Josh Kaminker
Director of OMNI Bioinformatics and Senior Scientist, Bioinformatics & Computational Biology
Postdoc Mentor
"Genentech is a place where Bioinformatics plays a very real and profound role in making scientific discoveries that may ultimately benefit patients."
16
Years at Genentech
32
Publications
1
Awards & Honors
I studied Mathematics and Biology as an undergraduate, moving on to pure bench work in graduate school. With a continued interest in computational biology, I moved to a genomics group at Berkeley for my postdoc. I joined the Bioinformatics department at Genentech in 2004 with the aim of having an impact on the treatment of human diseases. I have continued to be engaged in extremely interesting and rewarding scientific projects in oncology and neuroscience. Throughout my career I have been immensely impressed by the scientific talent and collaborative nature of research at Genentech.
Postdoctoral Mentor
Sensory neurons play a fundamental role in transducing external stimuli from the periphery to the central nervous system. We are interested in using cutting edge single cell-based approaches to understand the biology of sensory neurons in pain and airway inflammation. Our work is highly collaborative and we work closely with multiple laboratories in both neuroscience and immunology, creating a unique and stimulating environment that fully integrates computational biology with bench experimentation.
Featured Publication
Untangling the brain0s neuroinflammatory and neurodegenerative transcriptional responses.
Nat Commun. 2016 Apr 21;7:11295.
Srinivasan K, Friedman BA, Larson JL, Lauffer BE, Goldstein LD, Appling LL, Borneo J, Poon C, Ho T, Cai F, Steiner P, van der Brug MP, Modrusan Z, Kaminker JS, Hansen DV.
My Focus
My group is deeply interested in using bioinformatics approaches to understand how transcriptional changes at the cellular level impact disease biology. Within Neuroscience our efforts are focused on understanding the role of such changes in driving neurodegenerative disease such as Alzheimer’s and ALS. We collaborate very closely with bench scientists to develop and pursue computational and biological hypotheses. We are also applying similar computational approaches to help define the role of different populations of sensory neurons in pain perception.
Publications
Genome-wide analysis of differential gene expression and splicing in excitatory neurons and interneuron subtypes
Journal of Neuroscience, ISSN: 02706474
Melanie Huntley; Karpagam Srinivasan; Brad Friedman; Tzu-Ming Wang; Ada X. Yee; Yuanyuan Wang; Josh Kaminker; Morgan Sheng; David Hansen; Jesse E. Hanson
Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer's Disease Not Evident in Mouse Models
Cell Reports,
Brad Friedman; Karpagam Srinivasan; Gai Ayalon; Bill Meilandt; Han Lin; Melanie Huntley; Yi Cao; Seung-Hye Lee; Patrick Haddick; Hai Ngu; Zora Modrusan; Jessica L. Larson; Josh Kaminker; Marcel van der Brug; David Hansen
Science Translational Medicine, ISSN: 19466242 19466234
Claire Le Pichon; Bill Meilandt; Sara Dominguez; Hilda Solanoy; Han Lin; Hai Ngu; Alvin Gogineni; Arundhati Sengupta Ghosh; Zhiyu Jiang; Seung-Hye Lee; Janice Maloney; Vineela Gandham; Christine Pozniak; Bei Wang; Sebum Lee; Mike Siu; Snahel Patel; Zora Modrusan; Xingrong Liu; York Rudhard; Miriam Baca; Amy Gustafson; Josh Kaminker; Rick Carano; Eric J. Huang; Oded Foreman; Robby Weimer; Kimberly Scearce-Levie; Joe Lewcock
eLife, ISSN: 2050084X
Martin Larhammar; Sarah Huntwork-Rodriguez; Zhiyu Jiang; Hilda Solanoy; Arundhati Sengupta Ghosh; Bei Wang; Josh Kaminker; Kevin Huang; Jeff Eastham Anderson; Mike Siu; Zora Modrusan; Madeline M. Farley; Marc Tessier-Lavigne; Joe Lewcock; Trent Watkins
Journal of Alzheimer's Disease, ISSN: 18758908
Patrick Haddick; Jessica L. Larson; Nisha Rathore; Tushar Bhangale; Qui T. Phung; Karpagam Srinivasan; David Hansen; Jennie Lill; Margaret A. Pericak-Vance; Jonathan Haines; Lindsay A. Farrer; John S.K. Kauwe; Gerard D. Schellenberg; Carlos Cruchaga; Alison Goate; Tim Behrens; Ryan Watts; Robert R. Graham; Josh Kaminker; Marcel van der Brug
Journal of Experimental Medicine, ISSN: 15409538 00221007
Michael Chang; Karpagam Srinivasan; Brad Friedman; Eric Suto; Zora Modrusan; Wyne Lee; Josh Kaminker; David Hansen; Morgan Sheng
Nature Communications, ISSN: 20411723
Karpagam Srinivasan; Brad Friedman; Jessica L. Larson; Ben Lauffer; Leonard Goldstein; Laurie L. Appling; Jovencio Borneo; CK Poon; Terence Ho; Fang Cai; Pascal Steiner; Marcel van der Brug; Zora Modrusan; Josh Kaminker; David Hansen
BMC Genomics, ISSN: 14712164
Melanie Huntley; Melanie Lou; Leonard Goldstein; Michael Lawrence; Peter Dijkgraaf; Josh Kaminker; Robert Gentleman
Nature, ISSN: 14764687
Mamie Yu; Suresh Selvaraj; May Liang-Chu; Sahar Aghajani; Matthew Busse; Jean Yuan; Genee Lee; Frank Peale; Christiaan Klijn; Richard Bourgon; Josh Kaminker; Rich Neve
Neuron, ISSN: 10974199
Yelin Chen; Yuanyuan Wang; Ali Erturk; Dara Kallop; Zhiyu Jiang; Robby Weimer; Josh Kaminker; Morgan Sheng
Journal of Neuroscience, ISSN: 15292401
Yelin Chen; Yuanyuan Wang; Zora Modrusan; Morgan Sheng; Josh Kaminker
Bioinformatics, ISSN: 14602059
Melanie Huntley; Jessica L. Larson; Christina Chaivorapol; Gabriel Becker; Michael Lawrence; Jason Hackney; Josh Kaminker; Martin Bishop
Clinical Cancer Research, ISSN: 10780432
Matt Brauer; Guanglei Zhuang; Maike Schmidt; Jenny Yao; Xiumin Wu; Josh Kaminker; Stefanie S. Jurinka; Ganesh Kolumam; Alicia Chung; Adrian Jubb; Zora Modrusan; Tomoko Ozawa; C. David James; Heidi Phillips; Benjamin Haley; Nga Wan Rachel Tam; Anne Clermont; Jason Cheng; Sherry X. Yang; Sandra M. Swain; Daniel Chen; Stefan Scherer; Hartmut Koeppen; Ru-Fang Yeh; Peng Yue; Daniel Stephan; Priti Hegde; Napoleone Ferrara; Mallika Singh; Carlos Bais
Proceedings of the National Academy of Sciences of the United States of America, ISSN: 00278424
Trent Watkins; Bei Wang; Sarah Huntwork-Rodriguez; Jing Yang; Zhiyu Jiang; Jeff Eastham Anderson; Zora Modrusan; Josh Kaminker; Marc Tessier-Lavigne; Joe Lewcock
Proceedings of the 2012 IEEE 16th International Enterprise Distributed Object Computing Conference Workshops, EDOCW 2012,
Rebecca Lawler; Hui Yang; Kathryn Woods; Josh Kaminker
Journal of Neuroscience, ISSN: 02706474
Mark Chen; Janice Maloney; Dara Kallop; Jasi Atwal; Stephen Tam; Kristin Baer; Holger Kissel; Josh Kaminker; Joe Lewcock; Robby Weimer; Ryan Watts
Developmental Cell, ISSN: 15345807
Stephen Tam; David L. Richmond; Josh Kaminker; Zora Modrusan; Baby Martin-Mcnulty; Tim Cao; Robby Weimer; Rick Carano; Nicholas Vanbruggen; Ryan Watts
Nature, ISSN: 00280836
Ingrid Wertz; Saritha Kusam; Cynthia Lam; Toru Okamoto; Wendy Sandoval; Daniel Anderson; Elizabeth Helgason; James Ernst; Mike Eby; Jinfeng Liu; Lisa Belmont; Josh Kaminker; Karen O'Rourke; Kanan Pujara; Pawan Bir Kohli; Adam Johnson; Mark L. Chiu; Jennie Lill; Peter Jackson; Wayne Fairbrother; Somasekar Seshagiri; Mary Ludlam; Kevin Leong; Erin Dueber; Heather Maecker; David C.S. Huang; Vishva Dixit
Proceedings of the National Academy of Sciences of the United States of America, ISSN: 00278424
Marcin Kowanetz; Xiumin Wu; John Lee; Martha Tan; Thijs Hagenbeek; Xueping Qu; Lanlan Yu; Jed Ross; Nina Korsisaari; Tim Cao; Hani Bou-Reslan; Dara Kallop; Robby Weimer; Mary Ludlam; Josh Kaminker; Zora Modrusan; Nick Van Bruggen; Frank Peale; Rick Carano; Gloria Meng; Napoleone Ferrara
Blood, ISSN: 00064971
Raquel Del Toro; Claudia Prahst; Thomas Mathivet; Geraldine Siegfried; Josh Kaminker; Bruno Larrivee; Christiane Bréant; Antonio Duarte; Nobuyuki Takakura; Akiyoshi Fukamizu; Josef Penninger; Anne Eichmann
Nature, ISSN: 00280836
Zhengyan Kan; Bijay Jaiswal; Jeremy Stinson; Vasant Janakiraman; Deepali Bhatt; Howard Stern; Peng Yue; Pete Haverty; Richard Bourgon; Jianbiao Zheng; Martin Moorhead; Subhra Chaudhuri; Lynn P. Tomsho; Brock Peters; Kanan Pujara; Shaun Cordes; David Davis; Victoria E. H. Carlton; Wenlin Yuan; Li Li; Weiru Wang; Charles Eigenbrot; Josh Kaminker; David Eberhard; Paul Waring; Stephan C. Schuster; Zora Modrusan; Zhen Zhang; David Stokoe; Frederic De Sauvage; Malek Faham; Somasekar Seshagiri
Blood, ISSN: 00064971
Geraldine Strasser; Josh Kaminker; Marc Tessier-Lavigne
Human Mutation, ISSN: 10597794
Peng Yue; Bill Forrest; Josh Kaminker; Scott Lohr; Zhen Zhang; Guy Cavet
Cancer Cell, ISSN: 15356108
Bijay Jaiswal; Vasant Janakiraman; Noelyn Kljavin; Subhra Chaudhuri; Howard Stern; Weiru Wang; Zhengyan Kan; Hashem A. Dbouk; Brock Peters; Paul Waring; Trisha Dela Vega; Denise M. Kenski; Krista Bowman; Maria Lorenzo; Hong Li; Jiansheng Wu; Zora Modrusan; Jeremy Stinson; Mike Eby; Peng Yue; Josh Kaminker; Frederic De Sauvage; Jonathan M. Backer; Somasekar Seshagiri
BMC Medical Genomics, ISSN: 17558794
Pete Haverty; Lawrence Hon; Josh Kaminker; John Chant; Zhen Zhang
Cancer Cell, ISSN: 15356108
Yongping Crawford; Ian Kasman; Lanlan Yu; Cuiling Zhong; Xiumin Wu; Zora Modrusan; Josh Kaminker; Napoleone Ferrara
Human Mutation, ISSN: 10597794
Lawrence Hon; Yan Zhang; Josh Kaminker; Zhen Zhang
Current Bioinformatics, ISSN: 15748936
Lawrence Hon; Josh Kaminker; Zhen Zhang
Science, ISSN: 00368075
Laura D. Wood; D. Williams Parsons; Siân Jones; Jimmy Lin; Tobias Sjöblom; Rebecca J. Leary; Dong Shen; Simina M. Boca; Thomas Barber; Janine Ptak; Natalie Silliman; Steve Szabo; Zoltan Dezso; Vadim Ustyanksky; Tatiana Nikolskaya; Yuri Nikolsky; Karchin; Paul A. Wilson; Josh Kaminker; Zhen Zhang; Randal Croshaw; Joseph Willis; Dawn Dawson; Michail Shipitsin; James K. V. Willson; Saraswati Sukumar; Kornelia Polyak; Ben H. Park; Charit L. Pethiyagoda; P. V. Krishna Pant; Dennis G. Ballinger; Andrew B. Sparks; James Hartigan; Douglas R. Smith; Erick Suh; Nickolas Papadopoulos; Phillip Buckhaults; Sanford D. Markowitz; Giovanni Parmigiani; Kenneth W. Kinzler; Victor E. Velculescu; Bert Vogelstein
Nucleic Acids Research, ISSN: 03051048
Josh Kaminker; Yan Zhang; Colin Watanabe; Zhen Zhang
Cancer Research, ISSN: 00085472
Josh Kaminker; Yan Zhang; Allison Waugh; Pete Haverty; Brock Peters; Dragan Sebisanovic; Jeremy Stinson; Bill Forrest; Fernando Bazan; Somasekar Seshagiri; Zhen Zhang
PLoS Computational Biology, ISSN: 1553734X
Mark Yandell; Chris J. Mungall; Chris Smith; Simon Prochnik; Josh Kaminker; George Hartzell; Suzanna E. Lewis; Gerald M. Rubin
Education
- University of California, Berkeley, Postdoctoral Fellow – 2004
- University of California, Los Angeles, PhD in Molecular, Cell, and Developmental Biology – 2001
- Indiana University, B.S. in Mathematics – 1995
- Indiana University, B.S. in Biology – 1995
Awards & Honors
- NIH Research Training in Cellular and Molecular Biology – 1996