Microbiome Award Judges

  

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2017 Microbiome Award Judges

David Coil Elisabeth Bik Emily Hollister Lauren Ambrogio

 

 


 

David Coil

Project Scientist at University of California, Davis

BIO:

David Coil is a Project Scientist responsible for supervising undergraduate research projects in microbiology, microbial ecology, and genomics in the lab of Jonathan Eisen. Also managing research projects/collaborations in the lab including microbial sampling, metagenomics, and bacterial genome assembly. And finally, performing public outreach in microbiology through the microBEnet project, which is focused on communication in the context of studies of microbiology of the built environment (including sending bacteria into space). David is the creator of “Gut Check: The Microbiome GameĀ.

David received his PhD in 2005 from the Fred Hutchinson Cancer Research Center/University of Washington, working on retroviruses. Since then he has lectured at the UW, done a post-doc in Belgium working on Legionella, and helps direct a non-profit in Alaska called Ground Truth Trekking.

PUBLICATIONS:

To see publications visit Google Scholar


 

Elisabeth Bik

Science Editor at uBiome, Inc, San Francisco

BIO:

After receiving her PhD at Utrecht University in The Netherlands with work on epidemic Vibrio cholerae strains, she worked at the Dutch National Institute for Health and the St. Antonius Hospital in Nieuwegein, where she set up a molecular microbiology unit for the detection and typing of clinical and nosocomical strains. In 2001, she joined the School of Medicine at Stanford, where she worked on the characterization of the human microbiome in oral, gastric, and intestinal samples. In addition, she studied the microbiome of marine mammals, including dolphins and sea lions. In November 2016, Elisabeth joined uBiome as a Science Editor. When she is not in the lab or writing, she can be found working on her blog Microbiome Digest, an almost daily compilation of scientific papers in the rapidly growing microbiome field, or on Twitter at @MicrobiomDigest. She also searches the biomedical literature for inappropriatedly duplicated or manipulated photographic images and plagiarized text.

Twitter:@microbiomdigest

Website: http://www.microbiomedigest.com

PUBLICATIONS:

Bik EM. The Hoops, Hopes, and Hypes of Human Microbiome Research. Yale J Biol Med. 2016 Sep 30;89(3):363-373. eCollection 2016 Sep 30. Review. PubMed PMID: 27698620; PubMed Central PMCID: PMC5045145.

Bik EM, Casadevall A, Fang FC. The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications. MBio. 2016 Jun 7;7(3). pii: e00809-16. doi: 10.1128/mBio.00809-16. PubMed PMID: 27273827; PubMed Central PMCID: PMC4941872.

Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun. 2016 Feb 3;7:10516. doi: 10.1038/ncomms10516. PubMed PMID: 26839246; PubMed Central PMCID: PMC4742810.

Hoy YE, Bik EM, Lawley TD, Holmes SP, Monack DM, Theriot JA, Relman DA. Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time. PLoS One. 2015 Nov 13;10(11):e0142825. doi: 10.1371/journal.pone.0142825. eCollection 2015 Nov 13. PubMed PMID: 26565698; PubMed Central PMCID: PMC4643986.

Bik EM. You Lose Some, You Win Some: Weight Loss Induces Microbiota and Metabolite Shifts. EBioMedicine. 2015 Jul 30;2(8):806-7. doi: 10.1016/j.ebiom.2015.07.037. eCollection 2015 Jul 30. Review. PubMed PMID: 26425686; PubMed Central PMCID: PMC4563139.

Bik EM, Relman DA. Unrest at home: diarrheal disease and microbiota disturbance. Genome Biol. 2014 Jun 27;15(6):120. doi: 10.1186/gb4182. PubMed PMID: 25002208; PubMed Central PMCID: PMC4072979.

Costello EK, Carlisle EM, Bik EM, Morowitz MJ, Relman DA. Microbiome assembly across multiple body sites in low-birthweight infants. MBio. 2013 Oct 29;4(6):e00782-13. doi: 10.1128/mBio.00782-13. PubMed PMID: 24169577; PubMed Central PMCID: PMC3809564.

Diaz MA, Bik EM, Carlin KP, Venn-Watson SK, Jensen ED, Jones SE, Gaston EP, Relman DA, Versalovic J. Identification of Lactobacillus strains with probiotic features from the bottlenose dolphin (Tursiops truncatus). J Appl Microbiol. 2013 Oct;115(4):1037-51. doi: 10.1111/jam.12305. Epub 2013 Aug 1. PubMed PMID: 23855505; PubMed Central PMCID: PMC4063339.

Staubach F, Baines JF, Künzel S, Bik EM, Petrov DA. Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment. PLoS One. 2013 Aug 13;8(8):e70749. doi: 10.1371/journal.pone.0070749. eCollection 2013 Aug 13. PubMed PMID: 23967097; PubMed Central PMCID: PMC3742674.

Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA, Singh U. Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One. 2013;8(1):e53838. doi: 10.1371/journal.pone.0053838. Epub 2013 Jan 22. PubMed PMID: 23349750; PubMed Central PMCID: PMC3551965.

Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH. Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets. Res Microbiol. 2012 Jul;163(6-7):407-12. doi: 10.1016/j.resmic.2012.07.001. Epub 2012 Jul 21. PubMed PMID: 22824070.

Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J. 2010 Aug;4(8):962-74. doi: 10.1038/ismej.2010.30. Epub 2010 Mar 25. PubMed PMID: 20336157; PubMed Central PMCID: PMC2941673.

DiGiulio DB, Romero R, Kusanovic JP, Gómez R, Kim CJ, Seok KS, Gotsch F, Mazaki-Tovi S, Vaisbuch E, Sanders K, Bik EM, Chaiworapongsa T, Oyarzún E, Relman DA. Prevalence and diversity of microbes in the amniotic fluid, the fetal inflammatory response, and pregnancy outcome in women with preterm pre-labor rupture of membranes. Am J Reprod Immunol. 2010 Jul 1;64(1):38-57. doi: 10.1111/j.1600-0897.2010.00830.x. Epub 2010 Mar 21. PubMed PMID: 20331587; PubMed Central PMCID: PMC2907911.

Bik EM. Composition and function of the human-associated microbiota. Nutr Rev. 2009 Nov;67 Suppl 2:S164-71. doi: 10.1111/j.1753-4887.2009.00237.x. Review. Erratum in: Nutr Rev. 2010 Mar;68(3):189. PubMed PMID: 19906220.

DiGiulio DB, Romero R, Amogan HP, Kusanovic JP, Bik EM, Gotsch F, Kim CJ, Erez O, Edwin S, Relman DA. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS One. 2008 Aug 26;3(8):e3056. doi: 10.1371/journal.pone.0003056. PubMed PMID: 18725970; PubMed Central PMCID: PMC2516597.

Bik EM. [The microbiotics of the human body]. Ned Tijdschr Geneeskd. 2008 Mar 22;152(12):668-73. Review. Dutch. PubMed PMID: 18438061.

Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11889-94. Epub 2007 Jul 9. PubMed PMID: 17620602; PubMed Central PMCID: PMC1924555.

Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007 Jul;5(7):e177. Epub 2007 Jun 26. PubMed PMID: 17594176; PubMed Central PMCID: PMC1896187.

Dethlefsen L, Eckburg PB, Bik EM, Relman DA. Assembly of the human intestinal microbiota. Trends Ecol Evol. 2006 Sep;21(9):517-23. Epub 2006 Jul 3. Review. PubMed PMID: 16820245.

Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA. Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):732-7. Epub 2006 Jan 4. PubMed PMID: 16407106; PubMed Central PMCID: PMC1334644.

Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, Wolber PK, Relman DA, Brown PO. Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res. 2006 Jan 10;34(1):e5. PubMed PMID: 16407321; PubMed Central PMCID: PMC1326253.

Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science. 2005 Jun 10;308(5728):1635-8. Epub 2005 Apr 14. PubMed PMID: 15831718; PubMed Central PMCID: PMC1395357.

v Dijk Y, Bik EM, Hochstenbach-Vernooij S, v d Vlist GJ, Savelkoul PH, Kaan JA, Diepersloot RJ. Management of an outbreak of Enterobacter cloacae in a neonatal unit using simple preventive measures. J Hosp Infect. 2002 May;51(1):21-6. PubMed PMID: 12009816.

Visser IJ, Vellema P, Weitenberg AM, Bik EM. [Severe watery diarrhea caused by Vibrio cholerae in lambs]. Tijdschr Diergeneeskd. 1997 Nov 1;122(21):600-3. Dutch. PubMed PMID: 9534795.

Mooi FR, Bik EM. The evolution of epidemic Vibrio cholerae strains. Trends Microbiol. 1997 Apr;5(4):161-5. Review. PubMed PMID: 9141191.

Bik EM, Gouw RD, Mooi FR. DNA fingerprinting of Vibrio cholerae strains with a novel insertion sequence element: a tool to identify epidemic strains. J Clin Microbiol. 1996 Jun;34(6):1453-61. PubMed PMID: 8735097; PubMed Central PMCID: PMC229041.

Bik EM, Bunschoten AE, Willems RJ, Chang AC, Mooi FR. Genetic organization and functional analysis of the otn DNA essential for cell-wall polysaccharide synthesis in Vibrio cholerae O139. Mol Microbiol. 1996 May;20(4):799-811. PubMed PMID: 8793876.

Bik EM, Bunschoten AE, Gouw RD, Mooi FR. Genesis of the novel epidemic Vibrio cholerae O139 strain: evidence for horizontal transfer of genes involved in polysaccharide synthesis. EMBO J. 1995 Jan 16;14(2):209-16. PubMed PMID: 7835331; PubMed Central PMCID: PMC398072.

Rijpkema SG, Bik EM, Jansen WH, Gielen H, Versluis LF, Stouthamer AH, Guinée PA, Mooi FR. Construction and analysis of a Vibrio cholerae delta-aminolevulinic acid auxotroph which confers protective immunity in a rabbit model. Infect Immun. 1992 Jun;60(6):2188-93. PubMed PMID: 1587587; PubMed Central PMCID: PMC257142.

Hermans PW, van Soolingen D, Bik EM, de Haas PE, Dale JW, van Embden JD. Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect Immun. 1991 Aug;59(8):2695-705. PubMed PMID: 1649798; PubMed Central PMCID: PMC258075.

Hermans PW, Schuitema AR, Van Soolingen D, Verstynen CP, Bik EM, Thole JE, Kolk AH, van Embden JD. Specific detection of Mycobacterium tuberculosis complex strains by polymerase chain reaction. J Clin Microbiol. 1990 Jun;28(6):1204-13. PubMed PMID: 2116445; PubMed Central PMCID: PMC267906.


 

 

Emily Hollister

Assistant Professor at Baylor College of Medicine

BIO:

Situated at the interface of microbial ecology, bioinformatics, and biostatistics, my research group is dedicated to the study of the structure and function of mixed microbial communities. Our work includes the study of the human microbiome and microbiome-environment interactions, as well as the development and improvement of bioinformatics approaches for microbiome analysis.

PUBLICATIONS:

(Selected)
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartman M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, and Weber CF. 2009. Introducing mothur: Open source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541.

Hollister EB, Engledow AS, Hammett AM, Provin TL, Wilkinson HH, and Gentry TJ. 2010. Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. The ISME Journal 4: 829-838.

Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Malfatti SA, Tringe SG, Holtzapple MT, and Gentry TJ. 2010. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Applied Microbiology and Biotechnology 88: 389-399.

Hollister EB, Gao C, Versalovic J. 2014. Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Gastroenterology doi:10.1053/j.gastro.2014.01.052

Hollister EB, Riehle K, Luna RA, Wiedler EM, Rubio-Gonzalez M, Mistretta TA, Raza S, Doddapaneni HV, Metcalf GA, Muzny DM, Gibbs RA, Petrosino J, Shulman RJ, Versalovic J. 2015. Structure and function of the healthy pre-adolescent pediatric gut microbiome. Microbiome doi: 10.1186/s40168-015-0101-x

Durgan DJ, Ganesh BP, Cope JL, Adjami NJ, Phillips SC, Petrosino JF, Hollister EB, Bryan RM. 2016. Role of the gut microbiome in obstructive sleep apnea-induced hypertension. Hypertension 67: 469-474.

Kao CC, Cope JL, Hsu JW, Dwarkanath P, Karmes JM, Luna RA, Hollister EB, Thame MM, Kurpad AV, Jahoor F. 2016. The gut microbiome and its relationship to gut function, arginine, and citrulline metabolism in American, Indian, and Jamaican women. The Journal of Nutrition. doi:10.3945/jn.115.227579

Chehoud C, Dryga A, Hwang Y, Nagy-Szakal D, Hollister EB, Luna RA, Versalovic J, Kellermayer R, Bushman FD. 2016. Transfer of viral communities between human individuals during fecal microbiota transplantation. mBio doi:10.1128/mbio.00322-16.

Shulman RJ, Hollister EB, Cain K, Czyzewski D, Self M, Weidler EM, Devaraj S, Luna RA, Versalovic J, Heitkemper MM. 2016. Randomized, double blind trial of psyllium fiber in children with irritable bowel syndrome. Clinical Gastroenterology and Hepatology doi: 10.1016/j.cgh.2016.03.045.

Pammi M, Cope JL, Tarr P, Warner B, Morrow AL, Gregory KE, Kroll JS, Ferris MJ, Engstrand L, Lilja HE, Hollister EB, Versalovic J, Neu J. 2017. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: A systematic review and meta-analysis. Microbiome 5:31. doi: 10.1186/s40168-017-0248-8.

Shah M, DeSantis TZ, Weinmaier T, McMurdie PJ, Cope JL, Altrichter A, Yamal J, Hollister EB. 2017. Leveraging sequence-based fecal microbial community survey data to identify a composite biomarker for colorectal cancer from the fecal microbiome. Gut (manuscript accepted)


 

 

Lauren Ambrogio

Chief Operating Officer at AOBiome

BIO:

Lauren Ambrogio joined AOBiome in May of 2016, overseeing the company's Research and Operational efforts. Prior to AOBiome, she was Chief Operating Officer at Q-State Biosciences where she provided leadership and oversight for a successful, fast-growing biotechnology start-up. In addition to her most recent roles, Ms. Ambrogio has held several management positions over the last 10 years merging her love for cutting-edge science and technology with operational excellence, including roles at the Dana Farber Cancer Institute, the Broad Institute, and Claritas Genomics. She brings expertise in genomics, project and portfolio management, product development, and corporate operations to the AOBiome team.

Ms. Ambrogio is an author on numerous scientific papers, holds a BS in Molecular Genetics from the University of Rochester, and is a Certified Project Management Professional.

PUBLICATIONS:

Selected Publications
Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. Perry JA, Kiezun A, Tonzi P, Van Allen EM, Carter SL, Baca SC, Cowley GS, Bhatt AS, Rheinbay E, Pedamallu CS, Helman E, Taylor-Weiner A, McKenna A, DeLuca DS, Lawrence MS, Ambrogio L, Sougnez C, Sivachenko A, Walensky LD, Wagle N, Mora J, de Torres C, Lavarino C, Dos Santos Aguiar S, Yunes JA, Brandalise SR, Mercado-Celis GE, Melendez-Zajgla J, Cárdenas-Cardós R, Velasco-Hidalgo L, Roberts CW, Garraway LA, Rodriguez-Galindo C, Gabriel SB, Lander ES, Golub TR, Orkin SH, Getz G, Janeway KA. Proc Natl Acad Sci U S A. 2014 Dec 23

The genomic landscape of pediatric Ewing sarcoma. Crompton BD, Stewart C, Taylor-Weiner A, Alexe G, Kurek KC, Calicchio ML, Kiezun A, Carter SL, Shukla SA, Mehta SS, Thorner AR, de Torres C, Lavarino C, Suñol M, McKenna A, Sivachenko A, Cibulskis K, Lawrence MS, Stojanov P, Rosenberg M, Ambrogio L, Auclair D, Seepo S, Blumenstiel B, DeFelice M, Imaz-Rosshandler I, Schwarz-Cruz Y Celis A, Rivera MN, Rodriguez-Galindo C, Fleming MD, Golub TR, Getz G, Mora J, Stegmaier K. Cancer Discov. 2014 Nov

Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors. Shern JF, Chen L, Chmielecki J, Wei JS, Patidar R, Rosenberg M, Ambrogio L, Auclair D, Wang J, Song YK, Tolman C, Hurd L, Liao H, Zhang S, Bogen D, Brohl AS, Sindiri S, Catchpoole D, Badgett T, Getz G, Mora J, Anderson JR, Skapek SX, Barr FG, Meyerson M, Hawkins DS, Khan J. Cancer Discov. 2014 Feb.

Landscape of genomic alterations in cervical carcinomas. Ojesina AI, Lichtenstein L, Freeman SS, Pedamallu CS, Imaz-Rosshandler I, Pugh TJ, Cherniack AD, Ambrogio L, Cibulskis K, Bertelsen B, Romero-Cordoba S, Treviño V, Vazquez-Santillan K, Guadarrama AS, Wright AA, Rosenberg MW, Duke F, Kaplan B, Wang R, Nickerson E, Walline HM, Lawrence MS, Stewart C, Carter SL, McKenna A, Rodriguez-Sanchez IP, Espinosa-Castilla M, Woie K, Bjorge L, Wik E, Halle MK, Hoivik EA, Krakstad C, Gabiño NB, Gómez-Macías GS, Valdez-Chapa LD, Garza-Rodríguez ML, Maytorena G, Vazquez J, Rodea C, Cravioto A, Cortes ML, Greulich H, Crum CP, Neuberg DS, Hidalgo-Miranda A, Escareno CR, Akslen LA, Carey TE, Vintermyr OK, Gabriel SB, Barrera-Saldaña HA, Melendez-Zajgla J, Getz G, Salvesen HB, Meyerson M. Nature. 2014 Feb 20

Mutational heterogeneity in cancer and the search for new cancer-associated genes. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Lee RS, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CW, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Nature. 2013 Jul 11

Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors. Chmielecki J, Crago AM, Rosenberg M, O'Connor R, Walker SR, Ambrogio L, Auclair D, McKenna A, Heinrich MC, Frank DA, Meyerson M. Nat Genet. 2013 Feb

Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2. Greulich H, Kaplan B, Mertins P, Chen TH, Tanaka KE, Yun CH, Zhang X, Lee SH, Cho J, Ambrogio L, Liao R, Imielinski M, Banerji S, Berger AH, Lawrence MS, Zhang J, Pho NH, Walker SR, Winckler W, Getz G, Frank D, Hahn WC, Eck MJ, Mani DR, Jaffe JD, Carr SA, Wong KK, Meyerson M. Proc Natl Acad Sci 2012 Aug 20 A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. Lee RS, Stewart C, Carter SL, Ambrogio L, Cibulskis K, Sougnez C, Lawrence MS, Auclair D, Mora J, Golub TR, Biegel JA, Getz G, Roberts CW. J Clin Invest. 2012 Aug 1 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

Predicting Relapse in Patients With Medulloblastoma by Integrating Evidence From Clinical and Genomic Features. Tamayo P, Cho YJ, Tsherniak A, Greulich H, Ambrogio L, Schouten-van Meeteren N, Zhou T, Buxton A, Kool M, Meyerson M, Pomeroy SL, Mesirov JP. J Clin Oncol. 2011 Feb 28.

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, Sougnez C, 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

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Sheila Fisher, Andrew Barry, Justin Abreu, Brian Minie, Toni M. Delorey, Jillian Nolan, Alexander Allen, Geneva Young, Zac Zwirko, Ryan Johnson, Frank Juhn, Chris Friedrich, Lauren Ambrogio, Timothy J. Fennell, Andrew Zimmer, John Stalker, Ramy Shammas, John Walsh, Jon Thompson, Brian Reilly, Brendan Blumensteil, Kristian Cibulskis, Stacey Gabriel, Robert Nicol and Chad Nusbaum. Genome Biol. 2011 Jan 4

A map of human genome variation from population-scale sequencing. 1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. Nature. 2010 Oct 28

Exome Sequencing, ANGPTL3 Mutations, and Familial Combined Hypolipidemia. Musunuru K, Pirruccello JP, Do R, Peloso GM, Guiducci C, Sougnez C, Garimella KV, Fisher S, Abreu J, Barry AJ, Fennell T, Banks E, Ambrogio L, Cibulskis K, Kernytsky A, Gonzalez E, Rudzicz N, Engert JC, Depristo MA, Daly MJ, Cohen JC, Hobbs HH, Altshuler D, Schonfeld G, Gabriel SB, Yue P, Kathiresan S. N Engl J Med. 2010 Oct 3.

BIBW2992, an irreversible EGFR/HER2 inhibitor highly effective in preclinical lung cancer models. Li D, Ambrogio L, Shimamura T, Kubo S, Takahashi M, Chirieac LR, Padera RF, Shapiro GI, Baum A, Himmelsbach F, Rettig WJ, Meyerson M, Solca F, Greulich H, Wong KK. Oncogene. 2008 Aug 7

Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Boehm JS, Zhao JJ, Yao J, Kim SY, Firestein R, Dunn IF, Sjostrom SK, Garraway LA, Weremowicz S, Richardson AL, Greulich H, Stewart CJ, Mulvey LA, Shen RR, Ambrogio L, Hirozane-Kishikawa T, Hill DE, Vidal M, Meyerson M, Grenier JK, Hinkle G, Root DE, Roberts TM, Lander ES, Polyak K, Hahn WC.. Cell 2007 Jun 15