Pronounsshe, her, her, hers, herself

Department/College/UnitPhysical & Biological Sciences Division

TitleActing Professor of Molecular, Cell, & Developmental Biology
Faculty Director of Diversity, UC Santa Cruz Genomics Institute

AffiliationFaculty

Other UCSC Campus AffiliationBiomolecular Science & Engineering

Web SiteFaculty
Lab

Primary Office LocationBiomedical Sciences
440

Additional Location(s)Biomed 465

Mail StopGenomics Institute

Biography, Education and Training

My research involves using pluripotent stem cells from a variety of primate species and high throughput sequencing methods to study how genome evolution affects human development and disease. My lab is located in the Institute for the Biology of Stem Cells. With funding from NIH-NHGRI, we are exploring the mechanisms by which transposable elements lead to new gene regulatory programs important for the evolution of new traits. With funding from NIH-NIMH we are studying the role of human-specific genomic innovations on brain development and disease. With Professor David Haussler, Scientific Director of the Genomics Institute, and Computer, Electrical Engineering Professor Mircea Teodorescu and BME Professor Tal Sharf, I lead UCSC’s Braingeneers project funded by the Schmidt Futures Foundation and NSF. This interdisciplinary team aims to develop stem cell derived 3D cell culture models of the brain to study the development and behavior of human neural circuits at a scale that enables the application of modern artificial intelligence (AI) approaches to this research. I am also Co-PI with Haussler and ECE Professor Holger Schmidt of the Genomics Institute’s Center for Live Cell Genomics, an NIH-NHGRI Center for Excellence in Genomic Science.  I am also part of the UCSC Treehouse Pediatric Cancer Initiative, where my group is developing organoid models of pediatric glioma. 

Summary of Expertise

molecular biology, stem cell biology, genomics, high throughput sequencing assays

Selected Publications

1. Field AR, Jacobs FMJ, Fiddes IT, Phillips APR, Reyes-Ortiz AM, LaMontagne E, Whitehead L, Meng V, Rosenkrantz, JL, Haeussler M, Katzman S, Salama SR*, Haussler D. Structurally conserved primate lncRNAs are transiently expressed during human cortical differentiation and influence cell type specific genes. Stem Cell Reports. 2019 Feb 12;12(2):245-257.
2. Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A, Bishara A, Rosenkrantz JL, Lorig-Roach R, Field AR, Haeussler M, Russo L, Bhaduri A, Nowakowski TJ, Pollen AA, Dougherty ML, Nuttle X, Addor MC, Zwolinski S, Katzman S, Kriegstein A, Eichler EE, Salama SR*, Jacobs FMJ, Haussler D. Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell. 2018; 173(6):1356-1369.
3. Toor JS, Rao AA, McShan AC, Yarmarkovich M, Nerli S, Yamaguchi K, Madejska AA, Nguyen S, Tripathi S, Maris JM, Salama SR, Haussler D, Sgourakis NG. A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. Frontiers in immunology. 2018; 9:99. 
4. Newton Y, Novak AM, Swatloski T, McColl DC, Chopra S, Graim K, Weinstein AS, Baertsch R, Salama SR, Ellrott K, Chopra M, Goldstein TC, Haussler D, Morozova O, Stuart JM. TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal. Cancer research. 2017; 77(21):e111-e114. 
5. Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, et al.; TCGA  Research Network, Noushmehr H, Iavarone A, Verhaak RG. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell. 2016 Jan 28;164(3):550-63.
6. Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, et al. 2015. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 372(26):2481-98. 
7. Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 2014 Sep 28. doi: 10.1038/nature13760. [Epub ahead of print]
8. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, et al.; TCGA Research Network. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10;155(2):462-77. doi: 10.1016/j.cell.2013.09.034. 
9. Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer Res. 2013 Oct 1;73(19):6036-45. doi: 10.1158/0008-5472.CAN-13-0186.
10. Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science. 2011 Aug 19;333(6045):1019-24. doi: 10.1126/science.1202702.
11. Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010 Dec;7(12):995-1001. doi: 10.1038/nmeth.1529.
12. Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. Human genome ultraconserved elements are ultraselected. Science. 2007 Aug 17;317(5840):915.
13. Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14;443(7108):167-72.
14. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006 May 4;441(7089):87-90.