Papers related to cancer genomics from the Gerstein Lab

Compression-based Network Interpretability Schemes
J Warrell, H Mohsen, M Gerstein (2020). bioRxiv.

Latent Evolutionary Signatures: A General Framework for Analyzing Music and Cultural Evolution
J Warrell, L Salichos, M Gancz, MB Gerstein (2024). J R Soc Interface 21: 20230647.

Recurrent repeat expansions in human cancer genomes
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.

Network propagation-based prioritization of long tail genes in 17 cancer types.
H Mohsen, V Gunasekharan, T Qing, M Seay, Y Surovtseva, S Negahban, Z Szallasi, L Pusztai, MB Gerstein (2021). Genome Biol 22: 287.

Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers.
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.

Molecular medicine tumor board: whole-genome sequencing to inform on personalized medicine for a man with advanced prostate cancer.
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.

Weight-based Neural Network Interpretability using Activation Tuning and Personalized Products
H Mohsen, J Warrell, MR Min, S Negahban, M Gerstein (2020). The 15th Machine Learning in Computational Biology Workshop.

Cyclic and Multilevel Causation in Evolutionary Processes
J Warrell, M Gerstein (2020). Biology & Philosophy, 35(5), pp.1-36.

An integrative ENCODE resource for cancer genomics.
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.

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins.
J Zhang, J Liu, D Lee, JJ Feng, L Lochovsky, S Lou, M Rutenberg-Schoenberg, M Gerstein (2020). Genome Biol 21: 151.

Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood.
S Li, FW Crawford, MB Gerstein (2020). Nat Commun 11: 3575.

Origins and characterization of variants shared between databases of somatic and germline human mutations.
W Meyerson, J Leisman, FCP Navarro, M Gerstein (2020). BMC Bioinformatics 21: 227.

Estimation of the carrier frequency of fumarate hydratase alterations and implications for kidney cancer risk in hereditary leiomyomatosis and renal cancer.
B Shuch, S Li, H Risch, RS Bindra, PD McGillivray, M Gerstein (2020). Cancer 126: 3657-3666.

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.
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.

Pan-cancer analysis of whole genomes.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Nature 578: 82-93.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
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.

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.
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.

Estimating growth patterns and driver effects in tumor evolution from individual samples.
L Salichos, W Meyerson, J Warrell, M Gerstein (2020). Nat Commun 11: 732.

Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures.
S Kumar, D Clarke, MB Gerstein (2019). Proc Natl Acad Sci U S A 116: 18962-18970.

MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool.
L Lochovsky, J Zhang, M Gerstein (2017). Bioinformatics 34: 1031-1033.

Cancer genomics: Less is more in the hunt for driver mutations.
S Kumar, M Gerstein (2017). Nature 547: 40-41.

Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations.
S Li, BM Shuch, MB Gerstein (2017). PLoS Genet 13: e1006685.

The Molecular Taxonomy of Primary Prostate Cancer.
Cancer Genome Atlas Research Network (2015). Cell 163: 1011-25.

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.
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.

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.
L Lochovsky, J Zhang, Y Fu, E Khurana, M Gerstein (2015). Nucleic Acids Res 43: 8123-34.

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.
JC Mu, M Mohiyuddin, J Li, N Bani Asadi, MB Gerstein, A Abyzov, WH Wong, HY Lam (2014). Bioinformatics 31: 1469-71.

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
Y Fu, Z Liu, S Lou, J Bedford, XJ Mu, KY Yip, E Khurana, M Gerstein (2014). Genome Biol 15: 480.

Integrative annotation of variants from 1092 humans: application to cancer genomics.
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 comprehensive nuclear receptor network for breast cancer cells.
R Kittler, J Zhou, S Hua, L Ma, Y Liu, E Pendleton, C Cheng, M Gerstein, KP White (2013). Cell Rep 3: 538-51.

Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression.
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.

Identification of a disease-defining gene fusion in epithelioid hemangioendothelioma.
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.

The genomic complexity of primary human prostate cancer.
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.

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.
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.

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.
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.

Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis.
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.

Molecular sampling of prostate cancer: a dilemma for predicting disease progression.
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.

mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer.
C Cheng, X Fu, P Alves, M Gerstein (2009). Genome Biol 10: R90.

N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer.
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.

Systematic identification of transcription factors associated with patient survival in cancers.
C Cheng, LM Li, P Alves, M Gerstein (2009). BMC Genomics 10: 225.

Distinct genomic aberrations associated with ERG rearranged prostate cancer.
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.

Targeting the human cancer pathway protein interaction network by structural genomics.
YJ Huang, D Hang, LJ Lu, L Tong, MB Gerstein, GT Montelione (2008). Mol Cell Proteomics 7: 2048-60.

Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer.
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.

Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer.
SR Setlur, TE Royce, A Sboner, JM Mosquera, F Demichelis, MD Hofer, KD Mertz, M Gerstein, MA Rubin (2007). Cancer Res 67: 10296-303.

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