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Kathleen Fisch

TitleExecutive Director
InstitutionUniversity of California San Diego
DepartmentMedicine
Address9500 Gilman Drive #0681
La Jolla CA 92093
Phone858-534-9452
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    Collapse Biography 
    Collapse Education and Training
    University of California, BerkeleyB.A.Integrative Biology
    University of California, DavisPh.D.Ecology: Population Genetics

    Collapse Overview 
    Collapse Overview
    Dr. Kathleen Fisch is the Executive Director of the UC San Diego Center for Computational Biology & Bioinformatics (CCBB) in the Department of Medicine and serves as the Co-Director of the ACTRI Center for Accelerating Drug Development (CADD). Dr. Fisch spearheads the development of a vibrant, leading edge vision for computational biology, bioinformatics support and infrastructure at UCSD Health Sciences.


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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Finger AJ, Mahardja B, Fisch K, Benjamin A, Lindberg J, Ellison L, Ghebremariam T, Hung TC, May B. A conservation hatchery population of Delta Smelt shows evidence of genetic adaptation to captivity after 9 generations. J Hered. 2018 Jul 17. PMID: 30016452.
      View in: PubMed
    2. Liu C, Guo T, Xu G, Sakai A, Ren S, Fukusumi T, Ando M, Sadat SH, Saito Y, Khan Z, Fisch K, Califano J. Characterization of alternative splicing events in HPV negative head and neck squamous cell carcinoma identifies an oncogenic DOCK5 variant. Clin Cancer Res. 2018 Jun 26. PMID: 29945995.
      View in: PubMed
    3. Velimezi G, Robinson-Garcia L, Muñoz-Martínez F, Wiegant WW, Ferreira da Silva J, Owusu M, Moder M, Wiedner M, Rosenthal SB, Fisch K, Moffat J, Menche J, van Attikum H, Jackson SP, Loizou JI. Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48. Nat Commun. 2018 Jun 11; 9(1):2280. PMID: 29891926.
      View in: PubMed
    4. Birmingham A, Mark AM, Mazzaferro C, Xu G, Fisch K. Efficient population-scale variant analysis and prioritization with VAPr. Bioinformatics. 2018 Apr 06. PMID: 29659724.
      View in: PubMed
    5. Gibbons MC, Fisch K, Pichika R, Cheng T, Engler AJ, Schenk S, Lane JG, Singh A, Ward SR. Heterogeneous muscle gene expression patterns in patients with massive rotator cuff tears. PLoS One. 2018; 13(1):e0190439. PMID: 29293645.
      View in: PubMed
    6. Rosenthal SB, Len J, Webster M, Gary A, Birmingham A, Fisch K. Interactive network visualization in Jupyter notebooks: visJS2jupyter. Bioinformatics. 2018 01 01; 34(1):126-128. PMID: 28968701.
      View in: PubMed
    7. Isoda T, Moore AJ, He Z, Chandra V, Aida M, Denholtz M, Piet van Hamburg J, Fisch K, Chang AN, Fahl SP, Wiest DL, Murre C. Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate. Cell. 2017 Sep 21; 171(1):103-119.e18. PMID: 28938112.
      View in: PubMed
    8. Widjaja CE, Olvera JG, Metz PJ, Phan AT, Savas JN, de Bruin G, Leestemaker Y, Berkers CR, de Jong A, Florea BI, Fisch K, Lopez J, Kim SH, Garcia DA, Searles S, Bui JD, Chang AN, Yates JR, Goldrath AW, Overkleeft HS, Ovaa H, Chang JT. Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification. J Clin Invest. 2017 Oct 02; 127(10):3609-3623. PMID: 28846070.
      View in: PubMed
    9. Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch K, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov. 2017 04; 7(4):410-423. PMID: 28188128.
      View in: PubMed
    10. Cowell AN, Loy DE, Sundararaman SA, Valdivia H, Fisch K, Lescano AG, Baldeviano GC, Durand S, Gerbasi V, Sutherland CJ, Nolder D, Vinetz JM, Hahn BH, Winzeler EA. Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples. MBio. 2017 02 07; 8(1). PMID: 28174312.
      View in: PubMed
    11. Akagi R, Akatsu Y, Fisch K, Alvarez-Garcia O, Teramura T, Muramatsu Y, Saito M, Sasho T, Su AI, Lotz MK. Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-ß signaling in chondrocytes. Osteoarthritis Cartilage. 2017 Jun; 25(6):943-951. PMID: 27884645.
      View in: PubMed
    12. Chen S, Miyazaki M, Chandra V, Fisch K, Chang AN, Murre C. Id3 Orchestrates Germinal Center B Cell Development. Mol Cell Biol. 2016 Oct 15; 36(20):2543-52. PMID: 27457619.
      View in: PubMed
    13. Alvarez-Garcia O, Fisch K, Wineinger NE, Akagi R, Saito M, Sasho T, Su AI, Lotz MK. Increased DNA Methylation and Reduced Expression of Transcription Factors in Human Osteoarthritis Cartilage. Arthritis Rheumatol. 2016 08; 68(8):1876-86. PMID: 26881698; PMCID: PMC4963260 [Available on 08/01/17].
    14. Alvarez-Garcia O, Olmer M, Akagi R, Akasaki Y, Fisch K, Shen T, Su AI, Lotz MK. Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy. Osteoarthritis Cartilage. 2016 Sep; 24(9):1639-47. PMID: 27118398.
      View in: PubMed
    15. Banno A, Garcia DA, van Baarsel ED, Metz PJ, Fisch K, Widjaja CE, Kim SH, Lopez J, Chang AN, Geurink PP, Florea BI, Overkleeft HS, Ovaa H, Bui JD, Yang J, Chang JT. Downregulation of 26S proteasome catalytic activity promotes epithelial-mesenchymal transition. Oncotarget. 2016 Apr 19; 7(16):21527-41. PMID: 26930717; PMCID: PMC5008303.
    16. Meißner T, Fisch K, Gioia L, Su AI. OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing. BMC Med Genomics. 2015 May 21; 8:24. PMID: 25989980; PMCID: PMC4494802.
    17. Fisch K, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI. Omics Pipe: a community-based framework for reproducible multi-omics data analysis. Bioinformatics. 2015 Jun 01; 31(11):1724-8. PMID: 25637560; PMCID: PMC4443682.
    18. Fisch, K., Kozfkay, C., Ivy, J., Ryder, O., R. Waples.Fish hatchery genetic management techniques: Integrating Theory with Implementation. North American Journal of Aquaculture: HaMAR Special Section. 2015; 3(77):343-357.
    19. LaCava, M., Fisch, K., Nagel, M., Lindberg, J., May, B., Finger, A.Spawning behavior of cultured delta smelt (Hypomesus transpacificus) in a conservation hatchery. North American Journal of Aquaculture. 2015; 3(77):255-266.
    20. Wei N, Shi Y, Truong LN, Fisch K, Xu T, Gardiner E, Fu G, Hsu YO, Kishi S, Su AI, Wu X, Yang XL. Oxidative stress diverts tRNA synthetase to nucleus for protection against DNA damage. Mol Cell. 2014 Oct 23; 56(2):323-332. PMID: 25284223.
      View in: PubMed
    21. Fisch, K., Mahardja, B., Burton, R., May, B.Hybridization between delta smelt and two other species within the family Osmeridae in the San Francisco Bay-Delta. Conservation Genetics. 2014; (15):489-494.
    22. Lindberg, J., Tigan, G., Ellison, L., Rettinghouse, T., Nagel, M., Fisch, K.Aquaculture methods for a genetically managed population of endangered delta smelt. North American Journal of Aquaculture. 2013; 2(75):186-196.
    23. Fisch K, Ivy JA, Burton RS, May B. Evaluating the performance of captive breeding techniques for conservation hatcheries: a case study of the delta smelt captive breeding program. J Hered. 2013 Jan-Feb; 104(1):92-104. PMID: 23125405.
      View in: PubMed
    24. Fisch, K., Henderson, J., Burton, R., May, B.Population genetics and conservation implications for the endangered delta smelt in the San Francisco Bay-Delta. Conservation Genetics. 2011; 6(12):1421-1434.
    25. Israel, J., Fisch, K., Turner, T., Waples, R.Conservation of native Bay-Delta fishes: past experience and future considerations for artificial propagation of Chinook salmon, delta smelt, and green sturgeon. San Francisco Estuary & Watershed Science. 2011; 1(9):1-20.
    26. Fisch K, Petersen JL, Baerwald MR, Pedroia JK, May B. Characterization of 24 microsatellite loci in delta smelt, Hypomesus transpacificus, and their cross-species amplification in two other smelt species of the Osmeridae family. Mol Ecol Resour. 2009 Jan; 9(1):405-8. PMID: 21564663.
      View in: PubMed