georgetown Journal of International Affairs 23.2 (2022): 246-253..
Z Chen, WC King, A Hwang, M Gerstein, J Zhang (2022). Sci Adv 8: eabq3745.
CY Lee, Y Chen, Z Duan, M Xu, MJ Girgenti, K Xu, M Gerstein, J Zhang (2022). PLoS Comput Biol 18: e1010636.
MJ Gandal, JR Haney, B Wamsley, CX Yap, S Parhami, PS Emani, N Chang, GT Chen, GD Hoftman, D de Alba, G Ramaswami, CL Hartl, A Bhattacharya, C Luo, T Jin, D Wang, R Kawaguchi, D Quintero, J Ou, YE Wu, NN Parikshak, V Swarup, TG Belgard, M Gerstein, B Pasaniuc, DH Geschwind (2022). Nature 611: 532-539.
H Zhou, T Arapoglou, X Li, Z Li, X Zheng, J Moore, A Asok, S Kumar, EE Blue, S Buyske, N Cox, A Felsenfeld, M Gerstein, E Kenny, B Li, T Matise, A Philippakis, HL Rehm, HJ Sofia, G Snyder, NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Z Weng, B Neale, SR Sunyaev, X Lin (2022). Nucleic Acids Res 51: D1300-D1311.
A Khanna, V Schaffer, G Gursoy, M Gerstein (2022). Annu Int Conf IEEE Eng Med Biol Soc 2022: 1358-1361.
B Mateescu, JC Jones, RP Alexander, E Alsop, JY An, M Asghari, A Boomgarden, L Bouchareychas, A Cayota, HC Chang, A Charest, DT Chiu, RJ Coffey, S Das, P De Hoff, A deMello, C D'Souza-Schorey, D Elashoff, KR Eliato, JL Franklin, DJ Galas, MB Gerstein, IH Ghiran, DB Go, S Gould, TR Grogan, JN Higginbotham, F Hladik, TJ Huang, X Huo, E Hutchins, DK Jeppesen, T Jovanovic-Talisman, BYS Kim, S Kim, KM Kim, Y Kim, RR Kitchen, V Knouse, EL LaPlante, CB Lebrilla, LJ Lee, KM Lennon, G Li, F Li, T Li, T Liu, Z Liu, AL Maddox, K McCarthy, B Meechoovet, N Maniya, Y Meng, A Milosavljevic, BH Min, A Morey, M Ng, J Nolan, GP De Oliveira Junior, ME Paulaitis, TA Phu, RL Raffai, E Reategui, ME Roth, DA Routenberg, J Rozowsky, J Rufo, S Senapati, S Shachar, H Sharma, AK Sood, S Stavrakis, A Sturchler, M Tewari, JP Tosar, AK Tucker-Schwartz, A Turchinovich, N Valkov, K Van Keuren-Jensen, KC Vickers, L Vojtech, WN Vreeland, C Wang, K Wang, Z Wang, JA Welsh, KW Witwer, DTW Wong, J Xia, YH Xie, K Yang, MP Zaborowski, C Zhang, Q Zhang, AM Zivkovic, LC Laurent (2022). iScience 25: 104653.
JM Mudge, J Ruiz-Orera, JR Prensner, MA Brunet, F Calvet, I Jungreis, JM Gonzalez, M Magrane, TF Martinez, JF Schulz, YT Yang, MM Alba, JL Aspden, PV Baranov, AA Bazzini, E Bruford, MJ Martin, L Calviello, AR Carvunis, J Chen, JP Couso, EW Deutsch, P Flicek, A Frankish, M Gerstein, N Hubner, NT Ingolia, M Kellis, G Menschaert, RL Moritz, U Ohler, X Roucou, A Saghatelian, JS Weissman, S van Heesch (2022). Nat Biotechnol 40: 994-999.
J Park, M Gerstein (2022). Nature.
G Gursoy, CM Brannon, E Ni, S Wagner, A Khanna, M Gerstein (2022). Genome Biol 23: 134.
Z Chen, J Goldwasser, P Tuckman, J Liu, J Zhang, M Gerstein (2022). Nat Commun 13: 3538.
T Qing, H Mohsen, VL Cannataro, M Marczyk, M Rozenblit, J Foldi, M Murray, JP Townsend, Y Kluger, M Gerstein, L Pusztai (2022). J Natl Cancer Inst 114: 988-995.
D Greenbaum, M Gerstein (2022). Science 375: 983.
SM Baxter, JE Posey, NJ Lake, N Sobreira, JX Chong, S Buyske, EE Blue, LH Chadwick, ZH Coban-Akdemir, KF Doheny, CP Davis, M Lek, C Wellington, SN Jhangiani, M Gerstein, RA Gibbs, RP Lifton, DG MacArthur, TC Matise, JR Lupski, D Valle, MJ Bamshad, A Hamosh, S Mane, DA Nickerson, Centers for Mendelian Genomics Consortium, HL Rehm, A O'Donnell-Luria (2022). Genet Med 24: 784-797.



2021 (19)

P Ebert, PA Audano, Q Zhu, B Rodriguez-Martin, D Porubsky, MJ Bonder, A Sulovari, J Ebler, W Zhou, R Serra Mari, F Yilmaz, X Zhao, P Hsieh, J Lee, S Kumar, J Lin, T Rausch, Y Chen, J Ren, M Santamarina, W Hops, H Ashraf, NT Chuang, X Yang, KM Munson, AP Lewis, S Fairley, LJ Tallon, WE Clarke, AO Basile, M Byrska-Bishop, A Corvelo, US Evani, TY Lu, MJP Chaisson, J Chen, C Li, H Brand, AM Wenger, M Ghareghani, WT Harvey, B Raeder, P Hasenfeld, AA Regier, HJ Abel, IM Hall, P Flicek, O Stegle, MB Gerstein, JMC Tubio, Z Mu, YI Li, X Shi, AR Hastie, K Ye, Z Chong, AD Sanders, MC Zody, ME Talkowski, RE Mills, SE Devine, C Lee, JO Korbel, T Marschall, EE Eichler (2021). Science 372.
G Wang, T Kitaoka, A Crawford, Q Mao, A Hesketh, FM Guppy, GI Ash, J Liu, MB Gerstein, YP Pitsiladis (2021). Sci Rep 11: 21705.
E Sarkar, E Chielle, G Gursoy, O Mazonka, M Gerstein, M Maniatakos (2021). IEEE Access 9: 93097-93110.
X Zhao, RL Collins, WP Lee, AM Weber, Y Jun, Q Zhu, B Weisburd, Y Huang, PA Audano, H Wang, M Walker, C Lowther, J Fu, Human Genome Structural Variation Consortium, MB Gerstein, SE Devine, T Marschall, JO Korbel, EE Eichler, MJP Chaisson, C Lee, RE Mills, H Brand, ME Talkowski (2021). Am J Hum Genet 108: 919-928.
TN Aung, B Acs, J Warrell, Y Bai, P Gaule, S Martinez-Morilla, I Vathiotis, S Shafi, M Moutafi, M Gerstein, B Freiberg, R Fulton, DL Rimm (2021). Mod Pathol 34: 1261-1270.
G Gursoy, T Li, S Liu, E Ni, CM Brannon, MB Gerstein (2021). Nat Rev Genet 23: 245-258.
G Gursoy, E Chielle, CM Brannon, M Maniatakos, M Gerstein (2021). Cell Syst 13: 173-182e3.
C Amaya, CJF Cameron, SC Devarkar, SJH Seager, MB Gerstein, Y Xiong, C Schlieker (2021). J Biol Chem 297: 100937.
K Xiong, M Gerstein, J Masel (2021). Genetics 219.
Z Chen, J Zhang, J Liu, Y Dai, D Lee, MR Min, M Xu, M Gerstein (2021). Bioinformatics 37: i280-i288.
G Gursoy, N Lu, S Wagner, M Gerstein (2021). Genome Biol 22: 263.
H Mohsen, V Gunasekharan, T Qing, M Seay, Y Surovtseva, S Negahban, Z Szallasi, L Pusztai, MB Gerstein (2021). Genome Biol 22: 287.
GI Ash, M Stults-Kolehmainen, MA Busa, AE Gaffey, K Angeloudis, B Muniz-Pardos, R Gregory, RA Huggins, NS Redeker, SA Weinzimer, LA Grieco, K Lyden, E Megally, I Vogiatzis, L Scher, X Zhu, JS Baker, C Brandt, MS Businelle, LM Fucito, S Griggs, R Jarrin, BJ Mortazavi, T Prioleau, W Roberts, EK Spanakis, LM Nally, A Debruyne, N Bachl, F Pigozzi, F Halabchi, DA Ramagole, DC Janse van Rensburg, B Wolfarth, C Fossati, S Rozenstoka, K Tanisawa, M Borjesson, JA Casajus, A Gonzalez-Aguero, I Zelenkova, J Swart, G Gursoy, W Meyerson, J Liu, D Greenbaum, YP Pitsiladis, MB Gerstein (2021). Sports Med 51: 2237-2250.
J Liu, DJ Spakowicz, GI Ash, R Hoyd, R Ahluwalia, A Zhang, S Lou, D Lee, J Zhang, C Presley, A Greene, M Stults-Kolehmainen, LM Nally, JS Baker, LM Fucito, SA Weinzimer, AV Papachristos, M Gerstein (2021). PLoS Comput Biol 17: e1009303.
X Li, S Kumar, A Harmanci, S Li, RR Kitchen, Y Zhang, VB Wali, SM Reddy, WA Woodward, JM Reuben, J Rozowsky, C Hatzis, NT Ueno, S Krishnamurthy, L Pusztai, M Gerstein (2021). Genome Med 13: 70.
S Lou, T Li, J Liu, M Gerstein (2021). Bioinformatics 37: 2998-3000.
Z Chen, J Zhang, J Liu, Z Zhang, J Zhu, D Lee, M Xu, M Gerstein (2021). Bioinformatics 37: 1756-1758.
AJ Armstrong, X Li, M Tucker, S Li, XJ Mu, KW Eng, A Sboner, M Rubin, M Gerstein (2021). Prostate Cancer Prostatic Dis 24: 786-793.
PS Emani, J Warrell, A Anticevic, S Bekiranov, M Gandal, MJ McConnell, G Sapiro, A Aspuru-Guzik, JT Baker, M Bastiani, JD Murray, SN Sotiropoulos, J Taylor, G Senthil, T Lehner, MB Gerstein, AW Harrow (2021). Nat Methods 18: 701-709.



2020 (41)

T Qing, H Mohsen, M Marczyk, Y Ye, T O'Meara, H Zhao, JP Townsend, M Gerstein, C Hatzis, Y Kluger, L Pusztai (2020). Nat Commun 11: 2438.
J Xu, MM Kudron, A Victorsen, J Gao, HN Ammouri, FCP Navarro, L Gevirtzman, RH Waterston, KP White, V Reinke, M Gerstein (2020). Nucleic Acids Res 49: e17.
H Mohsen, J Warrell, MR Min, S Negahban, M Gerstein (2020). The 15th Machine Learning in Computational Biology Workshop.
D Lee, M Shi, J Moran, M Wall, J Zhang, J Liu, D Fitzgerald, Y Kyono, L Ma, KP White, M Gerstein (2020). Genome Biol 21: 298.
A Frankish, M Diekhans, I Jungreis, J Lagarde, JE Loveland, JM Mudge, C Sisu, JC Wright, J Armstrong, I Barnes, A Berry, A Bignell, C Boix, S Carbonell Sala, F Cunningham, T Di Domenico, S Donaldson, IT Fiddes, C Garcia Giron, JM Gonzalez, T Grego, M Hardy, T Hourlier, KL Howe, T Hunt, OG Izuogu, R Johnson, FJ Martin, L Martinez, S Mohanan, P Muir, FCP Navarro, A Parker, B Pei, F Pozo, FC Riera, M Ruffier, BM Schmitt, E Stapleton, MM Suner, I Sycheva, B Uszczynska-Ratajczak, MY Wolf, J Xu, YT Yang, A Yates, D Zerbino, Y Zhang, JS Choudhary, M Gerstein, R Guigo, TJP Hubbard, M Kellis, B Paten, ML Tress, P Flicek (2020). Nucleic Acids Res 49: D916-D923.
B Li, YT Yang, JA Capra, MB Gerstein (2020). PLoS Comput Biol 16: e1008291.
G Gursoy, P Emani, CM Brannon, OA Jolanki, A Harmanci, JS Strattan, JM Cherry, AD Miranker, M Gerstein (2020). Cell 183: 905-917e16.
S Kumar, A Harmanci, J Vytheeswaran, MB Gerstein (2020). Genome Biol 21: 274.
J Zhang, J Liu, P McGillivray, C Yi, L Lochovsky, D Lee, M Gerstein (2020). BMC Bioinformatics 21: 474.
S Lou, T Li, D Spakowicz, X Yan, GL Chupp, M Gerstein (2020). BMC Bioinformatics 21: 457.
D Greenbaum, M Gerstein (2020). Science. 370 (6513):178.
MH Bailey, WU Meyerson, LJ Dursi, LB Wang, G Dong, WW Liang, A Weerasinghe, S Li, Y Li, S Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, G Saksena, K Ellrott, MC Wendl, DA Wheeler, G Getz, JT Simpson, MB Gerstein, L Ding, PCAWG Consortium (2020). Nat Commun 11: 4748.
D Galeano, S Li, M Gerstein, A Paccanaro (2020). Nat Commun 11: 4575.
CH Li, SD Prokopec, RX Sun, F Yousif, N Schmitz, PCAWG Tumour Subtypes and Clinical Translation, PC Boutros, PCAWG Consortium (2020). Nat Commun 11: 4330.
J Warrell, M Gerstein (2020). Biology & Philosophy, 35(5), pp.1-36.
ENCODE Project Consortium, JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, CA Davis, A Dobin, R Kaul, J Halow, EL Van Nostrand, P Freese, DU Gorkin, Y Shen, Y He, M Mackiewicz, F Pauli-Behn, BA Williams, A Mortazavi, CA Keller, XO Zhang, SI Elhajjajy, J Huey, DE Dickel, V Snetkova, X Wei, X Wang, JC Rivera-Mulia, J Rozowsky, J Zhang, SB Chhetri, J Zhang, A Victorsen, KP White, A Visel, GW Yeo, CB Burge, E Lecuyer, DM Gilbert, J Dekker, J Rinn, EM Mendenhall, JR Ecker, M Kellis, RJ Klein, WS Noble, A Kundaje, R Guigo, PJ Farnham, JM Cherry, RM Myers, B Ren, BR Graveley, MB Gerstein, LA Pennacchio, MP Snyder, BE Bernstein, B Wold, RC Hardison, TR Gingeras, JA Stamatoyannopoulos, Z Weng (2020). Nature 583: 699-710.
ENCODE Project Consortium, MP Snyder, TR Gingeras, JE Moore, Z Weng, MB Gerstein, B Ren, RC Hardison, JA Stamatoyannopoulos, BR Graveley, EA Feingold, MJ Pazin, M Pagan, DA Gilchrist, BC Hitz, JM Cherry, BE Bernstein, EM Mendenhall, DR Zerbino, A Frankish, P Flicek, RM Myers (2020). Nature 583: 693-698.
J Zhang, D Lee, V Dhiman, P Jiang, J Xu, P McGillivray, H Yang, J Liu, W Meyerson, D Clarke, M Gu, S Li, S Lou, J Xu, L Lochovsky, M Ung, L Ma, S Yu, Q Cao, A Harmanci, KK Yan, A Sethi, G Gursoy, MR Schoenberg, J Rozowsky, J Warrell, P Emani, YT Yang, T Galeev, X Kong, S Liu, X Li, J Krishnan, Y Feng, JC Rivera-Mulia, J Adrian, JR Broach, M Bolt, J Moran, D Fitzgerald, V Dileep, T Liu, S Mei, T Sasaki, C Trevilla-Garcia, S Wang, Y Wang, C Zang, D Wang, RJ Klein, M Snyder, DM Gilbert, K Yip, C Cheng, F Yue, XS Liu, KP White, M Gerstein (2020). Nat Commun 11: 3696.
C Sisu, P Muir, A Frankish, I Fiddes, M Diekhans, D Thybert, DT Odom, P Flicek, TM Keane, T Hubbard, J Harrow, M Gerstein (2020). Nat Commun 11: 3695.
J Zhang, J Liu, D Lee, JJ Feng, L Lochovsky, S Lou, M Rutenberg-Schoenberg, M Gerstein (2020). Genome Biol 21: 151.
A Sethi, M Gu, E Gumusgoz, L Chan, KK Yan, J Rozowsky, I Barozzi, V Afzal, JA Akiyama, I Plajzer-Frick, C Yan, CS Novak, M Kato, TH Garvin, Q Pham, A Harrington, BJ Mannion, EA Lee, Y Fukuda-Yuzawa, A Visel, DE Dickel, KY Yip, R Sutton, LA Pennacchio, M Gerstein (2020). Nat Methods 17: 807-814.
G Gursoy, CM Brannon, FCP Navarro, M Gerstein (2020). Bioinformatics 36: 5145-5150.
G Gursoy, R Bjornson, ME Green, M Gerstein (2020). BMC Med Genomics 13: 78.
S Li, FW Crawford, MB Gerstein (2020). Nat Commun 11: 3575.
J Zhang, J Liu, D Lee, S Lou, Z Chen, G Gursoy, M Gerstein (2020). BMC Bioinformatics 21: 281.
D Spakowicz, S Lou, B Barron, JL Gomez, T Li, Q Liu, N Grant, X Yan, R Hoyd, G Weinstock, GL Chupp, M Gerstein (2020). Genome Biol 21: 150.
S Lou, T Li, X Kong, J Zhang, J Liu, D Lee, M Gerstein (2020). Bioinformatics 36: i474-i481.
D Lee, J Zhang, J Liu, M Gerstein (2020). PLoS Comput Biol 16: e1008006.
W Meyerson, J Leisman, FCP Navarro, M Gerstein (2020). BMC Bioinformatics 21: 227.
G Gursoy, CM Brannon, M Gerstein (2020). BMC Med Genomics 13: 74.
C Ye, A Paccanaro, M Gerstein, KK Yan (2020). BMC Bioinformatics 21: 222.
BA Shook, RR Wasko, O Mano, M Rutenberg-Schoenberg, MC Rudolph, B Zirak, GC Rivera-Gonzalez, F Lopez-Giraldez, S Zarini, A Rezza, DA Clark, M Rendl, MD Rosenblum, MB Gerstein, V Horsley (2020). Cell Stem Cell 26: 880-895e6.
B Shuch, S Li, H Risch, RS Bindra, PD McGillivray, M Gerstein (2020). Cancer 126: 3657-3666.
KK Yan, D Wang, K Xiong, M Gerstein (2020). Cell Syst 10: 219-222.
S Kumar, J Warrell, S Li, PD McGillivray, W Meyerson, L Salichos, A Harmanci, A Martinez-Fundichely, CWY Chan, MM Nielsen, L Lochovsky, Y Zhang, X Li, S Lou, JS Pedersen, C Herrmann, G Getz, E Khurana, MB Gerstein (2020). Cell 180: 915-927e16.
T Chen, Y Chen, M Yuan, M Gerstein, T Li, H Liang, T Froehlich, L Lu (2020). JMIR Med Inform 8: e15767.
GI Ash, M Stults-Kolehmainen, MA Busa, R Gregory, CE Garber, J Liu, M Gerstein, JA Casajus, A Gonzalez-Aguero, D Constantinou, M Geistlinger, FM Guppy, F Pigozzi, YP Pitsiladis (2020). Curr Sports Med Rep 19: 45-49.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Nature 578: 82-93.
E Rheinbay, MM Nielsen, F Abascal, JA Wala, O Shapira, G Tiao, H Hornshj, JM Hess, RI Juul, Z Lin, L Feuerbach, R Sabarinathan, T Madsen, J Kim, L Mularoni, S Shuai, A Lanzos, C Herrmann, YE Maruvka, C Shen, SB Amin, P Bandopadhayay, J Bertl, KA Boroevich, J Busanovich, J Carlevaro-Fita, D Chakravarty, CWY Chan, D Craft, P Dhingra, K Diamanti, NA Fonseca, A Gonzalez-Perez, Q Guo, MP Hamilton, NJ Haradhvala, C Hong, K Isaev, TA Johnson, M Juul, A Kahles, A Kahraman, Y Kim, J Komorowski, K Kumar, S Kumar, D Lee, KV Lehmann, Y Li, EM Liu, L Lochovsky, K Park, O Pich, ND Roberts, G Saksena, SE Schumacher, N Sidiropoulos, L Sieverling, N Sinnott-Armstrong, C Stewart, D Tamborero, JMC Tubio, HM Umer, L Uuskula-Reimand, C Wadelius, L Wadi, X Yao, CZ Zhang, J Zhang, JE Haber, A Hobolth, M Imielinski, M Kellis, MS Lawrence, C von Mering, H Nakagawa, BJ Raphael, MA Rubin, C Sander, LD Stein, JM Stuart, T Tsunoda, DA Wheeler, R Johnson, J Reimand, M Gerstein, E Khurana, PJ Campbell, N Lopez-Bigas, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, J Weischenfeldt, R Beroukhim, I Martincorena, JS Pedersen, G Getz, PCAWG Consortium (2020). Nature 578: 102-111.
B Rodriguez-Martin, EG Alvarez, A Baez-Ortega, J Zamora, F Supek, J Demeulemeester, M Santamarina, YS Ju, J Temes, D Garcia-Souto, H Detering, Y Li, J Rodriguez-Castro, A Dueso-Barroso, AL Bruzos, SC Dentro, MG Blanco, G Contino, D Ardeljan, M Tojo, ND Roberts, S Zumalave, PA Edwards, J Weischenfeldt, M Puiggros, Z Chong, K Chen, EA Lee, JA Wala, KM Raine, A Butler, SM Waszak, FCP Navarro, SE Schumacher, J Monlong, F Maura, N Bolli, G Bourque, M Gerstein, PJ Park, DC Wedge, R Beroukhim, D Torrents, JO Korbel, I Martincorena, RC Fitzgerald, P Van Loo, HH Kazazian, KH Burns, PCAWG Structural Variation Working Group, PJ Campbell, JMC Tubio, PCAWG Consortium (2020). Nat Genet 52: 306-319.
L Salichos, W Meyerson, J Warrell, M Gerstein (2020). Nat Commun 11: 732.



2019 (19)

JS Johnson, DJ Spakowicz, BY Hong, LM Petersen, P Demkowicz, L Chen, SR Leopold, BM Hanson, HO Agresta, M Gerstein, E Sodergren, GM Weinstock (2019). Nat Commun 10: 5029.
J Warrell, MB Gerstein (2019). Bayesian Deep Learning Workshop at NeurIPS.
M Koupenova, E Mick, HA Corkrey, A Singh, SE Tanriverdi, O Vitseva, D Levy, AM Keeler, M Ezzaty Mirhashemi, MK ElMallah, M Gerstein, J Rozowsky, K Tanriverdi, JE Freedman (2019). iScience 19: 916-926.
S Lou, KA Cotter, T Li, J Liang, H Mohsen, J Liu, J Zhang, S Cohen, J Xu, H Yu, MA Rubin, M Gerstein (2019). PLoS Genet 15: e1007860.
S Kumar, D Clarke, MB Gerstein (2019). Proc Natl Acad Sci U S A 116: 18962-18970.
D Greenbaum, M Gerstein (2019). Science 365 (6455):764.
FC Navarro, J Hoops, L Bellfy, E Cerveira, Q Zhu, C Zhang, C Lee, MB Gerstein (2019). PLoS Comput Biol 15: e1007293.
D Polioudakis, L de la Torre-Ubieta, J Langerman, AG Elkins, X Shi, JL Stein, CK Vuong, S Nichterwitz, M Gevorgian, CK Opland, D Lu, W Connell, EK Ruzzo, JK Lowe, T Hadzic, FI Hinz, S Sabri, WE Lowry, MB Gerstein, K Plath, DH Geschwind (2019). Neuron 103: 785-801e8.
B Wang, C Yan, S Lou, P Emani, B Li, M Xu, X Kong, W Meyerson, YT Yang, D Lee, M Gerstein (2019). Structure 27: 1469-1481e3.
FCP Navarro, H Mohsen, C Yan, S Li, M Gu, W Meyerson, M Gerstein (2019). Genome Biol 20: 109.
MJP Chaisson, AD Sanders, X Zhao, A Malhotra, D Porubsky, T Rausch, EJ Gardner, OL Rodriguez, L Guo, RL Collins, X Fan, J Wen, RE Handsaker, S Fairley, ZN Kronenberg, X Kong, F Hormozdiari, D Lee, AM Wenger, AR Hastie, D Antaki, T Anantharaman, PA Audano, H Brand, S Cantsilieris, H Cao, E Cerveira, C Chen, X Chen, CS Chin, Z Chong, NT Chuang, CC Lambert, DM Church, L Clarke, A Farrell, J Flores, T Galeev, DU Gorkin, M Gujral, V Guryev, WH Heaton, J Korlach, S Kumar, JY Kwon, ET Lam, JE Lee, J Lee, WP Lee, SP Lee, S Li, P Marks, K Viaud-Martinez, S Meiers, KM Munson, FCP Navarro, BJ Nelson, C Nodzak, A Noor, S Kyriazopoulou-Panagiotopoulou, AWC Pang, Y Qiu, G Rosanio, M Ryan, A Stutz, DCJ Spierings, A Ward, AE Welch, M Xiao, W Xu, C Zhang, Q Zhu, X Zheng-Bradley, E Lowy, S Yakneen, S McCarroll, G Jun, L Ding, CL Koh, B Ren, P Flicek, K Chen, MB Gerstein, PY Kwok, PM Lansdorp, GT Marth, J Sebat, X Shi, A Bashir, K Ye, SE Devine, ME Talkowski, RE Mills, T Marschall, JO Korbel, EE Eichler, C Lee (2019). Nat Commun 10: 1784.
J Rozowsky, RR Kitchen, JJ Park, TR Galeev, J Diao, J Warrell, W Thistlethwaite, SL Subramanian, A Milosavljevic, M Gerstein (2019). Cell Syst 8: 352-357e3.
OD Murillo, W Thistlethwaite, J Rozowsky, SL Subramanian, R Lucero, N Shah, AR Jackson, S Srinivasan, A Chung, CD Laurent, RR Kitchen, T Galeev, J Warrell, JA Diao, JA Welsh, K Hanspers, A Riutta, S Burgstaller-Muehlbacher, RV Shah, A Yeri, LM Jenkins, ME Ahsen, C Cordon-Cardo, N Dogra, SM Gifford, JT Smith, G Stolovitzky, AK Tewari, BH Wunsch, KK Yadav, KM Danielson, J Filant, C Moeller, P Nejad, A Paul, B Simonson, DK Wong, X Zhang, L Balaj, R Gandhi, AK Sood, RP Alexander, L Wang, C Wu, DTW Wong, DJ Galas, K Van Keuren-Jensen, T Patel, JC Jones, S Das, KH Cheung, AR Pico, AI Su, RL Raffai, LC Laurent, ME Roth, MB Gerstein, A Milosavljevic (2019). Cell 177: 463-477e15.
S Das, Extracellular RNA Communication Consortium, KM Ansel, M Bitzer, XO Breakefield, A Charest, DJ Galas, MB Gerstein, M Gupta, A Milosavljevic, MT McManus, T Patel, RL Raffai, J Rozowsky, ME Roth, JA Saugstad, K Van Keuren-Jensen, AM Weaver, LC Laurent (2019). Cell 177: 231-242.
EY Ho, Q Cao, M Gu, RW Chan, Q Wu, M Gerstein, KY Yip (2019). Brief Bioinform 21: 836-850.
GG Yardmc, H Ozadam, MEG Sauria, O Ursu, KK Yan, T Yang, A Chakraborty, A Kaul, BR Lajoie, F Song, Y Zhan, F Ay, M Gerstein, A Kundaje, Q Li, J Taylor, F Yue, J Dekker, WS Noble (2019). Genome Biol 20: 57.
A Moro, TP Driscoll, LC Boraas, W Armero, DM Kasper, N Baeyens, C Jouy, V Mallikarjun, J Swift, SJ Ahn, D Lee, J Zhang, M Gu, M Gerstein, M Schwartz, S Nicoli (2019). Nat Cell Biol 21: 348-358.
JE Posey, AH O'Donnell-Luria, JX Chong, T Harel, SN Jhangiani, ZH Coban Akdemir, S Buyske, D Pehlivan, CMB Carvalho, S Baxter, N Sobreira, P Liu, N Wu, JA Rosenfeld, S Kumar, D Avramopoulos, JJ White, KF Doheny, PD Witmer, C Boehm, VR Sutton, DM Muzny, E Boerwinkle, M Gunel, DA Nickerson, S Mane, DG MacArthur, RA Gibbs, A Hamosh, RP Lifton, TC Matise, HL Rehm, M Gerstein, MJ Bamshad, D Valle, JR Lupski, Centers for Mendelian Genomics (2019). Genet Med 21: 798-812.
S Li, MB Gerstein (2019). N Engl J Med 380: 200.



2018 (25)

J Warrell, MB Gerstein (2018). Uncertainty in Artificial Intelligence Workshop on Uncertainty in Deep Learning.
J Warrell, H Mohsen, MB Gerstein (2018). NeurIPS Workshop on Machine Learning for Health.
PsychENCODE Consortium (2018). Science 362: 1262-1263.
D Wang, S Liu, J Warrell, H Won, X Shi, FCP Navarro, D Clarke, M Gu, P Emani, YT Yang, M Xu, MJ Gandal, S Lou, J Zhang, JJ Park, C Yan, SK Rhie, K Manakongtreecheep, H Zhou, A Nathan, M Peters, E Mattei, D Fitzgerald, T Brunetti, J Moore, Y Jiang, K Girdhar, GE Hoffman, S Kalayci, ZH Gumus, GE Crawford, PsychENCODE Consortium, P Roussos, S Akbarian, AE Jaffe, KP White, Z Weng, N Sestan, DH Geschwind, JA Knowles, MB Gerstein (2018). Science 362.
MJ Gandal, P Zhang, E Hadjimichael, RL Walker, C Chen, S Liu, H Won, H van Bakel, M Varghese, Y Wang, AW Shieh, J Haney, S Parhami, J Belmont, M Kim, P Moran Losada, Z Khan, J Mleczko, Y Xia, R Dai, D Wang, YT Yang, M Xu, K Fish, PR Hof, J Warrell, D Fitzgerald, K White, AE Jaffe, PsychENCODE Consortium, MA Peters, M Gerstein, C Liu, LM Iakoucheva, D Pinto, DH Geschwind (2018). Science 362.
M Li, G Santpere, Y Imamura Kawasawa, OV Evgrafov, FO Gulden, S Pochareddy, SM Sunkin, Z Li, Y Shin, Y Zhu, AMM Sousa, DM Werling, RR Kitchen, HJ Kang, M Pletikos, J Choi, S Muchnik, X Xu, D Wang, B Lorente-Galdos, S Liu, P Giusti-Rodriguez, H Won, CA de Leeuw, AF Pardinas, BrainSpan Consortium, PsychENCODE Consortium, PsychENCODE Developmental Subgroup, M Hu, F Jin, Y Li, MJ Owen, MC O'Donovan, JTR Walters, D Posthuma, MA Reimers, P Levitt, DR Weinberger, TM Hyde, JE Kleinman, DH Geschwind, MJ Hawrylycz, MW State, SJ Sanders, PF Sullivan, MB Gerstein, ES Lein, JA Knowles, N Sestan (2018). Science 362.
A Amiri, G Coppola, S Scuderi, F Wu, T Roychowdhury, F Liu, S Pochareddy, Y Shin, A Safi, L Song, Y Zhu, AMM Sousa, PsychENCODE Consortium, M Gerstein, GE Crawford, N Sestan, A Abyzov, FM Vaccarino (2018). Science 362.
X Kong, M Gerstein (2018). Current Opinion in Systems Biology 11:117-122.
W Shi, CKY Ng, RS Lim, T Jiang, S Kumar, X Li, VB Wali, S Piscuoglio, MB Gerstein, AB Chagpar, B Weigelt, L Pusztai, JS Reis-Filho, C Hatzis (2018). Cell Rep 25: 1446-1457.
A Frankish, M Diekhans, AM Ferreira, R Johnson, I Jungreis, J Loveland, JM Mudge, C Sisu, J Wright, J Armstrong, I Barnes, A Berry, A Bignell, S Carbonell Sala, J Chrast, F Cunningham, T Di Domenico, S Donaldson, IT Fiddes, C Garcia Giron, JM Gonzalez, T Grego, M Hardy, T Hourlier, T Hunt, OG Izuogu, J Lagarde, FJ Martin, L Martinez, S Mohanan, P Muir, FCP Navarro, A Parker, B Pei, F Pozo, M Ruffier, BM Schmitt, E Stapleton, MM Suner, I Sycheva, B Uszczynska-Ratajczak, J Xu, A Yates, D Zerbino, Y Zhang, B Aken, JS Choudhary, M Gerstein, R Guigo, TJP Hubbard, M Kellis, B Paten, A Reymond, ML Tress, P Flicek (2018). Nucleic Acids Res 47: D766-D773.
J Lilue, AG Doran, IT Fiddes, M Abrudan, J Armstrong, R Bennett, W Chow, J Collins, S Collins, A Czechanski, P Danecek, M Diekhans, DD Dolle, M Dunn, R Durbin, D Earl, A Ferguson-Smith, P Flicek, J Flint, A Frankish, B Fu, M Gerstein, J Gilbert, L Goodstadt, J Harrow, K Howe, X Ibarra-Soria, M Kolmogorov, CJ Lelliott, DW Logan, J Loveland, CE Mathews, R Mott, P Muir, S Nachtweide, FCP Navarro, DT Odom, N Park, S Pelan, SK Pham, M Quail, L Reinholdt, L Romoth, L Shirley, C Sisu, M Sjoberg-Herrera, M Stanke, C Steward, M Thomas, G Threadgold, D Thybert, J Torrance, K Wong, J Wood, B Yalcin, F Yang, DJ Adams, B Paten, TM Keane (2018). Nat Genet 50: 1574-1583.
D Greenbaum, M Gerstein (2018). Science 362 (6415):648.
D Greenbaum, M Gerstein (2018). Cell 174:1043-1044.
V Onuchic, E Lurie, I Carrero, P Pawliczek, RY Patel, J Rozowsky, T Galeev, Z Huang, RC Altshuler, Z Zhang, RA Harris, C Coarfa, L Ashmore, JW Bertol, WD Fakhouri, F Yu, M Kellis, M Gerstein, A Milosavljevic (2018). Science 361.
BC Carlyle, RR Kitchen, J Zhang, RS Wilson, TT Lam, JS Rozowsky, KR Williams, N Sestan, MB Gerstein, AC Nairn (2018). J Proteome Res 17: 3431-3444.
AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, P Dehal, D Ware, F Perez, S Canon, MW Sneddon, ML Henderson, WJ Riehl, D Murphy-Olson, SY Chan, RT Kamimura, S Kumari, MM Drake, TS Brettin, EM Glass, D Chivian, D Gunter, DJ Weston, BH Allen, J Baumohl, AA Best, B Bowen, SE Brenner, CC Bun, JM Chandonia, JM Chia, R Colasanti, N Conrad, JJ Davis, BH Davison, M DeJongh, S Devoid, E Dietrich, I Dubchak, JN Edirisinghe, G Fang, JP Faria, PM Frybarger, W Gerlach, M Gerstein, A Greiner, J Gurtowski, HL Haun, F He, R Jain, MP Joachimiak, KP Keegan, S Kondo, V Kumar, ML Land, F Meyer, M Mills, PS Novichkov, T Oh, GJ Olsen, R Olson, B Parrello, S Pasternak, E Pearson, SS Poon, GA Price, S Ramakrishnan, P Ranjan, PC Ronald, MC Schatz, SMD Seaver, M Shukla, RA Sutormin, MH Syed, J Thomason, NL Tintle, D Wang, F Xia, H Yoo, S Yoo, D Yu (2018). Nat Biotechnol 36: 566-569.
A Harmanci, M Gerstein (2018). Nat Commun 9: 2453.
KW Barber, P Muir, RV Szeligowski, S Rogulina, M Gerstein, JR Sampson, FJ Isaacs, J Rinehart (2018). Nat Biotechnol 36: 638-644.
P McGillivray, D Clarke, W Meyerson, J Zhang, D Lee, M Gu, S Kumar, H Zhou, MB Gerstein (2018). Annual Review of Biomedical Data Science Vol. 1.
D Thybert, M Roller, FCP Navarro, I Fiddes, I Streeter, C Feig, D Martin-Galvez, M Kolmogorov, V Janousek, W Akanni, B Aken, S Aldridge, V Chakrapani, W Chow, L Clarke, C Cummins, A Doran, M Dunn, L Goodstadt, K Howe, M Howell, AA Josselin, RC Karn, CM Laukaitis, L Jingtao, F Martin, M Muffato, S Nachtweide, MA Quail, C Sisu, M Stanke, K Stefflova, C Van Oosterhout, F Veyrunes, B Ward, F Yang, G Yazdanifar, A Zadissa, DJ Adams, A Brazma, M Gerstein, B Paten, S Pham, TM Keane, DT Odom, P Flicek (2018). Genome Res 28: 448-459.
P McGillivray, R Ault, M Pawashe, R Kitchen, S Balasubramanian, M Gerstein (2018). Nucleic Acids Res 46: 3326-3338.
T Becker, WP Lee, J Leone, Q Zhu, C Zhang, S Liu, J Sargent, K Shanker, A Mil-Homens, E Cerveira, M Ryan, J Cha, FCP Navarro, T Galeev, M Gerstein, RE Mills, DG Shin, C Lee, A Malhotra (2018). Genome Biol 19: 38.
MJ Gandal, JR Haney, NN Parikshak, V Leppa, G Ramaswami, C Hartl, AJ Schork, V Appadurai, A Buil, TM Werge, C Liu, KP White, CommonMind Consortium, PsychENCODE Consortium, iPSYCH-BROAD Working Group, S Horvath, DH Geschwind (2018). Science 359: 693-697.
MB Gerstein, FCP Navarro (2018). Nature 553: 405.
BD Piening, W Zhou, K Contrepois, H Rost, GJ Gu Urban, T Mishra, BM Hanson, EJ Bautista, S Leopold, CY Yeh, D Spakowicz, I Banerjee, C Chen, K Kukurba, D Perelman, C Craig, E Colbert, D Salins, S Rego, S Lee, C Zhang, J Wheeler, MR Sailani, L Liang, C Abbott, M Gerstein, A Mardinoglu, U Smith, DL Rubin, S Pitteri, E Sodergren, TL McLaughlin, GM Weinstock, MP Snyder (2018). Cell Syst 6: 157-170e8.



2017 (20)

KE Kaczor-Urbanowicz, Y Kim, F Li, T Galeev, RR Kitchen, M Gerstein, K Koyano, SH Jeong, X Wang, D Elashoff, SY Kang, SM Kim, K Kim, S Kim, D Chia, X Xiao, J Rozowsky, DTW Wong (2017). Bioinformatics 34: 1-8.
MM Kudron, A Victorsen, L Gevirtzman, LW Hillier, WW Fisher, D Vafeados, M Kirkey, AS Hammonds, J Gersch, H Ammouri, ML Wall, J Moran, D Steffen, M Szynkarek, S Seabrook-Sturgis, N Jameel, M Kadaba, J Patton, R Terrell, M Corson, TJ Durham, S Park, S Samanta, M Han, J Xu, KK Yan, SE Celniker, KP White, L Ma, M Gerstein, V Reinke, RH Waterston (2017). Genetics 208: 937-949.
BC Carlyle, RR Kitchen, JE Kanyo, EZ Voss, M Pletikos, AMM Sousa, TT Lam, MB Gerstein, N Sestan, AC Nairn (2017). Nat Neurosci 20: 1787-1795.
AMM Sousa, Y Zhu, MA Raghanti, RR Kitchen, M Onorati, ATN Tebbenkamp, B Stutz, KA Meyer, M Li, YI Kawasawa, F Liu, RG Perez, M Mele, T Carvalho, M Skarica, FO Gulden, M Pletikos, A Shibata, AR Stephenson, MK Edler, JJ Ely, JD Elsworth, TL Horvath, PR Hof, TM Hyde, JE Kleinman, DR Weinberger, M Reimers, RP Lifton, SM Mane, JP Noonan, MW State, ES Lein, JA Knowles, T Marques-Bonet, CC Sherwood, MB Gerstein, N Sestan (2017). Science 358: 1027-1032.
L Lochovsky, J Zhang, M Gerstein (2017). Bioinformatics 34: 1031-1033.
Q Cao, C Anyansi, X Hu, L Xu, L Xiong, W Tang, MTS Mok, C Cheng, X Fan, M Gerstein, ASL Cheng, KY Yip (2017). Nat Genet 49: 1428-1436.
S Balasubramanian, Y Fu, M Pawashe, P McGillivray, M Jin, J Liu, KJ Karczewski, DG MacArthur, M Gerstein (2017). Nat Commun 8: 382.
KK Yan, S Lou, M Gerstein (2017). PLoS Comput Biol 13: e1005647.
SME Sahraeian, M Mohiyuddin, R Sebra, H Tilgner, PT Afshar, KF Au, N Bani Asadi, MB Gerstein, WH Wong, MP Snyder, E Schadt, HYK Lam (2017). Nat Commun 8: 59.
Y Zhang, S Li, A Abyzov, MB Gerstein (2017). PLoS Comput Biol 13: e1005567.
S Kumar, M Gerstein (2017). Nature 547: 40-41.
P Dhingra, Y Fu, M Gerstein, E Khurana (2017). Curr Protoc Bioinformatics 57: 15111-151117.
P Alves, S Liu, D Wang, M Gerstein (2017). IEEE/ACM Trans Comput Biol Bioinform 15: 926-933.
V Despic, M Dejung, M Gu, J Krishnan, J Zhang, L Herzel, K Straube, MB Gerstein, F Butter, KM Neugebauer (2017). Genome Res 27: 1184-1194.
D Greenbaum, J Rozowsky, V Stodden, M Gerstein (2017). Genome Biol 18: 64.
KK Yan, GG Yardimci, C Yan, WS Noble, M Gerstein (2017). Bioinformatics 33: 2199-2201.
S Li, BM Shuch, MB Gerstein (2017). PLoS Genet 13: e1006685.
DM Kasper, A Moro, E Ristori, A Narayanan, G Hill-Teran, E Fleming, M Moreno-Mateos, CE Vejnar, J Zhang, D Lee, M Gu, M Gerstein, A Giraldez, S Nicoli (2017). Dev Cell 40: 552-565e5.
E Mick, R Shah, K Tanriverdi, V Murthy, M Gerstein, J Rozowsky, R Kitchen, MG Larson, D Levy, JE Freedman (2017). Stroke 48: 828-834.
A Abyzov, L Tomasini, B Zhou, N Vasmatzis, G Coppola, M Amenduni, R Pattni, M Wilson, M Gerstein, S Weissman, AE Urban, FM Vaccarino (2017). Genome Res 27: 512-523.



2016 (19)

J Chen, B Wang, L Regan, M Gerstein (2016). J Mol Biol 429: 435-445.
S Kumar, D Clarke, M Gerstein (2016). Nucleic Acids Res 44: 10062-10073.
D Wang, F He, S Maslov, M Gerstein (2016). PLoS Comput Biol 12: e1005146.
D Greenbaum, M Gerstein (2016). The Scientist (30 Aug).
CC Yang, EH Andrews, MH Chen, WY Wang, JJ Chen, M Gerstein, CC Liu, C Cheng (2016). BMC Genomics 17: 632.
SW Choo, M Rayko, TK Tan, R Hari, A Komissarov, WY Wee, AA Yurchenko, S Kliver, G Tamazian, A Antunes, RK Wilson, WC Warren, KP Koepfli, P Minx, K Krasheninnikova, A Kotze, DL Dalton, E Vermaak, IC Paterson, P Dobrynin, FT Sitam, JJ Rovie-Ryan, WE Johnson, AM Yusoff, SJ Luo, KV Karuppannan, G Fang, D Zheng, MB Gerstein, L Lipovich, SJ O'Brien, GJ Wong (2016). Genome Res 26: 1312-1322.
R Shah, K Tanriverdi, D Levy, M Larson, M Gerstein, E Mick, J Rozowsky, R Kitchen, V Murthy, E Mikalev, JE Freedman (2016). PLoS One 11: e0153691.
JE Freedman, M Gerstein, E Mick, J Rozowsky, D Levy, R Kitchen, S Das, R Shah, K Danielson, L Beaulieu, FC Navarro, Y Wang, TR Galeev, A Holman, RY Kwong, V Murthy, SE Tanriverdi, M Koupenova-Zamor, E Mikhalev, K Tanriverdi (2016). Nat Commun 7: 11106.
KH Cheung, S Keerthikumar, P Roncaglia, SL Subramanian, ME Roth, M Samuel, S Anand, L Gangoda, S Gould, R Alexander, D Galas, MB Gerstein, AF Hill, RR Kitchen, J Lotvall, T Patel, DC Procaccini, P Quesenberry, J Rozowsky, RL Raffai, A Shypitsyna, AI Su, C Thery, K Vickers, MH Wauben, S Mathivanan, A Milosavljevic, LC Laurent (2016). J Biomed Semantics 7: 19.
J Chen, J Rozowsky, TR Galeev, A Harmanci, R Kitchen, J Bedford, A Abyzov, Y Kong, L Regan, M Gerstein (2016). Nat Commun 7: 11101.
D Clarke, A Sethi, S Li, S Kumar, RWF Chang, J Chen, M Gerstein (2016). Structure 24: 826-837.
KK Yan, D Wang, A Sethi, P Muir, R Kitchen, C Cheng, M Gerstein (2016). Cell Syst 2: 147-157.
D Greenbaum, M Gerstein (2016). Cell 165:257-258.
F He, S Yoo, D Wang, S Kumari, M Gerstein, D Ware, S Maslov (2016). Plant J 86: 472-80.
P Muir, S Li, S Lou, D Wang, DJ Spakowicz, L Salichos, J Zhang, GM Weinstock, F Isaacs, J Rozowsky, M Gerstein (2016). Genome Biol 17: 53.
D Wang, KK Yan, J Rozowsky, E Pan, M Gerstein (2016). Trends Genet 32: 251-253.
A Harmanci, M Gerstein (2016). Nat Methods 13: 251-6.
E Khurana, Y Fu, D Chakravarty, F Demichelis, MA Rubin, M Gerstein (2016). Nat Rev Genet 17: 93-108.
A Abyzov, S Li, MB Gerstein (2016). Oncotarget 7: 7370-1.



2015 (19)

S Purushotham, MR Min, CJ Kuo, M Gerstein (2015). NIPS Workshop on Machine Learning in Computational Biology.
Cancer Genome Atlas Research Network (2015). Cell 163: 1011-25.
A Sethi, D Clarke, J Chen, S Kumar, TR Galeev, L Regan, M Gerstein (2015). Curr Opin Struct Biol 35: 125-34.
PsychENCODE Consortium, S Akbarian, C Liu, JA Knowles, FM Vaccarino, PJ Farnham, GE Crawford, AE Jaffe, D Pinto, S Dracheva, DH Geschwind, J Mill, AC Nairn, A Abyzov, S Pochareddy, S Prabhakar, S Weissman, PF Sullivan, MW State, Z Weng, MA Peters, KP White, MB Gerstein, A Amiri, C Armoskus, AE Ashley-Koch, T Bae, A Beckel-Mitchener, BP Berman, GA Coetzee, G Coppola, N Francoeur, M Fromer, R Gao, K Grennan, J Herstein, DH Kavanagh, NA Ivanov, Y Jiang, RR Kitchen, A Kozlenkov, M Kundakovic, M Li, Z Li, S Liu, LM Mangravite, E Mattei, E Markenscoff-Papadimitriou, FC Navarro, N North, L Omberg, D Panchision, N Parikshak, J Poschmann, AJ Price, M Purcaro, TE Reddy, P Roussos, S Schreiner, S Scuderi, R Sebra, M Shibata, AW Shieh, M Skarica, W Sun, V Swarup, A Thomas, J Tsuji, H van Bakel, D Wang, Y Wang, K Wang, DM Werling, AJ Willsey, H Witt, H Won, CC Wong, GA Wray, EY Wu, X Xu, L Yao, G Senthil, T Lehner, P Sklar, N Sestan (2015). Nat Neurosci 18: 1707-12.
D Greenbaum, M Gerstein (2015). Cell 163:1047-1048.
Cancer Genome Atlas Research Network, WM Linehan, PT Spellman, CJ Ricketts, CJ Creighton, SS Fei, C Davis, DA Wheeler, BA Murray, L Schmidt, CD Vocke, M Peto, AA Al Mamun, E Shinbrot, A Sethi, S Brooks, WK Rathmell, AN Brooks, KA Hoadley, AG Robertson, D Brooks, R Bowlby, S Sadeghi, H Shen, DJ Weisenberger, M Bootwalla, SB Baylin, PW Laird, AD Cherniack, G Saksena, S Haake, J Li, H Liang, Y Lu, GB Mills, R Akbani, MD Leiserson, BJ Raphael, P Anur, D Bottaro, L Albiges, N Barnabas, TK Choueiri, B Czerniak, AK Godwin, AA Hakimi, TH Ho, J Hsieh, M Ittmann, WY Kim, B Krishnan, MJ Merino, KR Mills Shaw, VE Reuter, E Reznik, CS Shelley, B Shuch, S Signoretti, R Srinivasan, P Tamboli, G Thomas, S Tickoo, K Burnett, D Crain, J Gardner, K Lau, D Mallery, S Morris, JD Paulauskis, RJ Penny, C Shelton, WT Shelton, M Sherman, E Thompson, P Yena, MT Avedon, J Bowen, JM Gastier-Foster, M Gerken, KM Leraas, TM Lichtenberg, NC Ramirez, T Santos, L Wise, E Zmuda, JA Demchok, I Felau, CM Hutter, M Sheth, HJ Sofia, R Tarnuzzer, Z Wang, L Yang, JC Zenklusen, J Zhang, B Ayala, J Baboud, S Chudamani, J Liu, L Lolla, R Naresh, T Pihl, Q Sun, Y Wan, Y Wu, A Ally, M Balasundaram, S Balu, R Beroukhim, T Bodenheimer, C Buhay, YS Butterfield, R Carlsen, SL Carter, H Chao, E Chuah, A Clarke, KR Covington, M Dahdouli, N Dewal, N Dhalla, HV Doddapaneni, JA Drummond, SB Gabriel, RA Gibbs, R Guin, W Hale, A Hawes, DN Hayes, RA Holt, AP Hoyle, SR Jefferys, SJ Jones, CD Jones, D Kalra, C Kovar, L Lewis, J Li, Y Ma, MA Marra, M Mayo, S Meng, M Meyerson, PA Mieczkowski, RA Moore, D Morton, LE Mose, AJ Mungall, D Muzny, JS Parker, CM Perou, J Roach, JE Schein, SE Schumacher, Y Shi, JV Simons, P Sipahimalani, T Skelly, MG Soloway, C Sougnez, A Tam, D Tan, N Thiessen, U Veluvolu, M Wang, MD Wilkerson, T Wong, J Wu, L Xi, J Zhou, J Bedford, F Chen, Y Fu, M Gerstein, D Haussler, K Kasaian, P Lai, S Ling, A Radenbaugh, D Van Den Berg, JN Weinstein, J Zhu, M Albert, I Alexopoulou, JJ Andersen, JT Auman, J Bartlett, S Bastacky, J Bergsten, ML Blute, L Boice, RJ Bollag, J Boyd, E Castle, YB Chen, JC Cheville, E Curley, B Davies, A DeVolk, R Dhir, L Dike, J Eckman, J Engel, J Harr, R Hrebinko, M Huang, L Huelsenbeck-Dill, M Iacocca, B Jacobs, M Lobis, JK Maranchie, S McMeekin, J Myers, J Nelson, J Parfitt, A Parwani, N Petrelli, B Rabeno, S Roy, AL Salner, J Slaton, M Stanton, RH Thompson, L Thorne, K Tucker, PM Weinberger, C Winemiller, LA Zach, R Zuna (2015). N Engl J Med 374: 135-45.
1000 Genomes Project Consortium, A Auton, LD Brooks, RM Durbin, EP Garrison, HM Kang, JO Korbel, JL Marchini, S McCarthy, GA McVean, GR Abecasis (2015). Nature 526: 68-74.
PH Sudmant, T Rausch, EJ Gardner, RE Handsaker, A Abyzov, J Huddleston, Y Zhang, K Ye, G Jun, MH Fritz, MK Konkel, A Malhotra, AM Stutz, X Shi, FP Casale, J Chen, F Hormozdiari, G Dayama, K Chen, M Malig, MJP Chaisson, K Walter, S Meiers, S Kashin, E Garrison, A Auton, HYK Lam, XJ Mu, C Alkan, D Antaki, T Bae, E Cerveira, P Chines, Z Chong, L Clarke, E Dal, L Ding, S Emery, X Fan, M Gujral, F Kahveci, JM Kidd, Y Kong, EW Lameijer, S McCarthy, P Flicek, RA Gibbs, G Marth, CE Mason, A Menelaou, DM Muzny, BJ Nelson, A Noor, NF Parrish, M Pendleton, A Quitadamo, B Raeder, EE Schadt, M Romanovitch, A Schlattl, R Sebra, AA Shabalin, A Untergasser, JA Walker, M Wang, F Yu, C Zhang, J Zhang, X Zheng-Bradley, W Zhou, T Zichner, J Sebat, MA Batzer, SA McCarroll, 1000 Genomes Project Consortium, RE Mills, MB Gerstein, A Bashir, O Stegle, SE Devine, C Lee, EE Eichler, JO Korbel (2015). Nature 526: 75-81.
JC Mu, P Tootoonchi Afshar, M Mohiyuddin, X Chen, J Li, N Bani Asadi, MB Gerstein, WH Wong, HY Lam (2015). Sci Rep 5: 14493.
LT Fang, PT Afshar, A Chhibber, M Mohiyuddin, Y Fan, JC Mu, G Gibeling, S Barr, NB Asadi, MB Gerstein, DC Koboldt, W Wang, WH Wong, HY Lam (2015). Genome Biol 16: 197.
EE Duffy, M Rutenberg-Schoenberg, CD Stark, RR Kitchen, MB Gerstein, MD Simon (2015). Mol Cell 59: 858-66.
L Lochovsky, J Zhang, Y Fu, E Khurana, M Gerstein (2015). Nucleic Acids Res 43: 8123-34.
PP Kuksa, MR Min, R Dugar, M Gerstein (2015). Bioinformatics 31: 3600-7.
J Mariani, G Coppola, P Zhang, A Abyzov, L Provini, L Tomasini, M Amenduni, A Szekely, D Palejev, M Wilson, M Gerstein, EL Grigorenko, K Chawarska, KA Pelphrey, JR Howe, FM Vaccarino (2015). Cell 162: 375-390.
A Abyzov, S Li, DR Kim, M Mohiyuddin, AM Stutz, NF Parrish, XJ Mu, W Clark, K Chen, M Hurles, JO Korbel, HY Lam, C Lee, MB Gerstein (2015). Nat Commun 6: 7256.
D Greenbaum, M Gerstein (2015). Science 347: 956.
M Mohiyuddin, JC Mu, J Li, N Bani Asadi, MB Gerstein, A Abyzov, WH Wong, HY Lam (2015). Bioinformatics 31: 2741-4.
D Wang, KK Yan, C Sisu, C Cheng, J Rozowsky, W Meyerson, MB Gerstein (2015). PLoS Comput Biol 11: e1004132.
C Cheng, E Andrews, KK Yan, M Ung, D Wang, M Gerstein (2015). Genome Biol 16: 63.



2014 (15)

D Greenbaum, A Harmanci, M Gerstein (2014). IEEE IEEE International Symposium on Ethics in Science, Technology and Engineering.
MR Min, X Ning, Y Qi, C Cheng, A Bonner, M Gerstein (2014). NIPS Workshop on Machine Learning in Computational Biology.
MR Min, X Ning, C Cheng, M Gerstein (2014). JMLR W&CP 33:614-622 (AISTATS 2014).
JC Mu, M Mohiyuddin, J Li, N Bani Asadi, MB Gerstein, A Abyzov, WH Wong, HY Lam (2014). Bioinformatics 31: 1469-71.
RR Kitchen, JS Rozowsky, MB Gerstein, AC Nairn (2014). Nat Neurosci 17: 1491-9.
A Harmanci, J Rozowsky, M Gerstein (2014). Genome Biol 15: 474.
Y Fu, Z Liu, S Lou, J Bedford, XJ Mu, KY Yip, E Khurana, M Gerstein (2014). Genome Biol 15: 480.
AP Boyle, CL Araya, C Brdlik, P Cayting, C Cheng, Y Cheng, K Gardner, LW Hillier, J Janette, L Jiang, D Kasper, T Kawli, P Kheradpour, A Kundaje, JJ Li, L Ma, W Niu, EJ Rehm, J Rozowsky, M Slattery, R Spokony, R Terrell, D Vafeados, D Wang, P Weisdepp, YC Wu, D Xie, KK Yan, EA Feingold, PJ Good, MJ Pazin, H Huang, PJ Bickel, SE Brenner, V Reinke, RH Waterston, M Gerstein, KP White, M Kellis, M Snyder (2014). Nature 512: 453-6.
MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, CA Davis, L Hillier, C Sisu, JJ Li, B Pei, AO Harmanci, MO Duff, S Djebali, RP Alexander, BH Alver, R Auerbach, K Bell, PJ Bickel, ME Boeck, NP Boley, BW Booth, L Cherbas, P Cherbas, C Di, A Dobin, J Drenkow, B Ewing, G Fang, M Fastuca, EA Feingold, A Frankish, G Gao, PJ Good, R Guigo, A Hammonds, J Harrow, RA Hoskins, C Howald, L Hu, H Huang, TJ Hubbard, C Huynh, S Jha, D Kasper, M Kato, TC Kaufman, RR Kitchen, E Ladewig, J Lagarde, E Lai, J Leng, Z Lu, M MacCoss, G May, R McWhirter, G Merrihew, DM Miller, A Mortazavi, R Murad, B Oliver, S Olson, PJ Park, MJ Pazin, N Perrimon, D Pervouchine, V Reinke, A Reymond, G Robinson, A Samsonova, GI Saunders, F Schlesinger, A Sethi, FJ Slack, WC Spencer, MH Stoiber, P Strasbourger, A Tanzer, OA Thompson, KH Wan, G Wang, H Wang, KL Watkins, J Wen, K Wen, C Xue, L Yang, K Yip, C Zaleski, Y Zhang, H Zheng, SE Brenner, BR Graveley, SE Celniker, TR Gingeras, R Waterston (2014). Nature 512: 445-8.
C Sisu, B Pei, J Leng, A Frankish, Y Zhang, S Balasubramanian, R Harte, D Wang, M Rutenberg-Schoenberg, W Clark, M Diekhans, J Rozowsky, T Hubbard, J Harrow, MB Gerstein (2014). Proc Natl Acad Sci U S A 111: 13361-6.
KK Yan, D Wang, J Rozowsky, H Zheng, C Cheng, M Gerstein (2014). Genome Biol 15: R100.
DG MacArthur, TA Manolio, DP Dimmock, HL Rehm, J Shendure, GR Abecasis, DR Adams, RB Altman, SE Antonarakis, EA Ashley, JC Barrett, LG Biesecker, DF Conrad, GM Cooper, NJ Cox, MJ Daly, MB Gerstein, DB Goldstein, JN Hirschhorn, SM Leal, LA Pennacchio, JA Stamatoyannopoulos, SR Sunyaev, D Valle, BF Voight, W Winckler, C Gunter (2014). Nature 508: 469-76.
M Kellis, B Wold, MP Snyder, BE Bernstein, A Kundaje, GK Marinov, LD Ward, E Birney, GE Crawford, J Dekker, I Dunham, LL Elnitski, PJ Farnham, EA Feingold, M Gerstein, MC Giddings, DM Gilbert, TR Gingeras, ED Green, R Guigo, T Hubbard, J Kent, JD Lieb, RM Myers, MJ Pazin, B Ren, JA Stamatoyannopoulos, Z Weng, KP White, RC Hardison (2014). Proc Natl Acad Sci U S A 111: 6131-8.
JA Miller, SL Ding, SM Sunkin, KA Smith, L Ng, A Szafer, A Ebbert, ZL Riley, JJ Royall, K Aiona, JM Arnold, C Bennet, D Bertagnolli, K Brouner, S Butler, S Caldejon, A Carey, C Cuhaciyan, RA Dalley, N Dee, TA Dolbeare, BA Facer, D Feng, TP Fliss, G Gee, J Goldy, L Gourley, BW Gregor, G Gu, RE Howard, JM Jochim, CL Kuan, C Lau, CK Lee, F Lee, TA Lemon, P Lesnar, B McMurray, N Mastan, N Mosqueda, T Naluai-Cecchini, NK Ngo, J Nyhus, A Oldre, E Olson, J Parente, PD Parker, SE Parry, A Stevens, M Pletikos, M Reding, K Roll, D Sandman, M Sarreal, S Shapouri, NV Shapovalova, EH Shen, N Sjoquist, CR Slaughterbeck, M Smith, AJ Sodt, D Williams, L Zollei, B Fischl, MB Gerstein, DH Geschwind, IA Glass, MJ Hawrylycz, RF Hevner, H Huang, AR Jones, JA Knowles, P Levitt, JW Phillips, N Sestan, P Wohnoutka, C Dang, A Bernard, JG Hohmann, ES Lein (2014). Nature 508: 199-206.
C Chen, BH Ha, AF Thevenin, HJ Lou, R Zhang, KY Yip, JR Peterson, M Gerstein, PM Kim, P Filippakopoulos, S Knapp, TJ Boggon, BE Turk (2014). Mol Cell 53: 140-7.



2013 (14)

MR Min, X Ning, C Cheng, M Gerstein (2013). NIPS Workshop on Machine Learning in Computational Biology.
T Steijger, JF Abril, PG Engstrom, F Kokocinski, RGASP Consortium, TJ Hubbard, R Guigo, J Harrow, P Bertone (2013). Nat Methods 10: 1177-84.
D Greenbaum, J Chen, M Gerstein (2013). Science 342: 560.
E Khurana, Y Fu, V Colonna, XJ Mu, HM Kang, T Lappalainen, A Sboner, L Lochovsky, J Chen, A Harmanci, J Das, A Abyzov, S Balasubramanian, K Beal, D Chakravarty, D Challis, Y Chen, D Clarke, L Clarke, F Cunningham, US Evani, P Flicek, R Fragoza, E Garrison, R Gibbs, ZH Gumus, J Herrero, N Kitabayashi, Y Kong, K Lage, V Liluashvili, SM Lipkin, DG MacArthur, G Marth, D Muzny, TH Pers, GRS Ritchie, JA Rosenfeld, C Sisu, X Wei, M Wilson, Y Xue, F Yu, 1000 Genomes Project Consortium, ET Dermitzakis, H Yu, MA Rubin, C Tyler-Smith, M Gerstein (2013). Science 342: 1235587.
A Abyzov, R Iskow, O Gokcumen, DW Radke, S Balasubramanian, B Pei, L Habegger, 1000 Genomes Project Consortium, C Lee, M Gerstein (2013). Genome Res 23: 2042-52.
D Greenbaum, M Gerstein (2013). The Scientist 27:26 (1 Oct.)
C Cheng, Y Fu, L Shen, M Gerstein (2013). BMC Syst Biol 7: 70.
Y Zhang, R Haraksingh, F Grubert, A Abyzov, M Gerstein, S Weissman, AE Urban (2013). Child Dev 84: 34-48.
R Kittler, J Zhou, S Hua, L Ma, Y Liu, E Pendleton, C Cheng, M Gerstein, KP White (2013). Cell Rep 3: 538-51.
H Tilgner, D Raha, L Habegger, M Mohiuddin, M Gerstein, M Snyder (2013). G3 (Bethesda) 3: 387-97.
SB Montgomery, DL Goode, E Kvikstad, CA Albers, ZD Zhang, XJ Mu, G Ananda, B Howie, KJ Karczewski, KS Smith, V Anaya, R Richardson, J Davis, 1000 Genomes Project Consortium, DG MacArthur, A Sidow, L Duret, M Gerstein, KD Makova, J Marchini, G McVean, G Lunter (2013). Genome Res 23: 749-61.
WF Doolittle, P Fraser, MB Gerstein, BR Graveley, S Henikoff, C Huttenhower, A Oshlack, CP Ponting, JL Rinn, MC Schatz, J Ule, D Weigel, GM Weinstock (2013). Genome Biol 14: 113.
KY Yip, C Cheng, M Gerstein (2013). Genome Biol 14: 205.
E Khurana, Y Fu, J Chen, M Gerstein (2013). PLoS Comput Biol 9: e1002886.



2012 (26)

PC Lin, YL Chiu, S Banerjee, K Park, JM Mosquera, E Giannopoulou, P Alves, AK Tewari, MB Gerstein, H Beltran, AM Melnick, O Elemento, F Demichelis, MA Rubin (2012). Cancer Res 73: 1232-44.
A Abyzov, J Mariani, D Palejev, Y Zhang, MS Haney, L Tomasini, AF Ferrandino, LA Rosenberg Belmaker, A Szekely, M Wilson, A Kocabas, NE Calixto, EL Grigorenko, A Huttner, K Chawarska, S Weissman, AE Urban, M Gerstein, FM Vaccarino (2012). Nature 492: 438-42.
1000 Genomes Project Consortium, GR Abecasis, A Auton, LD Brooks, MA DePristo, RM Durbin, RE Handsaker, HM Kang, GT Marth, GA McVean (2012). Nature 491: 56-65.
M Gerstein (2012). Nature 489: 208.
ENCODE Project Consortium (2012). Nature 489: 57-74.
MB Gerstein, A Kundaje, M Hariharan, SG Landt, KK Yan, C Cheng, XJ Mu, E Khurana, J Rozowsky, R Alexander, R Min, P Alves, A Abyzov, N Addleman, N Bhardwaj, AP Boyle, P Cayting, A Charos, DZ Chen, Y Cheng, D Clarke, C Eastman, G Euskirchen, S Frietze, Y Fu, J Gertz, F Grubert, A Harmanci, P Jain, M Kasowski, P Lacroute, JJ Leng, J Lian, H Monahan, H O'Geen, Z Ouyang, EC Partridge, D Patacsil, F Pauli, D Raha, L Ramirez, TE Reddy, B Reed, M Shi, T Slifer, J Wang, L Wu, X Yang, KY Yip, G Zilberman-Schapira, S Batzoglou, A Sidow, PJ Farnham, RM Myers, SM Weissman, M Snyder (2012). Nature 489: 91-100.
S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann, A Mortazavi, A Tanzer, J Lagarde, W Lin, F Schlesinger, C Xue, GK Marinov, J Khatun, BA Williams, C Zaleski, J Rozowsky, M Roder, F Kokocinski, RF Abdelhamid, T Alioto, I Antoshechkin, MT Baer, NS Bar, P Batut, K Bell, I Bell, S Chakrabortty, X Chen, J Chrast, J Curado, T Derrien, J Drenkow, E Dumais, J Dumais, R Duttagupta, E Falconnet, M Fastuca, K Fejes-Toth, P Ferreira, S Foissac, MJ Fullwood, H Gao, D Gonzalez, A Gordon, H Gunawardena, C Howald, S Jha, R Johnson, P Kapranov, B King, C Kingswood, OJ Luo, E Park, K Persaud, JB Preall, P Ribeca, B Risk, D Robyr, M Sammeth, L Schaffer, LH See, A Shahab, J Skancke, AM Suzuki, H Takahashi, H Tilgner, D Trout, N Walters, H Wang, J Wrobel, Y Yu, X Ruan, Y Hayashizaki, J Harrow, M Gerstein, T Hubbard, A Reymond, SE Antonarakis, G Hannon, MC Giddings, Y Ruan, B Wold, P Carninci, R Guigo, TR Gingeras (2012). Nature 489: 101-8.
J Harrow, A Frankish, JM Gonzalez, E Tapanari, M Diekhans, F Kokocinski, BL Aken, D Barrell, A Zadissa, S Searle, I Barnes, A Bignell, V Boychenko, T Hunt, M Kay, G Mukherjee, J Rajan, G Despacio-Reyes, G Saunders, C Steward, R Harte, M Lin, C Howald, A Tanzer, T Derrien, J Chrast, N Walters, S Balasubramanian, B Pei, M Tress, JM Rodriguez, I Ezkurdia, J van Baren, M Brent, D Haussler, M Kellis, A Valencia, A Reymond, M Gerstein, R Guigo, TJ Hubbard (2012). Genome Res 22: 1760-74.
KY Yip, C Cheng, N Bhardwaj, JB Brown, J Leng, A Kundaje, J Rozowsky, E Birney, P Bickel, M Snyder, M Gerstein (2012). Genome Biol 13: R48.
C Cheng, R Alexander, R Min, J Leng, KY Yip, J Rozowsky, KK Yan, X Dong, S Djebali, Y Ruan, CA Davis, P Carninci, T Lassman, TR Gingeras, R Guigo, E Birney, Z Weng, M Snyder, M Gerstein (2012). Genome Res 22: 1658-67.
SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, BE Bernstein, P Bickel, JB Brown, P Cayting, Y Chen, G DeSalvo, C Epstein, KI Fisher-Aylor, G Euskirchen, M Gerstein, J Gertz, AJ Hartemink, MM Hoffman, VR Iyer, YL Jung, S Karmakar, M Kellis, PV Kharchenko, Q Li, T Liu, XS Liu, L Ma, A Milosavljevic, RM Myers, PJ Park, MJ Pazin, MD Perry, D Raha, TE Reddy, J Rozowsky, N Shoresh, A Sidow, M Slattery, JA Stamatoyannopoulos, MY Tolstorukov, KP White, S Xi, PJ Farnham, JD Lieb, BJ Wold, M Snyder (2012). Genome Res 22: 1813-31.
B Pei, C Sisu, A Frankish, C Howald, L Habegger, XJ Mu, R Harte, S Balasubramanian, A Tanzer, M Diekhans, A Reymond, TJ Hubbard, J Harrow, MB Gerstein (2012). Genome Biol 13: R51.
X Dong, MC Greven, A Kundaje, S Djebali, JB Brown, C Cheng, TR Gingeras, M Gerstein, R Guigo, E Birney, Z Weng (2012). Genome Biol 13: R53.
JQ Wu, M Seay, VP Schulz, M Hariharan, D Tuck, J Lian, J Du, M Shi, Z Ye, M Gerstein, MP Snyder, S Weissman (2012). PLoS Genet 8: e1002565.
HY Lam, C Pan, MJ Clark, P Lacroute, R Chen, R Haraksingh, M O'Huallachain, MB Gerstein, JM Kidd, CD Bustamante, M Snyder (2012). Nat Biotechnol 30: 226-9.
J Cotney, J Leng, S Oh, LE DeMare, SK Reilly, MB Gerstein, JP Noonan (2012). Genome Res 22: 1069-80.
M Vidal, DW Chan, M Gerstein, M Mann, GS Omenn, D Tagle, S Sechi, Workshop Participants (2012). Clin Proteomics 9: 6.
MJ Bamshad, JA Shendure, D Valle, A Hamosh, JR Lupski, RA Gibbs, E Boerwinkle, RP Lifton, M Gerstein, M Gunel, S Mane, DA Nickerson, Centers for Mendelian Genomics (2012). Am J Med Genet A 158A: 1523-5.
L Habegger, S Balasubramanian, DZ Chen, E Khurana, A Sboner, A Harmanci, J Rozowsky, D Clarke, M Snyder, M Gerstein (2012). Bioinformatics 28: 2267-9.
G Zilberman-Schapira, J Chen, M Gerstein (2012). Recent Pat DNA Gene Seq 6: 180-8.
TA Gianoulis, MA Griffin, DJ Spakowicz, BF Dunican, CJ Alpha, A Sboner, AM Sismour, C Kodira, M Egholm, GM Church, MB Gerstein, SA Strobel (2012). PLoS Genet 8: e1002558.
R Chen, GI Mias, J Li-Pook-Than, L Jiang, HY Lam, R Chen, E Miriami, KJ Karczewski, M Hariharan, FE Dewey, Y Cheng, MJ Clark, H Im, L Habegger, S Balasubramanian, M O'Huallachain, JT Dudley, S Hillenmeyer, R Haraksingh, D Sharon, G Euskirchen, P Lacroute, K Bettinger, AP Boyle, M Kasowski, F Grubert, S Seki, M Garcia, M Whirl-Carrillo, M Gallardo, MA Blasco, PL Greenberg, P Snyder, TE Klein, RB Altman, AJ Butte, EA Ashley, M Gerstein, KC Nadeau, H Tang, M Snyder (2012). Cell 148: 1293-307.
DG MacArthur, S Balasubramanian, A Frankish, N Huang, J Morris, K Walter, L Jostins, L Habegger, JK Pickrell, SB Montgomery, CA Albers, ZD Zhang, DF Conrad, G Lunter, H Zheng, Q Ayub, MA DePristo, E Banks, M Hu, RE Handsaker, JA Rosenfeld, M Fromer, M Jin, XJ Mu, E Khurana, K Ye, M Kay, GI Saunders, MM Suner, T Hunt, IH Barnes, C Amid, DR Carvalho-Silva, AH Bignell, C Snow, B Yngvadottir, S Bumpstead, DN Cooper, Y Xue, IG Romero, 1000 Genomes Project Consortium, J Wang, Y Li, RA Gibbs, SA McCarroll, ET Dermitzakis, JK Pritchard, JC Barrett, J Harrow, ME Hurles, MB Gerstein, C Tyler-Smith (2012). Science 335: 823-8.
G Li, X Ruan, RK Auerbach, KS Sandhu, M Zheng, P Wang, HM Poh, Y Goh, J Lim, J Zhang, HS Sim, SQ Peh, FH Mulawadi, CT Ong, YL Orlov, S Hong, Z Zhang, S Landt, D Raha, G Euskirchen, CL Wei, W Ge, H Wang, C Davis, KI Fisher-Aylor, A Mortazavi, M Gerstein, T Gingeras, B Wold, Y Sun, MJ Fullwood, E Cheung, E Liu, WK Sung, M Snyder, Y Ruan (2012). Cell 148: 84-98.
D Clarke, N Bhardwaj, MB Gerstein (2012). J Struct Biol 179: 320-6.
J Du, J Leng, L Habegger, A Sboner, D McDermott, M Gerstein (2012). PLoS One 7: e29175.



2011 (40)

HY Lam, MJ Clark, R Chen, R Chen, G Natsoulis, M O'Huallachain, FE Dewey, L Habegger, EA Ashley, MB Gerstein, AJ Butte, HP Ji, M Snyder (2011). Nat Biotechnol 30: 78-82.
N Bhardwaj, D Clarke, M Gerstein (2011). Proc Natl Acad Sci U S A 108: 20279-80.
D Greenbaum, A Sboner, XJ Mu, M Gerstein (2011). PLoS Comput Biol 7: e1002278.
D Lipman, P Flicek, S Salzberg, M Gerstein, R Knight (2011). Genome Biol 12: 402.
RR Haraksingh, A Abyzov, M Gerstein, AE Urban, M Snyder (2011). PLoS One 6: e27859.
C Cheng, KK Yan, W Hwang, J Qian, N Bhardwaj, J Rozowsky, ZJ Lu, W Niu, P Alves, M Kato, M Snyder, M Gerstein (2011). PLoS Comput Biol 7: e1002190.
C Cheng, C Shou, KY Yip, MB Gerstein (2011). Genome Biol 12: R111.
D Greenbaum, M Gerstein (2011). Am J Bioeth 11: 39-41.
C Cheng, R Min, M Gerstein (2011). Bioinformatics 27: 3221-7.
SC Flores, MB Gerstein (2011). BMC Bioinformatics 12: 417.
KY Yip, L Utz, S Sitwell, X Hu, SS Sidhu, BE Turk, M Gerstein, PM Kim (2011). BMC Biol 9: 53.
C Cheng, M Gerstein (2011). Nucleic Acids Res 40: 553-68.
MR Tanas, A Sboner, AM Oliveira, MR Erickson-Johnson, J Hespelt, PJ Hanwright, J Flanagan, Y Luo, K Fenwick, R Natrajan, C Mitsopoulos, M Zvelebil, BL Hoch, SW Weiss, M Debiec-Rychter, R Sciot, RB West, AJ Lazar, A Ashworth, JS Reis-Filho, CJ Lord, MB Gerstein, MA Rubin, BP Rubin (2011). Sci Transl Med 3: 98ra82.
N Bhardwaj, A Abyzov, D Clarke, C Shou, MB Gerstein (2011). Protein Sci 20: 1745-54.
A Sboner, XJ Mu, D Greenbaum, RK Auerbach, MB Gerstein (2011). Genome Biol 12: 125.
J Rozowsky, A Abyzov, J Wang, P Alves, D Raha, A Harmanci, J Leng, R Bjornson, Y Kong, N Kitabayashi, N Bhardwaj, M Rubin, M Snyder, M Gerstein (2011). Mol Syst Biol 7: 522.
ZD Zhang, J Du, H Lam, A Abyzov, AE Urban, M Snyder, M Gerstein (2011). BMC Genomics 12: 375.
MB Clark, PP Amaral, FJ Schlesinger, ME Dinger, RJ Taft, JL Rinn, CP Ponting, PF Stadler, KV Morris, A Morillon, JS Rozowsky, MB Gerstein, C Wahlestedt, Y Hayashizaki, P Carninci, TR Gingeras, JS Mattick (2011). PLoS Biol 9: e1000625; discussion e1001102.
KK Yan, M Gerstein (2011). PLoS One 6: e19917.
XJ Mu, ZJ Lu, Y Kong, HY Lam, MB Gerstein (2011). Nucleic Acids Res 39: 7058-76.
D Greenbaum, M Gerstein (2011). Am J Bioeth 11: 31-2.
ENCODE Project Consortium (2011). PLoS Biol 9: e1001046.
J Fasolo, A Sboner, MG Sun, H Yu, R Chen, D Sharon, PM Kim, M Gerstein, M Snyder (2011). Genes Dev 25: 767-78.
TA Gianoulis, A Agarwal, M Snyder, MB Gerstein (2011). Genome Biol 12: R32.
N Negre, CD Brown, L Ma, CA Bristow, SW Miller, U Wagner, P Kheradpour, ML Eaton, P Loriaux, R Sealfon, Z Li, H Ishii, RF Spokony, J Chen, L Hwang, C Cheng, RP Auburn, MB Davis, M Domanus, PK Shah, CA Morrison, J Zieba, S Suchy, L Senderowicz, A Victorsen, NA Bild, AJ Grundstad, D Hanley, DM MacAlpine, M Mannervik, K Venken, H Bellen, R White, M Gerstein, S Russell, RL Grossman, B Ren, JW Posakony, M Kellis, KP White (2011). Nature 471: 527-31.
GM Euskirchen, RK Auerbach, E Davidov, TA Gianoulis, G Zhong, J Rozowsky, N Bhardwaj, MB Gerstein, M Snyder (2011). PLoS Genet 7: e1002008.
J Jee, J Rozowsky, KY Yip, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein (2011). Bioinformatics 27: 1152-4.
A Karpikov, J Rozowsky, M Gerstein (2011). BMC Bioinformatics 12: 57.
A Abyzov, AE Urban, M Snyder, M Gerstein (2011). Genome Res 21: 974-84.
C Cheng, KK Yan, KY Yip, J Rozowsky, R Alexander, C Shou, M Gerstein (2011). Genome Biol 12: R15.
MF Berger, MS Lawrence, F Demichelis, Y Drier, K Cibulskis, AY Sivachenko, A Sboner, R Esgueva, D Pflueger, C Sougnez, R Onofrio, SL Carter, K Park, L Habegger, L Ambrogio, T Fennell, M Parkin, G Saksena, D Voet, AH Ramos, TJ Pugh, J Wilkinson, S Fisher, W Winckler, S Mahan, K Ardlie, J Baldwin, JW Simons, N Kitabayashi, TY MacDonald, PW Kantoff, L Chin, SB Gabriel, MB Gerstein, TR Golub, M Meyerson, A Tewari, ES Lander, G Getz, MA Rubin, LA Garraway (2011). Nature 470: 214-20.
RE Mills, K Walter, C Stewart, RE Handsaker, K Chen, C Alkan, A Abyzov, SC Yoon, K Ye, RK Cheetham, A Chinwalla, DF Conrad, Y Fu, F Grubert, I Hajirasouliha, F Hormozdiari, LM Iakoucheva, Z Iqbal, S Kang, JM Kidd, MK Konkel, J Korn, E Khurana, D Kural, HY Lam, J Leng, R Li, Y Li, CY Lin, R Luo, XJ Mu, J Nemesh, HE Peckham, T Rausch, A Scally, X Shi, MP Stromberg, AM Stutz, AE Urban, JA Walker, J Wu, Y Zhang, ZD Zhang, MA Batzer, L Ding, GT Marth, G McVean, J Sebat, M Snyder, J Wang, K Ye, EE Eichler, MB Gerstein, ME Hurles, C Lee, SA McCarroll, JO Korbel, 1000 Genomes Project (2011). Nature 470: 59-65.
C Shou, N Bhardwaj, HY Lam, KK Yan, PM Kim, M Snyder, MB Gerstein (2011). PLoS Comput Biol 7: e1001050.
A Abyzov, M Gerstein (2011). Bioinformatics 27: 595-603.
S Balasubramanian, L Habegger, A Frankish, DG MacArthur, R Harte, C Tyler-Smith, J Harrow, M Gerstein (2011). Genes Dev 25: 1-10.
FM Vaccarino, AE Urban, HE Stevens, A Szekely, A Abyzov, EL Grigorenko, M Gerstein, S Weissman (2011). J Child Psychol Psychiatry 52: 504-16.
ZJ Lu, KY Yip, G Wang, C Shou, LW Hillier, E Khurana, A Agarwal, R Auerbach, J Rozowsky, C Cheng, M Kato, DM Miller, F Slack, M Snyder, RH Waterston, V Reinke, MB Gerstein (2011). Genome Res 21: 276-85.
W Niu, ZJ Lu, M Zhong, M Sarov, JI Murray, CM Brdlik, J Janette, C Chen, P Alves, E Preston, C Slightham, L Jiang, AA Hyman, SK Kim, RH Waterston, M Gerstein, M Snyder, V Reinke (2011). Genome Res 21: 245-54.
L Habegger, A Sboner, TA Gianoulis, J Rozowsky, A Agarwal, M Snyder, M Gerstein (2011). Bioinformatics 27: 281-3.
D Pflueger, S Terry, A Sboner, L Habegger, R Esgueva, PC Lin, MA Svensson, N Kitabayashi, BJ Moss, TY MacDonald, X Cao, T Barrette, AK Tewari, MS Chee, AM Chinnaiyan, DS Rickman, F Demichelis, MB Gerstein, MA Rubin (2011). Genome Res 21: 56-67.



2010 (32)

Yale Law School Roundtable on Data and Code Sharing (2010). Computing in Science & Engineering 12(5): 8-13 (Sept/Oct).
MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng, BI Arshinoff, T Liu, KY Yip, R Robilotto, A Rechtsteiner, K Ikegami, P Alves, A Chateigner, M Perry, M Morris, RK Auerbach, X Feng, J Leng, A Vielle, W Niu, K Rhrissorrakrai, A Agarwal, RP Alexander, G Barber, CM Brdlik, J Brennan, JJ Brouillet, A Carr, MS Cheung, H Clawson, S Contrino, LO Dannenberg, AF Dernburg, A Desai, L Dick, AC Dose, J Du, T Egelhofer, S Ercan, G Euskirchen, B Ewing, EA Feingold, R Gassmann, PJ Good, P Green, F Gullier, M Gutwein, MS Guyer, L Habegger, T Han, JG Henikoff, SR Henz, A Hinrichs, H Holster, T Hyman, AL Iniguez, J Janette, M Jensen, M Kato, WJ Kent, E Kephart, V Khivansara, E Khurana, JK Kim, P Kolasinska-Zwierz, EC Lai, I Latorre, A Leahey, S Lewis, P Lloyd, L Lochovsky, RF Lowdon, Y Lubling, R Lyne, M MacCoss, SD Mackowiak, M Mangone, S McKay, D Mecenas, G Merrihew, DM Miller, A Muroyama, JI Murray, SL Ooi, H Pham, T Phippen, EA Preston, N Rajewsky, G Ratsch, H Rosenbaum, J Rozowsky, K Rutherford, P Ruzanov, M Sarov, R Sasidharan, A Sboner, P Scheid, E Segal, H Shin, C Shou, FJ Slack, C Slightam, R Smith, WC Spencer, EO Stinson, S Taing, T Takasaki, D Vafeados, K Voronina, G Wang, NL Washington, CM Whittle, B Wu, KK Yan, G Zeller, Z Zha, M Zhong, X Zhou, modENCODE Consortium, J Ahringer, S Strome, KC Gunsalus, G Micklem, XS Liu, V Reinke, SK Kim, LW Hillier, S Henikoff, F Piano, M Snyder, L Stein, JD Lieb, RH Waterston (2010). Science 330: 1775-87.
N Bhardwaj, PM Kim, MB Gerstein (2010). Sci Signal 3: ra79.
X Li, TA Gianoulis, KY Yip, M Gerstein, M Snyder (2010). Cell 143: 639-50.
ZD Zhang, MB Gerstein (2010). BMC Bioinformatics 11: 539.
1000 Genomes Project Consortium, GR Abecasis, D Altshuler, A Auton, LD Brooks, RM Durbin, RA Gibbs, ME Hurles, GA McVean (2010). Nature 467: 1061-73.
A Sboner, L Habegger, D Pflueger, S Terry, DZ Chen, JS Rozowsky, AK Tewari, N Kitabayashi, BJ Moss, MS Chee, F Demichelis, MA Rubin, MB Gerstein (2010). Genome Biol 11: R104.
KH Cheung, M Samwald, RK Auerbach, MB Gerstein (2010). Mol Syst Biol 6: 403.
RP Alexander, G Fang, J Rozowsky, M Snyder, MB Gerstein (2010). Nat Rev Genet 11: 559-71.
E Khurana, HY Lam, C Cheng, N Carriero, P Cayting, MB Gerstein (2010). Nucleic Acids Res 38: 6997-7007.
A Agarwal, D Koppstein, J Rozowsky, A Sboner, L Habegger, LW Hillier, R Sasidharan, V Reinke, RH Waterston, M Gerstein (2010). BMC Genomics 11: 383.
ME Holford, E Khurana, KH Cheung, M Gerstein (2010). Bioinformatics 26: i71-8.
N Bhardwaj, MB Carson, A Abyzov, KK Yan, H Lu, MB Gerstein (2010). PLoS Comput Biol 6: e1000755.
NR Voss, M Gerstein (2010). Nucleic Acids Res 38: W555-62.
HY Lam, PM Kim, J Mok, R Tonikian, SS Sidhu, BE Turk, M Snyder, MB Gerstein (2010). BMC Bioinformatics 11: 243.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl Acad Sci U S A 107: 9186-91.
PV Patel, TA Gianoulis, RD Bjornson, KY Yip, DM Engelman, MB Gerstein (2010). Genome Res 20: 960-71.
Y Lee, X Yang, Y Huang, H Fan, Q Zhang, Y Wu, J Li, R Hasina, C Cheng, MW Lingen, MB Gerstein, RR Weichselbaum, HR Xing, YA Lussier (2010). PLoS Comput Biol 6: e1000730.
G Fang, N Bhardwaj, R Robilotto, MB Gerstein (2010). PLoS Comput Biol 6: e1000703.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107: 6841-6.
M Kasowski, F Grubert, C Heffelfinger, M Hariharan, A Asabere, SM Waszak, L Habegger, J Rozowsky, M Shi, AE Urban, MY Hong, KJ Karczewski, W Huber, SM Weissman, MB Gerstein, JO Korbel, M Snyder (2010). Science 328: 232-5.
A Sboner, F Demichelis, S Calza, Y Pawitan, SR Setlur, Y Hoshida, S Perner, HO Adami, K Fall, LA Mucci, PW Kantoff, M Stampfer, SO Andersson, E Varenhorst, JE Johansson, MB Gerstein, TR Golub, MA Rubin, O Andren (2010). BMC Med Genomics 3: 8.
ZD Zhang, A Frankish, T Hunt, J Harrow, M Gerstein (2010). Genome Biol 11: R26.
N Bhardwaj, M Gerstein, H Lu (2010). BMC Bioinformatics 11 Suppl 1: S6.
JQ Wu, L Habegger, P Noisa, A Szekely, C Qiu, S Hutchison, D Raha, M Egholm, H Lin, S Weissman, W Cui, M Gerstein, M Snyder (2010). Proc Natl Acad Sci U S A 107: 5254-9.
M Snyder, J Du, M Gerstein (2010). Genes Dev 24: 423-31.
M Zhong, W Niu, ZJ Lu, M Sarov, JI Murray, J Janette, D Raha, KL Sheaffer, HY Lam, E Preston, C Slightham, LW Hillier, T Brock, A Agarwal, R Auerbach, AA Hyman, M Gerstein, SE Mango, SK Kim, RH Waterston, V Reinke, M Snyder (2010). PLoS Genet 6: e1000848.
J Mok, PM Kim, HY Lam, S Piccirillo, X Zhou, GR Jeschke, DL Sheridan, SA Parker, V Desai, M Jwa, E Cameroni, H Niu, M Good, A Remenyi, JL Ma, YJ Sheu, HE Sassi, R Sopko, CS Chan, C De Virgilio, NM Hollingsworth, WA Lim, DF Stern, B Stillman, BJ Andrews, MB Gerstein, M Snyder, BE Turk (2010). Sci Signal 3: ra12.
D Raha, Z Wang, Z Moqtaderi, L Wu, G Zhong, M Gerstein, K Struhl, M Snyder (2010). Proc Natl Acad Sci U S A 107: 3639-44.
KY Yip, RP Alexander, KK Yan, M Gerstein (2010). PLoS One 5: e8121.
HY Lam, XJ Mu, AM Stutz, A Tanzer, PD Cayting, M Snyder, PM Kim, JO Korbel, MB Gerstein (2010). Nat Biotechnol 28: 47-55.
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2009 (39)

D Greenbaum, MB Gerstein (2009). Science 323: 210.
A Canaan, I Haviv, AE Urban, VP Schulz, S Hartman, Z Zhang, D Palejev, AB Deisseroth, J Lacy, M Snyder, M Gerstein, SM Weissman (2009). Proc Natl Acad Sci U S A 106: 22421-6.
D Greenbaum, M Gerstein (2009). Am J Bioeth 9: 15-9.
R Tonikian, X Xin, CP Toret, D Gfeller, C Landgraf, S Panni, S Paoluzi, L Castagnoli, B Currell, S Seshagiri, H Yu, B Winsor, M Vidal, MB Gerstein, GD Bader, R Volkmer, G Cesareni, DG Drubin, PM Kim, SS Sidhu, C Boone (2009). PLoS Biol 7: e1000218.
YJ Liu, D Zheng, S Balasubramanian, N Carriero, E Khurana, R Robilotto, MB Gerstein (2009). BMC Genomics 10: 480.
A Sboner, A Karpikov, G Chen, M Smith, D Mattoon, L Freeman-Cook, B Schweitzer, MB Gerstein (2009). J Proteome Res 8: 5451-64.
C Cheng, N Bhardwaj, M Gerstein (2009). BMC Genomics 10: 431.
Y Arinaminpathy, E Khurana, DM Engelman, MB Gerstein (2009). Drug Discov Today 14: 1130-5.
C Cheng, X Fu, P Alves, M Gerstein (2009). Genome Biol 10: R90.
RK Auerbach, G Euskirchen, J Rozowsky, N Lamarre-Vincent, Z Moqtaderi, P Lefrancois, K Struhl, M Gerstein, M Snyder (2009). Proc Natl Acad Sci U S A 106: 14926-31.
KY Yip, PM Kim, D McDermott, M Gerstein (2009). BMC Bioinformatics 10: 241.
A Rzhetsky, M Seringhaus, MB Gerstein (2009). PLoS Comput Biol 5: e1000411.
D Pflueger, DS Rickman, A Sboner, S Perner, CJ LaFargue, MA Svensson, BJ Moss, N Kitabayashi, Y Pan, A de la Taille, R Kuefer, AK Tewari, F Demichelis, MS Chee, MB Gerstein, MA Rubin (2009). Neoplasia 11: 804-11.
X Guo, Z Zhang, MB Gerstein, D Zheng (2009). PLoS Comput Biol 5: e1000449.
RP Alexander, PM Kim, T Emonet, MB Gerstein (2009). Sci Signal 2: pe44.
R Sasidharan, A Agarwal, J Rozowsky, M Gerstein (2009). BMC Res Notes 2: 150.
K Talbert-Slagle, S Marlatt, FN Barrera, E Khurana, J Oates, M Gerstein, DM Engelman, AM Dixon, D Dimaio (2009). J Virol 83: 9773-85.
JO Korbel, T Tirosh-Wagner, AE Urban, XN Chen, M Kasowski, L Dai, F Grubert, C Erdman, MC Gao, K Lange, EM Sobel, GM Barlow, AS Aylsworth, NJ Carpenter, RD Clark, MY Cohen, E Doran, T Falik-Zaccai, SO Lewin, IT Lott, BC McGillivray, JB Moeschler, MJ Pettenati, SM Pueschel, KW Rao, LG Shaffer, M Shohat, AJ Van Riper, D Warburton, S Weissman, MB Gerstein, M Snyder, JR Korenberg (2009). Proc Natl Acad Sci U S A 106: 12031-6.
J Du, RD Bjornson, ZD Zhang, Y Kong, M Snyder, MB Gerstein (2009). PLoS Comput Biol 5: e1000432.
SE Celniker, LA Dillon, MB Gerstein, KC Gunsalus, S Henikoff, GH Karpen, M Kellis, EC Lai, JD Lieb, DM MacAlpine, G Micklem, F Piano, M Snyder, L Stein, KP White, RH Waterston, modENCODE Consortium (2009). Nature 459: 927-30.
Y Xia, EA Franzosa, MB Gerstein (2009). PLoS Comput Biol 5: e1000413.
L Ni, C Bruce, C Hart, J Leigh-Bell, D Gelperin, L Umansky, MB Gerstein, M Snyder (2009). Genes Dev 23: 1351-63.
N Bhardwaj, M Gerstein (2009). Protein Sci 18: 1230-40.
M Snyder, S Weissman, M Gerstein (2009). Mol Syst Biol 5: 273.
C Cheng, LM Li, P Alves, M Gerstein (2009). BMC Genomics 10: 225.
Y Mishima, C Abreu-Goodger, AA Staton, C Stahlhut, C Shou, C Cheng, M Gerstein, AJ Enright, AJ Giraldez (2009). Genes Dev 23: 619-32.
JO Korbel, A Abyzov, XJ Mu, N Carriero, P Cayting, Z Zhang, M Snyder, MB Gerstein (2009). Genome Biol 10: R23.
KS Keating, SC Flores, MB Gerstein, LA Kuhn (2009). Protein Sci 18: 359-71.
TA Gianoulis, J Raes, PV Patel, R Bjornson, JO Korbel, I Letunic, T Yamada, A Paccanaro, LJ Jensen, M Snyder, P Bork, MB Gerstein (2009). Proc Natl Acad Sci U S A 106: 1374-9.
P Lefrancois, GM Euskirchen, RK Auerbach, J Rozowsky, T Gibson, CM Yellman, M Gerstein, M Snyder (2009). BMC Genomics 10: 37.
F Demichelis, SR Setlur, R Beroukhim, S Perner, JO Korbel, CJ Lafargue, D Pflueger, C Pina, MD Hofer, A Sboner, MA Svensson, DS Rickman, A Urban, M Snyder, M Meyerson, C Lee, MB Gerstein, R Kuefer, MA Rubin (2009). Genes Chromosomes Cancer 48: 366-80.
X Zhang, Z Lian, C Padden, MB Gerstein, J Rozowsky, M Snyder, TR Gingeras, P Kapranov, SM Weissman, PE Newburger (2009). Blood 113: 2526-34.
S Balasubramanian, D Zheng, YJ Liu, G Fang, A Frankish, N Carriero, R Robilotto, P Cayting, M Gerstein (2009). Genome Biol 10: R2.
J Rozowsky, G Euskirchen, RK Auerbach, ZD Zhang, T Gibson, R Bjornson, N Carriero, M Snyder, MB Gerstein (2009). Nat Biotechnol 27: 66-75.
SC Popescu, GV Popescu, S Bachan, Z Zhang, M Gerstein, M Snyder, SP Dinesh-Kumar (2009). Genes Dev 23: 80-92.
LY Wang, A Abyzov, JO Korbel, M Snyder, M Gerstein (2009). Genome Res 19: 106-17.
Z Wang, M Gerstein, M Snyder (2009). Nat Rev Genet 10: 57-63.
KY Yip, M Gerstein (2009). Bioinformatics 25: 243-50.
HY Lam, E Khurana, G Fang, P Cayting, N Carriero, KH Cheung, MB Gerstein (2009). Nucleic Acids Res 37: D738-43.



2008 (25)

M Seringhaus, M Gerstein (2008). American Scientist 96:466-473 (Nov-Dec)
M Seringhaus, J Rozowsky, T Royce, U Nagalakshmi, J Jee, M Snyder, M Gerstein (2008). BMC Genomics 9: 635.
AY Yam, Y Xia, HT Lin, A Burlingame, M Gerstein, J Frydman (2008). Nat Struct Mol Biol 15: 1255-62.
D Greenbaum, J Du, M Gerstein (2008). Am J Bioeth 8: 71-4.
Y Hasin, T Olender, M Khen, C Gonzaga-Jauregui, PM Kim, AE Urban, M Snyder, MB Gerstein, D Lancet, JO Korbel (2008). PLoS Genet 4: e1000249.
PM Kim, HY Lam, AE Urban, JO Korbel, J Affourtit, F Grubert, X Chen, S Weissman, M Snyder, MB Gerstein (2008). Genome Res 18: 1865-74.
ZD Zhang, J Rozowsky, M Snyder, J Chang, M Gerstein (2008). PLoS Comput Biol 4: e1000158.
R Sasidharan, A Smith, M Gerstein (2008). PLoS One 3: e2726.
A Rzhetsky, M Seringhaus, M Gerstein (2008). Cell 134: 9-13.
R Sasidharan, M Gerstein (2008). Nature 453: 729-31.
JO Korbel, PM Kim, X Chen, AE Urban, S Weissman, M Snyder, MB Gerstein (2008). Curr Opin Struct Biol 18: 366-74.
YJ Huang, D Hang, LJ Lu, L Tong, MB Gerstein, GT Montelione (2008). Mol Cell Proteomics 7: 2048-60.
Z Lian, A Karpikov, J Lian, MC Mahajan, S Hartman, M Gerstein, M Snyder, SM Weissman (2008). Genome Res 18: 1224-37.
KD Mertz, F Demichelis, A Sboner, MS Hirsch, P Dal Cin, K Struckmann, M Storz, S Scherrer, DM Schmid, RT Strebel, NM Probst-Hensch, M Gerstein, H Moch, MA Rubin (2008). Int J Cancer 123: 569-76.
U Nagalakshmi, Z Wang, K Waern, C Shou, D Raha, M Gerstein, M Snyder (2008). Science 320: 1344-9.
SC Flores, KS Keating, J Painter, F Morcos, K Nguyen, EA Merritt, LA Kuhn, MB Gerstein (2008). Proteins 73: 299-319.
ZD Zhang, G Weinstock, M Gerstein (2008). J Mol Evol 66: 446-56.
PE Bourne, JL Fink, M Gerstein (2008). PLoS Comput Biol 4: e1000037.
PM Kim, A Sboner, Y Xia, M Gerstein (2008). Mol Syst Biol 4: 179.
M Seringhaus, M Gerstein (2008). FEBS Lett 582: 1170.
DS Johnson, W Li, DB Gordon, A Bhattacharjee, B Curry, J Ghosh, L Brizuela, JS Carroll, M Brown, P Flicek, CM Koch, I Dunham, M Bieda, X Xu, PJ Farnham, P Kapranov, DA Nix, TR Gingeras, X Zhang, H Holster, N Jiang, RD Green, JS Song, SA McCuine, E Anton, L Nguyen, ND Trinklein, Z Ye, K Ching, D Hawkins, B Ren, PC Scacheri, J Rozowsky, A Karpikov, G Euskirchen, S Weissman, M Gerstein, M Snyder, A Yang, Z Moqtaderi, H Hirsch, HP Shulha, Y Fu, Z Weng, K Struhl, RM Myers, JD Lieb, XS Liu (2008). Genome Res 18: 393-403.
MR Seringhaus, PD Cayting, MB Gerstein (2008). Genome Biol 9: 401.
JQ Wu, J Du, J Rozowsky, Z Zhang, AE Urban, G Euskirchen, S Weissman, M Gerstein, M Snyder (2008). Genome Biol 9: R3.
ZD Zhang, P Cayting, G Weinstock, M Gerstein (2008). Mol Biol Evol 25: 131-43.
KY Yip, P Patel, PM Kim, DM Engelman, D McDermott, M Gerstein (2008). Bioinformatics 24: 290-2.



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KH Cheung, AK Smith, KYL Yip, CJO Baker, MB Gerstein (2007). in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 11-30
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SR Setlur, TE Royce, A Sboner, JM Mosquera, F Demichelis, MD Hofer, KD Mertz, M Gerstein, MA Rubin (2007). Cancer Res 67: 10296-303.
A Smith, K Cheung, M Krauthammer, M Schultz, M Gerstein (2007). Bioinformatics 23: 3073-9.
AJ McClellan, Y Xia, AM Deutschbauer, RW Davis, M Gerstein, J Frydman (2007). Cell 131: 121-35.
JO Korbel, AE Urban, JP Affourtit, B Godwin, F Grubert, JF Simons, PM Kim, D Palejev, NJ Carriero, L Du, BE Taillon, Z Chen, A Tanzer, AC Saunders, J Chi, F Yang, NP Carter, ME Hurles, SM Weissman, TT Harkins, MB Gerstein, M Egholm, M Snyder (2007). Science 318: 420-6.
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AR Borneman, TA Gianoulis, ZD Zhang, H Yu, J Rozowsky, MR Seringhaus, LY Wang, M Gerstein, M Snyder (2007). Science 317: 815-9.
S Orchard, L Salwinski, S Kerrien, L Montecchi-Palazzi, M Oesterheld, V Stumpflen, A Ceol, A Chatr-aryamontri, J Armstrong, P Woollard, JJ Salama, S Moore, J Wojcik, GD Bader, M Vidal, ME Cusick, M Gerstein, AC Gavin, G Superti-Furga, J Greenblatt, J Bader, P Uetz, M Tyers, P Legrain, S Fields, N Mulder, M Gilson, M Niepmann, L Burgoon, J De Las Rivas, C Prieto, VM Perreau, C Hogue, HW Mewes, R Apweiler, I Xenarios, D Eisenberg, G Cesareni, H Hermjakob (2007). Nat Biotechnol 25: 894-8.
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R Jansen, D Greenbaum, M Gerstein (2002). Genome Res 12: 37-46.
M Gerstein, N Lan, R Jansen (2002). Science 295: 284-7.
N Lan, R Jansen, M Gerstein (2002). Proceedings of the IEEE 90:1848-1858
M Gerstein, J Junker (2002). Nature Yearbook of Science and Technology 210-212 (ed. D Butler, Palgrave Macmillan Publishers)
P Berman, P Bertone, B DasGupta, M Gerstein, M-Y Kao, M Snyder (2002). Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics. Springer-Verlag LNCS 2452: 419-433
R Jansen, N Lan, J Qian, M Gerstein (2002). J Struct Funct Genomics 2: 71-81.
CE Horak, NM Luscombe, J Qian, P Bertone, S Piccirrillo, M Gerstein, M Snyder (2002). Genes Dev 16: 3017-33.
KH Cheung, K White, J Hager, M Gerstein, V Reinke, K Nelson, P Masiar, R Srivastava, Y Li, J Li, H Zhao, J Li, DB Allison, M Snyder, P Miller, K Williams (2002). Proc AMIA Symp : 140-4.
D Schneider, Y Liu, M Gerstein, DM Engelman (2002). FEBS Lett 532: 231-6.
A Mateos, J Dopazo, R Jansen, Y Tu, M Gerstein, G Stolovitzky (2002). Genome Res 12: 1703-15.
ZL Zhang, PM Harrison, M Gerstein (2002). J Mol Biol 323: 811-22.
J Lin, J Qian, D Greenbaum, P Bertone, R Das, N Echols, A Senes, B Stenger, M Gerstein (2002). Nucleic Acids Res 30: 4574-82.
Z Lian, Y Kluger, DS Greenbaum, D Tuck, M Gerstein, N Berliner, SM Weissman, PE Newburger (2002). Blood 100: 3209-20.
Y Liu, DM Engelman, M Gerstein (2002). Genome Biol 3: research0054.
Z Zhang, P Harrison, M Gerstein (2002). Genome Res 12: 1466-82.
AM Edwards, B Kus, R Jansen, D Greenbaum, J Greenblatt, M Gerstein (2002). Trends Genet 18: 529-36.
WG Krebs, V Alexandrov, CA Wilson, N Echols, H Yu, M Gerstein (2002). Proteins 48: 682-95.
NM Luscombe, J Qian, Z Zhang, T Johnson, M Gerstein (2002). Genome Biol 3: RESEARCH0040.
G Giaever, AM Chu, L Ni, C Connelly, L Riles, S Veronneau, S Dow, A Lucau-Danila, K Anderson, B Andre, AP Arkin, A Astromoff, M El-Bakkoury, R Bangham, R Benito, S Brachat, S Campanaro, M Curtiss, K Davis, A Deutschbauer, KD Entian, P Flaherty, F Foury, DJ Garfinkel, M Gerstein, D Gotte, U Guldener, JH Hegemann, S Hempel, Z Herman, DF Jaramillo, DE Kelly, SL Kelly, P Kotter, D LaBonte, DC Lamb, N Lan, H Liang, H Liao, L Liu, C Luo, M Lussier, R Mao, P Menard, SL Ooi, JL Revuelta, CJ Roberts, M Rose, P Ross-Macdonald, B Scherens, G Schimmack, B Shafer, DD Shoemaker, S Sookhai-Mahadeo, RK Storms, JN Strathern, G Valle, M Voet, G Volckaert, CY Wang, TR Ward, J Wilhelmy, EA Winzeler, Y Yang, G Yen, E Youngman, K Yu, H Bussey, JD Boeke, M Snyder, P Philippsen, RW Davis, M Johnston (2002). Nature 418: 387-91.
S Balasubramanian, P Harrison, H Hegyi, P Bertone, N Luscombe, N Echols, P McGarvey, Z Zhang, M Gerstein (2002). Pharmacogenomics 3: 393-402.
N Echols, P Harrison, S Balasubramanian, NM Luscombe, P Bertone, Z Zhang, M Gerstein (2002). Nucleic Acids Res 30: 2515-23.
CE Horak, MC Mahajan, NM Luscombe, M Gerstein, SM Weissman, M Snyder (2002). Proc Natl Acad Sci U S A 99: 2924-9.
Y Liu, NM Luscombe, V Alexandrov, P Bertone, P Harrison, Z Zhang, M Gerstein (2002). Genome Biol 3: REPORTS4004.
A Kumar, PM Harrison, KH Cheung, N Lan, N Echols, P Bertone, P Miller, MB Gerstein, M Snyder (2002). Nat Biotechnol 20: 58-63.



2001 (21)

J Qian, NM Luscombe, M Gerstein (2001). J Mol Biol 313: 673-81.
J Qian, M Dolled-Filhart, J Lin, H Yu, M Gerstein (2001). J Mol Biol 314: 1053-66.
H Hegyi, M Gerstein (2001). Genome Res 11: 1632-40.
NM Luscombe, D Greenbaum, M Gerstein (2001). Methods Inf Med 40: 346-58.
R Das, J Junker, D Greenbaum, MB Gerstein (2001). Pharmacogenomics J 1: 115-25.
H Zhu, M Bilgin, R Bangham, D Hall, A Casamayor, P Bertone, N Lan, R Jansen, S Bidlingmaier, T Houfek, T Mitchell, P Miller, RA Dean, M Gerstein, M Snyder (2001). Science 293: 2101-5.
V Alexandrov, M Gerstein (2001). International Journal of Quantum Chemistry 85:693-696
WK Olson, M Bansal, SK Burley, RE Dickerson, M Gerstein, SC Harvey, U Heinemann, XJ Lu, S Neidle, Z Shakked, H Sklenar, M Suzuki, CS Tung, E Westhof, C Wolberger, HM Berman (2001). J Mol Biol 313: 229-37.
J Tsai, N Voss, M Gerstein (2001). Bioinformatics 17: 949-56.
D Greenbaum, NM Luscombe, R Jansen, J Qian, M Gerstein (2001). Genome Res 11: 1463-8.
M Gerstein, F M Richards (2001). International Tables for Crystallography (Volume F, Chapter 22.1.1, pages 531-539; M Rossmann & E Arnold, editors; Dordrecht: Kluwer)
P Harrison, M Gerstein (2001). Trends Biochem Sci 26:204-205
P Bertone, M Gerstein (2001). IEEE Eng Med Biol Mag 20: 33-40.
Z Lian, L Wang, S Yamaga, W Bonds, Y Beazer-Barclay, Y Kluger, M Gerstein, PE Newburger, N Berliner, SM Weissman (2001). Blood 98: 513-24.
YV Subrahmanyam, S Yamaga, Y Prashar, HH Lee, NP Hoe, Y Kluger, M Gerstein, JD Goguen, PE Newburger, SM Weissman (2001). Blood 97: 2457-68.
P Bertone, Y Kluger, N Lan, D Zheng, D Christendat, A Yee, AM Edwards, CH Arrowsmith, GT Montelione, M Gerstein (2001). Nucleic Acids Res 29: 2884-98.
M Gerstein, B Honig (2001). Current Opinion in Structural Biology 11: 327-329.
N Luscombe, D Greenbaum, M Gerstein (2001). Intl. Medical Informatics Association (Yearbook, Pages 83-99)
PM Harrison, N Echols, MB Gerstein (2001). Nucleic Acids Res 29: 818-30.
J Qian, B Stenger, CA Wilson, J Lin, R Jansen, SA Teichmann, J Park, WG Krebs, H Yu, V Alexandrov, N Echols, M Gerstein (2001). Nucleic Acids Res 29: 1750-64.
Cheung KH, Liu Y, Kumar K, Snyder M, Gerstein M, Miller P (2001). IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE) pp. 97-103



2000 (18)

M Gerstein (2000). Nat Struct Biol 7 Suppl: 960-3.
R Das, H Hegyi, M Gerstein (2000). J Mol Microbiol Biotechnol 2: 387-92.
D Christendat, A Yee, A Dharamsi, Y Kluger, M Gerstein, CH Arrowsmith, AM Edwards (2000). Prog Biophys Mol Biol 73: 339-45.
H Zhu, JF Klemic, S Chang, P Bertone, A Casamayor, KG Klemic, D Smith, M Gerstein, MA Reed, M Snyder (2000). Nat Genet 26: 283-9.
A Drawid, R Jansen, M Gerstein (2000). Trends Genet 16: 426-30.
M Gerstein, R Jansen (2000). Curr Opin Struct Biol 10: 574-84.
R Das, M Gerstein (2000). Funct Integr Genomics 1: 76-88.
GJ Naylor, M Gerstein (2000). J Mol Evol 51: 223-33.
D Christendat, A Yee, A Dharamsi, Y Kluger, A Savchenko, JR Cort, V Booth, CD Mackereth, V Saridakis, I Ekiel, G Kozlov, KL Maxwell, N Wu, LP McIntosh, K Gehring, MA Kennedy, AR Davidson, EF Pai, M Gerstein, AM Edwards, CH Arrowsmith (2000). Nat Struct Biol 7: 903-9.
A Drawid, M Gerstein (2000). J Mol Biol 301: 1059-75.
S Balasubramanian, T Schneider, M Gerstein, L Regan (2000). Nucleic Acids Res 28: 3075-82.
M Gerstein, J Lin, H Hegyi (2000). Pac Symp Biocomput : 30-41.
M Gerstein (2000). Science 288: 1590.
J Lin, M Gerstein (2000). Genome Res 10: 808-18.
WG Krebs, M Gerstein (2000). Nucleic Acids Res 28: 1665-75.
A Senes, M Gerstein, DM Engelman (2000). J Mol Biol 296: 921-36.
CA Wilson, J Kreychman, M Gerstein (2000). J Mol Biol 297: 233-49.
R Jansen, M Gerstein (2000). Nucleic Acids Res 28: 1481-8.



1999 (10)

P Ross-Macdonald, PS Coelho, T Roemer, S Agarwal, A Kumar, R Jansen, KH Cheung, A Sheehan, D Symoniatis, L Umansky, M Heidtman, FK Nelson, H Iwasaki, K Hager, M Gerstein, P Miller, GS Roeder, M Snyder (1999). Nature 402: 413-8.
M Gerstein, C Chothia (1999). Science 285: 1682-3.
M Gerstein, R Jansen, T Johnson, J Tsai, W Krebs (1999). Rigidity Theory and Applications 401-442 (ed. M F Thorpe and P M Duxbury, Kluwer Academic/Plenum Publishers).
M Gerstein (1999). Bioinformatics 15: 429-31.
ES Brodkin, M Gerstein (1999). N Engl J Med 341: 1080; author reply 1081.
J Tsai, R Taylor, C Chothia, M Gerstein (1999). J Mol Biol 290: 253-66.
SA Teichmann, C Chothia, M Gerstein (1999). Curr Opin Struct Biol 9: 390-9.
M Gerstein (1999). Nature 399: 101.
H Hegyi, M Gerstein (1999). J Mol Biol 288: 147-64.
M Gerstein (1999). Nature 398: 20.



1998 (9)

M Gerstein, H Hegyi (1998). FEMS Microbiol Rev 22: 277-304.
M Gerstein (1998). Fold Des 3: 497-512.
M Gerstein (1998). Proteins 33: 518-34.
M Gerstein, M Levitt (1998). Sci Am 279: 100-5.
M Gerstein (1998). Bioinformatics 14: 707-14.
M Gerstein, W Krebs (1998). Nucleic Acids Res 26: 4280-90.
J Fu, M Gerstein, PR David, AL Gnatt, DA Bushnell, AM Edwards, RD Kornberg (1998). J Mol Biol 280: 317-22.
M Levitt, M Gerstein (1998). Proc Natl Acad Sci U S A 95: 5913-20.
M Gerstein, M Levitt (1998). Protein Sci 7: 445-56.



1997 (6)

M Gerstein (1997). J Mol Biol 274: 562-76.
J Tsai, M Gerstein, M Levitt (1997). Protein Sci 6: 2606-16.
M Gerstein, M Levitt (1997). Proc Natl Acad Sci U S A 94: 11911-6.
C Chothia, M Gerstein (1997). Nature 385: 579, 581.
M Levitt, M Gerstein, E Huang, S Subbiah, J Tsai (1997). Annu Rev Biochem 66: 549-79.
R Schmidt, M Gerstein, RB Altman (1997). Protein Sci 6: 246-8.



1996 (4)

R Becker, M Gerstein (1996). New Jersey Lawyer Magazine 179: 12-27 (September).
J Tsai, M Gerstein, M Levitt (1996). Journal of Chemical Physics 104: 9417-9430
M Gerstein, C Chothia (1996). Proc Natl Acad Sci U S A 93: 10167-72.
M Gerstein, M Levitt (1996). Proc Int Conf Intell Syst Mol Biol 4: 59-67.



1995 (7)

M Gerstein, RB Altman (1995). Comput Appl Biosci 11: 633-44.
M Suzuki, M Gerstein (1995). Proteins 23: 525-35.
M Gerstein, RB Altman (1995). J Mol Biol 251: 161-75.
M Gerstein, J Tsai, M Levitt (1995). J Mol Biol 249: 955-66.
RB Altman, C Hughes, MB Gerstein (1995). J Mol Graph 13: 142-52, 109-2.
M Suzuki, N Yagi, M Gerstein (1995). Protein Eng 8: 329-38.
M Suzuki, SE Brenner, M Gerstein, N Yagi (1995). Protein Eng 8: 319-28.



1994 (7)

M Gerstein (1994). American Journal of Physics 62: 596-601
M Suzuki, M Gerstein, N Yagi (1994). Nucleic Acids Res 22: 3397-405.
Y Harpaz, M Gerstein, C Chothia (1994). Structure 2: 641-9.
M Gerstein, AM Lesk, C Chothia (1994). Biochemistry 33: 6739-49.
M Suzuki, D Neuhaus, M Gerstein, S Aimoto (1994). Protein Eng 7: 461-70.
M Gerstein, EL Sonnhammer, C Chothia (1994). J Mol Biol 236: 1067-78.
RB Altman, M Gerstein (1994). Proc Int Conf Intell Syst Mol Biol 2: 19-27.



1993 (7)

M Gerstein, R Lynden-Bell (1993). Journal of Physical Chemistry 97: 2982-2991.
M Gerstein, R Lynden-Bell (1993). Journal of Physical Chemistry 97: 2991-2999.
M Gerstein, BF Anderson, GE Norris, EN Baker, AM Lesk, C Chothia (1993). J Mol Biol 234: 357-72.
M Suzuki, M Gerstein, T Johnson (1993). Protein Eng 6: 565-74.
M Gerstein, RM Lynden-Bell (1993). J Mol Biol 230: 641-50.
M Gerstein, G Schulz, C Chothia (1993). J Mol Biol 229: 494-501.
S Subramaniam, M Gerstein, D Oesterhelt, R Henderson (1993). EMBO J 12: 1-8.



1992 (2)

M Gerstein (1992). Acta Crystallographica A48: 271-276.
I De Baere, L Liu, L Moens, J Van Beeumen, C Gielens, J Richelle, C Trotman, J Finch, M Gerstein, M Perutz (1992). Proc Natl Acad Sci U S A 89: 4638-42.



1991 (1)

M Gerstein, C Chothia (1991). J Mol Biol 220: 133-49.



1987 (1)

N Fisch, A Kritz, M Gerstein (1987). Proceedings of the Sixth Joint Workshop on Electron Cyclotron Emission and Electron Cyclotron Resonance Heating. (eds. A Riviere, A Costley), 23-30 (Oxford, 16-17 September).