Melanoma genome sequencing reveals frequent PREX2 mutations. Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, Ramos AH, Pugh TJ, Stransky N, Parkin M, Winckler W, Mahan S, Ardlie K, Baldwin J, Wargo J, Schadendorf D, Meyerson M, Gabriel SB, Golub TR, Wagner SN, Lander ES, Getz G, Chin L, Garraway LA. Nature. 2012 May 9;485(7399):502-6. doi: 10.1038/nature11071.

High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing. Wagle N, Berger MF, Davis MJ, Blumenstiel B, DeFelice M, Pochanard P, Ducar M, Van Hummelen P, MacConaill LE, Hahn WC, Meyerson M, Gabriel SB, Garraway LA.. Cancer Discovery, January 2012, 2; 82.

Dissecting therapeutic resistance to RAF inhibition in melanoma by tumor genomic profiling. Wagle N, Emery C, Berger MF, Davis MJ, Sawyer A, Pochanard P, Kehoe SM, Johannessen C, MacConaill LE, Hahn WC, Meyerson M, Garraway LA. J Clin Oncol. 2011 Mar 7. (Epub ahead of print).

The genomic complexity of primary human prostate cancer. Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, SougnezC, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA. Nature. 2011 Feb 10;470(7333):214-20.

Integrative analysis of the melanoma transcriptome. Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, Maguire J, Johnson LA, Robinson J, Verhaak RG, Sougnez C, Onofrio RC, Ziaugra L, Cibulskis K, Laine E, Barretina J, Winckler W, Fisher DE, Getz G, Meyerson M, Jaffe DB, Gabriel SB, Lander ES, Dummer R, Gnirke A, Nusbaum C, Garraway LA. Genome Research. 2010 Apr;20(4):413-27. Epub 2010 Feb 23.

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, Garraway LA, Gnirke A. Genome Biology. 2009;10(10):R115. Epub 2009 Oct 16.

Diversity and complexity in DNA recognition by transcription factors. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML. Science. 2009 Jun 26;324(5935):1720-3. Epub 2009 May 14.

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR. Cell. 2008 Jun 27;133(7):1266-76.

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW 3rd, Bulyk ML. Nature Biotechnology. 2006 Nov;24(11):1429-35. Epub 2006 Sep 24.

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML. Nature Genetics. 2004 Dec;36(12):1331-9. Epub 2004 Nov 14.