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Kathleen Fisch

Title(s)Executive Director, Medicine
SchoolHealth Sciences
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.

    Collapse Research 
    Collapse Research Activities and Funding
    Omics Data Generation Center (ODGC) for the Acute to Chronic Pain Signatures (A2CPS) Program
    NIH/NIDA U54DA049115Sep 1, 2019 - Jul 31, 2023
    Role: Principal Investigator
    Comparative Study of Molecular Signatures in HIV-Related Neuropathogenesis and Alzheimer's Disease
    NIH R01AG061066Sep 30, 2018 - May 31, 2023
    Role: Co-Investigator
    UC San Diego Clinical and Translational Research Institute
    NIH 2UL1TR001442-06Aug 13, 2015 - Apr 30, 2025
    Role: Co-Investigator
    UC San Diego Clinical and Translational Research Institute
    NIH/NCATS UL1TR001442Aug 13, 2015 - Mar 31, 2020
    Role: Other Personnel
    Cytoscape: A Modeling Platform for Biomolecular Networks
    NIH/NHGRI R01HG009979Jun 1, 2004 - Jun 30, 2021
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
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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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing. PLoS One. 2020; 15(5):e0233380. Sakai A, Ando M, Fukusumi T, Ren S, Liu C, Qualliotine J, Haft S, Sadat S, Saito Y, Guo TW, Xu G, Sasik R, Fisch KM, Gutkind JS, Fertig EJ, Molinolo AA, Califano JA. PMID: 32437477.
      View in: PubMed   Mentions:    Fields:    
    2. Differential expression of nuclear genes encoding mitochondrial proteins from urban and rural populations in Morocco. Cell Stress Chaperones. 2020 Apr 21. Bickler SW, Prieto JM, Cauvi DM, De Cos V, Nasamran C, Ameh E, Amin S, Nicholson S, Din H, Mocumbi AO, Noormahomed EV, Tellez-Isaias G, Fisch KM, De Maio A. PMID: 32319023.
      View in: PubMed   Mentions:    Fields:    
    3. Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection. Front Genet. 2020; 11:358. Ryan AF, Nasamran CA, Pak K, Draf C, Fisch KM, Webster N, Kurabi A. PMID: 32351546.
      View in: PubMed   Mentions:
    4. Increased Fibrogenic Gene Expression in Multifidus Muscles of Patients With Chronic Versus Acute Lumbar Spine Pathology. Spine (Phila Pa 1976). 2020 Feb 15; 45(4):E189-E195. Shahidi B, Fisch KM, Gibbons MC, Ward SR. PMID: 31513095.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    5. Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma. Head Neck. 2020 Apr; 42(4):688-697. Saito Y, Favorov AV, Forman M, Ren S, Sakai A, Fukusumi T, Liu C, Sadat S, Ando M, Xu G, Khan Z, Pang J, Valsamakis A, Fisch KM, Califano JA. PMID: 31850594.
      View in: PubMed   Mentions:    Fields:    
    6. FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy. Elife. 2019 09 03; 8. Diaz Osterman CJ, Ozmadenci D, Kleinschmidt EG, Taylor KN, Barrie AM, Jiang S, Bean LM, Sulzmaier FJ, Jean C, Tancioni I, Anderson K, Uryu S, Cordasco EA, Li J, Chen XL, Fu G, Ojalill M, Rappu P, Heino J, Mark AM, Xu G, Fisch KM, Kolev VN, Weaver DT, Pachter JA, Gyorffy B, McHale MT, Connolly DC, Molinolo A, Stupack DG, Schlaepfer DD. PMID: 31478830.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    7. Mechanisms of vascular permeability and remodeling associated with hemarthrosis in factor VIII-deficient mice. J Thromb Haemost. 2019 11; 17(11):1815-1826. Cooke EJ, Wyseure T, Zhou JY, Gopal S, Nasamran CA, Fisch KM, Manon-Jensen T, Karsdal MA, Mosnier LO, von Drygalski A. PMID: 31301687.
      View in: PubMed   Mentions: 1     Fields:    
    8. Integrating Gene and Protein Expression Reveals Perturbed Functional Networks in Alzheimer's Disease. Cell Rep. 2019 07 23; 28(4):1103-1116.e4. Canchi S, Raao B, Masliah D, Rosenthal SB, Sasik R, Fisch KM, De Jager PL, Bennett DA, Rissman RA. PMID: 31340147.
      View in: PubMed   Mentions: 1     Fields:    
    9. Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun. 2019 May 29; 10(1):2415. Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. PMID: 31142745.
      View in: PubMed   Mentions:    Fields:    
    10. Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun. 2019 05 16; 10(1):2188. Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. PMID: 31097695.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    11. A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma. Cell. 2019 04 18; 177(3):572-586.e22. Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T. PMID: 30955884.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    12. Mutation of chromatin regulators and focal hotspot alterations characterize human papillomavirus-positive oropharyngeal squamous cell carcinoma. Cancer. 2019 07 15; 125(14):2423-2434. Haft S, Ren S, Xu G, Mark A, Fisch K, Guo TW, Khan Z, Pang J, Ando M, Liu C, Sakai A, Fukusumi T, Califano JA. PMID: 30933315.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    13. DNA methylation changes associated with Parkinson's disease progression: outcomes from the first longitudinal genome-wide methylation analysis in blood. Epigenetics. 2019 04; 14(4):365-382. Henderson-Smith A, Fisch KM, Hua J, Liu G, Ricciardelli E, Jepsen K, Huentelman M, Stalberg G, Edland SD, Scherzer CR, Dunckley T, Desplats P. PMID: 30871403.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    14. On entropy and information in gene interaction networks. Bioinformatics. 2019 03 01; 35(5):815-822. Wallace ZS, Rosenthal SB, Fisch KM, Ideker T, Sasik R. PMID: 30102349.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    15. Variations in HPV function are associated with survival in squamous cell carcinoma. JCI Insight. 2019 Jan 10; 4(1). Gleber-Netto FO, Rao X, Guo T, Xi Y, Gao M, Shen L, Erikson K, Kalu NN, Ren S, Xu G, Fisch KM, Akagi K, Seiwert T, Gillison M, Frederick MJ, Johnson FM, Wang J, Myers JN, Califano J, Skinner HD, Pickering CR. PMID: 30626753.
      View in: PubMed   Mentions: 5     Fields:    
    16. Biological Interpretation of Complex Genomic Data. Methods Mol Biol. 2019; 1908:61-71. Fisch KM. PMID: 30649721.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    17. A Conservation Hatchery Population of Delta Smelt Shows Evidence of Genetic Adaptation to Captivity After 9 Generations. J Hered. 2018 08 24; 109(6):689-699. Finger AJ, Mahardja B, Fisch KM, Benjamin A, Lindberg J, Ellison L, Ghebremariam T, Hung TC, May B. PMID: 30016452.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    18. Efficient population-scale variant analysis and prioritization with VAPr. Bioinformatics. 2018 08 15; 34(16):2843-2845. Birmingham A, Mark AM, Mazzaferro C, Xu G, Fisch KM. PMID: 29659724.
      View in: PubMed   Mentions: 1     Fields:    
    19. Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis. Osteoarthritis Cartilage. 2018 11; 26(11):1531-1538. Fisch KM, Gamini R, Alvarez-Garcia O, Akagi R, Saito M, Muramatsu Y, Sasho T, Koziol JA, Su AI, Lotz MK. PMID: 30081074.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    20. Characterization of Alternative Splicing Events in HPV-Negative Head and Neck Squamous Cell Carcinoma Identifies an Oncogenic DOCK5 Variant. Clin Cancer Res. 2018 10 15; 24(20):5123-5132. Liu C, Guo T, Xu G, Sakai A, Ren S, Fukusumi T, Ando M, Sadat S, Saito Y, Khan Z, Fisch KM, Califano J. PMID: 29945995.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    21. Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48. Nat Commun. 2018 06 11; 9(1):2280. Velimezi G, Robinson-Garcia L, Muñoz-Martínez F, Wiegant WW, Ferreira da Silva J, Owusu M, Moder M, Wiedner M, Rosenthal SB, Fisch KM, Moffat J, Menche J, van Attikum H, Jackson SP, Loizou JI. PMID: 29891926.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    22. Heterogeneous muscle gene expression patterns in patients with massive rotator cuff tears. PLoS One. 2018; 13(1):e0190439. Gibbons MC, Fisch KM, Pichika R, Cheng T, Engler AJ, Schenk S, Lane JG, Singh A, Ward SR. PMID: 29293645.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    23. Interactive network visualization in Jupyter notebooks: visJS2jupyter. Bioinformatics. 2018 01 01; 34(1):126-128. Rosenthal SB, Len J, Webster M, Gary A, Birmingham A, Fisch KM. PMID: 28968701.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    24. 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. Isoda T, Moore AJ, He Z, Chandra V, Aida M, Denholtz M, Piet van Hamburg J, Fisch KM, Chang AN, Fahl SP, Wiest DL, Murre C. PMID: 28938112.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    25. Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification. J Clin Invest. 2017 Oct 02; 127(10):3609-3623. 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. PMID: 28846070.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    26. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov. 2017 04; 7(4):410-423. Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. PMID: 28188128.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    27. 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). 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. PMID: 28174312.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    28. Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-ß signaling in chondrocytes. Osteoarthritis Cartilage. 2017 06; 25(6):943-951. Akagi R, Akatsu Y, Fisch KM, Alvarez-Garcia O, Teramura T, Muramatsu Y, Saito M, Sasho T, Su AI, Lotz MK. PMID: 27884645.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    29. Id3 Orchestrates Germinal Center B Cell Development. Mol Cell Biol. 2016 10 15; 36(20):2543-52. Chen S, Miyazaki M, Chandra V, Fisch KM, Chang AN, Murre C. PMID: 27457619.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCellsPHPublic Health
    30. Increased DNA Methylation and Reduced Expression of Transcription Factors in Human Osteoarthritis Cartilage. Arthritis Rheumatol. 2016 08; 68(8):1876-86. Alvarez-Garcia O, Fisch KM, Wineinger NE, Akagi R, Saito M, Sasho T, Su AI, Lotz MK. PMID: 26881698.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    31. Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy. Osteoarthritis Cartilage. 2016 09; 24(9):1639-47. Alvarez-Garcia O, Olmer M, Akagi R, Akasaki Y, Fisch KM, Shen T, Su AI, Lotz MK. PMID: 27118398.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    32. Downregulation of 26S proteasome catalytic activity promotes epithelial-mesenchymal transition. Oncotarget. 2016 Apr 19; 7(16):21527-41. 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. PMID: 26930717.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    33. 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. Meißner T, Fisch KM, Gioia L, Su AI. PMID: 25989980.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    34. Omics Pipe: a community-based framework for reproducible multi-omics data analysis. Bioinformatics. 2015 Jun 01; 31(11):1724-8. Fisch KM, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI. PMID: 25637560.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    35. Fish hatchery genetic management techniques: Integrating Theory with Implementation. North American Journal of Aquaculture: HaMAR Special Section. 2015; 3(77):343-357. Fisch, K., Kozfkay, C., Ivy, J., Ryder, O., R. Waples.
    36. Spawning behavior of cultured delta smelt (Hypomesus transpacificus) in a conservation hatchery. North American Journal of Aquaculture. 2015; 3(77):255-266. LaCava, M., Fisch, K., Nagel, M., Lindberg, J., May, B., Finger, A.
    37. Oxidative stress diverts tRNA synthetase to nucleus for protection against DNA damage. Mol Cell. 2014 Oct 23; 56(2):323-332. Wei N, Shi Y, Truong LN, Fisch KM, Xu T, Gardiner E, Fu G, Hsu YO, Kishi S, Su AI, Wu X, Yang XL. PMID: 25284223.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    38. Hybridization between delta smelt and two other species within the family Osmeridae in the San Francisco Bay-Delta. Conservation Genetics. 2014; (15):489-494. Fisch, K., Mahardja, B., Burton, R., May, B.
    39. Aquaculture methods for a genetically managed population of endangered delta smelt. North American Journal of Aquaculture. 2013; 2(75):186-196. Lindberg, J., Tigan, G., Ellison, L., Rettinghouse, T., Nagel, M., Fisch, K.
    40. 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. Fisch KM, Ivy JA, Burton RS, May B. PMID: 23125405.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    41. Population genetics and conservation implications for the endangered delta smelt in the San Francisco Bay-Delta. Conservation Genetics. 2011; 6(12):1421-1434. Fisch, K., Henderson, J., Burton, R., May, B.
    42. 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. Israel, J., Fisch, K., Turner, T., Waples, R.
    43. 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. Fisch KM, Petersen JL, Baerwald MR, Pedroia JK, May B. PMID: 21564663.
      View in: PubMed   Mentions: 1     Fields:    
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