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.

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.

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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