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Jill Hollenbach, PhD, MPH

TitleAssistant Professor
SchoolUCSF School of Medicine
DepartmentNeurology
Address675 Nelson Rising Lane
San Francisco CA 94158
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    Collapse Research 
    Collapse Research Activities and Funding
    MHC variation at high resolution in multiple sclerosis
    NIH/NINDS R01NS102153Aug 15, 2017 - Apr 30, 2022
    Role: Co-Principal Investigator
    Integrated Exchange and Storage of Current- and Future-Generation Immunogenomic Data
    NIH/NIAID R01AI128775Mar 1, 2017 - Feb 28, 2022
    Role: Principal Investigator
    Immunogenetic Determinants of Disease Risk in Neurological Disease
    NIH/NINDS U19NS095774Jul 1, 2015 - Jul 31, 2020
    Role: Co-Investigator
    Mapping the Intersection: Self-identification and Genetic Ancestry
    NIH/NHGRI R21HG008041Sep 9, 2014 - Jun 30, 2016
    Role: Principal Investigator
    Integrated Exchange & Storage of Current and Future-Generation Immunogenomic Data
    NIH/NIGMS R01GM109030Apr 1, 2014 - Feb 28, 2017
    Role: Co-Principal Investigator

    Collapse ORNG Applications 
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    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. Pappas DJ, Lizee A, Paunic V, Beutner KR, Motyer A, Vukcevic D, Leslie S, Biesiada J, Meller J, Taylor KD, Zheng X, Zhao LP, Gourraud PA, Hollenbach J, Mack SJ, Maiers M. Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest. Pharmacogenomics J. 2017 Apr 25. PMID: 28440342.
      View in: PubMed
    2. Norman PJ, Norberg SJ, Guethlein LA, Nemat-Gorgani N, Royce T, Wroblewski EE, Dunn T, Mann T, Alicata C, Hollenbach JA, Chang W, Shults Won M, Gunderson KL, Abi-Rached L, Ronaghi M, Parham P. Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II. Genome Res. 2017 May; 27(5):813-823. PMID: 28360230.
      View in: PubMed
    3. Steele NZ, Carr JS, Bonham LW, Geier EG, Damotte V, Miller ZA, Desikan RS, Boehme KL, Mukherjee S, Crane PK, Kauwe JS, Kramer JH, Miller BL, Coppola G, Hollenbach J, Huang Y, Yokoyama JS. Fine-mapping of the human leukocyte antigen locus as a risk factor for Alzheimer disease: A case-control study. PLoS Med. 2017 Mar; 14(3):e1002272. PMID: 28350795.
      View in: PubMed
    4. Norman PJ, Hollenbach JA, Nemat-Gorgani N, Marin WM, Norberg SJ, Ashouri E, Jayaraman J, Wroblewski EE, Trowsdale J, Rajalingam R, Oksenberg JR, Chiaroni J, Guethlein LA, Traherne JA, Ronaghi M, Parham P. Defining KIR and HLA Class I Genotypes at Highest Resolution via High-Throughput Sequencing. Am J Hum Genet. 2016 Aug 04; 99(2):375-91. PMID: 27486779; PMCID: PMC4974113 [Available on 02/04/17].
    5. Isobe N, Keshavan A, Gourraud PA, Zhu AH, Datta E, Schlaeger R, Caillier SJ, Santaniello A, Lizée A, Himmelstein DS, Baranzini SE, Hollenbach J, Cree BA, Hauser SL, Oksenberg JR, Henry RG, et al. Association of HLA Genetic Risk Burden With Disease Phenotypes in Multiple Sclerosis. JAMA Neurol. 2016 Jul 01; 73(7):795-802. PMID: 27244296.
      View in: PubMed
    6. Le Gall C, Laurent J, Vince N, Lizee A, Agrawal A, Walencik A, Rettman P, Gagne K, Retiere C, Hollenbach J, Cesbron A, Limou S, Gourraud PA. Multidimensional reduction of multicentric cohort heterogeneity: An alternative method to increase statistical power and robustness. Hum Immunol. 2016 Nov; 77(11):1024-1029. PMID: 27262455.
      View in: PubMed
    7. Hollenbach JA, Pando MJ, Caillier SJ, Gourraud PA, Oksenberg JR. The killer immunoglobulin-like receptor KIR3DL1 in combination with HLA-Bw4 is protective against multiple sclerosis in African Americans. Genes Immun. 2016 04; 17(3):199-202. PMID: 26866467.
      View in: PubMed
    8. Pappas DJ, Marin W, Hollenbach J, Mack SJ. Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): An integrated case-control analysis pipeline. Hum Immunol. 2016 Mar; 77(3):283-287. PMID: 26708359; PMCID: PMC4828284 [Available on 03/01/17].
    9. Milius RP, Heuer M, George M, Pollack J, Hollenbach J, Mack SJ, Maiers M. The GL service: Web service to exchange GL string encoded HLA & KIR genotypes with complete and accurate allele and genotype ambiguity. Hum Immunol. 2016 Mar; 77(3):249-56. PMID: 26621609; PMCID: PMC4828303 [Available on 03/01/17].
    10. Traherne JA, Jiang W, Valdes AM, Hollenbach J, Jayaraman J, Lane JA, Johnson C, Trowsdale J, Noble JA. KIR haplotypes are associated with late-onset type 1 diabetes in European-American families. Genes Immun. 2016 Jan-Feb; 17(1):8-12. PMID: 26492518; PMCID: PMC4746488.
    11. Mack SJ, Milius RP, Gifford BD, Sauter J, Hofmann J, Osoegawa K, Robinson J, Groeneweg M, Turenchalk GS, Adai A, Holcomb C, Rozemuller EH, Penning MT, Heuer ML, Wang C, Salit ML, Schmidt AH, Parham PR, Müller C, Hague T, Fischer G, Fernandez-Vina M, Hollenbach J, Norman PJ, Maiers M. Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing. Hum Immunol. 2015 Dec; 76(12):954-62. PMID: 26407912; PMCID: PMC4674382 [Available on 12/01/16].
    12. Milius RP, Heuer M, Valiga D, Doroschak KJ, Kennedy CJ, Bolon YT, Schneider J, Pollack J, Kim HR, Cereb N, Hollenbach J, Mack SJ, Maiers M. Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping. Hum Immunol. 2015 Dec; 76(12):963-74. PMID: 26319908; PMCID: PMC4674307 [Available on 12/01/16].
    13. Hilton HG, Norman PJ, Nemat-Gorgani N, Goyos A, Hollenbach JA, Henn BM, Gignoux CR, Guethlein LA, Parham P. Loss and Gain of Natural Killer Cell Receptor Function in an African Hunter-Gatherer Population. PLoS Genet. 2015 Aug; 11(8):e1005439. PMID: 26292085; PMCID: PMC4546388.
    14. Hollenbach JA, Saperstein A, Albrecht M, Vierra-Green C, Parham P, Norman PJ, Maiers M. Race, Ethnicity and Ancestry in Unrelated Transplant Matching for the National Marrow Donor Program: A Comparison of Multiple Forms of Self-Identification with Genetics. PLoS One. 2015; 10(8):e0135960. PMID: 26287376; PMCID: PMC4545604.
    15. Norman PJ, Norberg SJ, Nemat-Gorgani N, Royce T, Hollenbach JA, Shults Won M, Guethlein LA, Gunderson KL, Ronaghi M, Parham P. Very long haplotype tracts characterized at high resolution from HLA homozygous cell lines. Immunogenetics. 2015 Sep; 67(9):479-85. PMID: 26198775; PMCID: PMC4540692.
    16. Hollenbach J, Oksenberg JR. The immunogenetics of multiple sclerosis: A comprehensive review. J Autoimmun. 2015 Nov; 64:13-25. PMID: 26142251; PMCID: PMC4687745 [Available on 11/01/16].
    17. Pappas D, Hollenbach J, Coleman AL, Gorin MB, Yu F, Williams K, Noble J, Tranah GJ. HLA class II genotypes are not associated with age related macular degeneration in a case-control, population-based study. Hum Immunol. 2015 Mar; 76(2-3):142-5. PMID: 25665771; PMCID: PMC4476503.
    18. Augusto DG, Hollenbach JA, Petzl-Erler ML. A deep look at KIR-HLA in Amerindians: comprehensive meta-analysis reveals limited diversity of KIR haplotypes. Hum Immunol. 2015 Apr; 76(4):272-80. PMID: 25636566.
      View in: PubMed
    19. Nemat-Gorgani N, Edinur HA, Hollenbach JA, Traherne JA, Dunn PP, Chambers GK, Parham P, Norman PJ. KIR diversity in Maori and Polynesians: populations in which HLA-B is not a significant KIR ligand. Immunogenetics. 2014 Nov; 66(11):597-611. PMID: 25139336; PMCID: PMC4198482.
    20. Madbouly A, Gragert L, Freeman J, Leahy N, Gourraud PA, Hollenbach JA, Kamoun M, Fernandez-Vina M, Maiers M. Validation of statistical imputation of allele-level multilocus phased genotypes from ambiguous HLA assignments. Tissue Antigens. 2014 Sep; 84(3):285-92. PMID: 25040134.
      View in: PubMed
    21. Norman PJ, Hollenbach JA, Nemat-Gorgani N, Guethlein LA, Hilton HG, Pando MJ, Koram KA, Riley EM, Abi-Rached L, Parham P. Co-evolution of human leukocyte antigen (HLA) class I ligands with killer-cell immunoglobulin-like receptors (KIR) in a genetically diverse population of sub-Saharan Africans. PLoS Genet. 2013 Oct; 9(10):e1003938. PMID: 24204327; PMCID: PMC3814319.
    22. Milius RP, Mack SJ, Hollenbach JA, Pollack J, Heuer ML, Gragert L, Spellman S, Guethlein LA, Trachtenberg EA, Cooley S, Bochtler W, Mueller CR, Robinson J, Marsh SG, Maiers M. Genotype List String: a grammar for describing HLA and KIR genotyping results in a text string. Tissue Antigens. 2013 Aug; 82(2):106-12. PMID: 23849068; PMCID: PMC3715123.
    23. Mack SJ, Cano P, Hollenbach JA, He J, Hurley CK, Middleton D, Moraes ME, Pereira SE, Kempenich JH, Reed EF, Setterholm M, Smith AG, Tilanus MG, Torres M, Varney MD, Voorter CE, Fischer GF, Fleischhauer K, Goodridge D, Klitz W, Little AM, Maiers M, Marsh SG, Müller CR, Noreen H, Rozemuller EH, Sanchez-Mazas A, Senitzer D, Trachtenberg E, Fernandez-Vina M. Common and well-documented HLA alleles: 2012 update to the CWD catalogue. Tissue Antigens. 2013 Apr; 81(4):194-203. PMID: 23510415; PMCID: PMC3634360.
    24. Hollenbach JA, Augusto DG, Alaez C, Bubnova L, Fae I, Fischer G, Gonzalez-Galarza FF, Gorodezky C, Karabon L, Kusnierczyk P, Noble J, Rickards O, Roberts C, Schaffer M, Shi L, Tavoularis S, Trachtenberg E, Yao Y, Middleton D. 16(th) IHIW: population global distribution of killer immunoglobulin-like receptor (KIR) and ligands. Int J Immunogenet. 2013 Feb; 40(1):39-45. PMID: 23280119; PMCID: PMC3789603.
    25. Hollenbach JA, Holcomb C, Hurley CK, Mabdouly A, Maiers M, Noble JA, Robinson J, Schmidt AH, Shi L, Turner V, Yao Y, Mack SJ. 16(th) IHIW: immunogenomic data-management methods. report from the immunogenomic data analysis working group (IDAWG). Int J Immunogenet. 2013 Feb; 40(1):46-53. PMID: 23280068; PMCID: PMC3789600.
    26. Gonzalez-Galarza FF, Mack SJ, Hollenbach J, Fernandez-Vina M, Setterholm M, Kempenich J, Marsh SG, Jones AR, Middleton D. 16(th) IHIW: extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles. Int J Immunogenet. 2013 Feb; 40(1):60-5. PMID: 23198982.
      View in: PubMed
    27. Vierra-Green C, Roe D, Hou L, Hurley CK, Rajalingam R, Reed E, Lebedeva T, Yu N, Stewart M, Noreen H, Hollenbach JA, Guethlein LA, Wang T, Spellman S, Maiers M. Allele-level haplotype frequencies and pairwise linkage disequilibrium for 14 KIR loci in 506 European-American individuals. PLoS One. 2012; 7(11):e47491. PMID: 23139747; PMCID: PMC3489906.
    28. Hollenbach JA, Nocedal I, Ladner MB, Single RM, Trachtenberg EA. Killer cell immunoglobulin-like receptor (KIR) gene content variation in the HGDP-CEPH populations. Immunogenetics. 2012 Oct; 64(10):719-37. PMID: 22752190; PMCID: PMC3438391.
    29. Hollenbach JA, Madbouly A, Gragert L, Vierra-Green C, Flesch S, Spellman S, Begovich A, Noreen H, Trachtenberg E, Williams T, Yu N, Shaw B, Fleischhauer K, Fernandez-Vina M, Maiers M. A combined DPA1~DPB1 amino acid epitope is the primary unit of selection on the HLA-DP heterodimer. Immunogenetics. 2012 Aug; 64(8):559-69. PMID: 22526601; PMCID: PMC3395342.
    30. Fernandez Vina MA, Hollenbach JA, Lyke KE, Sztein MB, Maiers M, Klitz W, Cano P, Mack S, Single R, Brautbar C, Israel S, Raimondi E, Khoriaty E, Inati A, Andreani M, Testi M, Moraes ME, Thomson G, Stastny P, Cao K. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations. Philos Trans R Soc Lond B Biol Sci. 2012 Mar 19; 367(1590):820-9. PMID: 22312049; PMCID: PMC3267126.
    31. Gourraud PA, Hollenbach JA, Barnetche T, Single RM, Mack SJ. Standard methods for the management of immunogenetic data. Methods Mol Biol. 2012; 882:197-213. PMID: 22665236; PMCID: PMC4209945.
    32. Mack SJ, Gourraud PA, Single RM, Thomson G, Hollenbach JA. Analytical methods for immunogenetic population data. Methods Mol Biol. 2012; 882:215-44. PMID: 22665237; PMCID: PMC4209087.
    33. Hollenbach JA, Mack SJ, Thomson G, Gourraud PA. Analytical methods for disease association studies with immunogenetic data. Methods Mol Biol. 2012; 882:245-66. PMID: 22665238; PMCID: PMC4209949.
    34. Hollenbach JA, Mack SJ, Gourraud PA, Single RM, Maiers M, Middleton D, Thomson G, Marsh SG, Varney MD. A community standard for immunogenomic data reporting and analysis: proposal for a STrengthening the REporting of Immunogenomic Studies statement. Tissue Antigens. 2011 Nov; 78(5):333-44. PMID: 21988720; PMCID: PMC3636772.
    35. Sanchez-Mazas A, Fernandez-Viña M, Middleton D, Hollenbach JA, Buhler S, Di D, Rajalingam R, Dugoujon JM, Mack SJ, Thorsby E. Immunogenetics as a tool in anthropological studies. Immunology. 2011 Jun; 133(2):143-64. PMID: 21480890; PMCID: PMC3088978.
    36. Lyke KE, Fernández-Vina MA, Cao K, Hollenbach J, Coulibaly D, Kone AK, Guindo A, Burdett LA, Hartzman RJ, Wahl AR, Hildebrand WH, Doumbo OK, Plowe CV, Sztein MB. Association of HLA alleles with Plasmodium falciparum severity in Malian children. Tissue Antigens. 2011 Jun; 77(6):562-71. PMID: 21447146; PMCID: PMC3152196.
    37. Hollenbach JA, Thompson SD, Bugawan TL, Ryan M, Sudman M, Marion M, Langefeld CD, Thomson G, Erlich HA, Glass DN. Juvenile idiopathic arthritis and HLA class I and class II interactions and age-at-onset effects. Arthritis Rheum. 2010 Jun; 62(6):1781-91. PMID: 20191588; PMCID: PMC2917207.
    38. Mack SJ, Hollenbach JA. Allele Name Translation Tool and Update NomenCLature: software tools for the automated translation of HLA allele names between successive nomenclatures. Tissue Antigens. 2010 May; 75(5):457-61. PMID: 20412076; PMCID: PMC2966768.
    39. Hollenbach JA, Meenagh A, Sleator C, Alaez C, Bengoche M, Canossi A, Contreras G, Creary L, Evseeva I, Gorodezky C, Hardie RA, Karlsen TH, Lie B, Luo M, Martinetti M, Navarette C, de Oliveira DC, Ozzella G, Pasi A, Pavlova E, Pinto S, Porto LC, Santos P, Slavcev A, Srinak D, Tavoularis S, Tonks S, Trachtenberg E, Vejbaesya S, Middleton D. Report from the killer immunoglobulin-like receptor (KIR) anthropology component of the 15th International Histocompatibility Workshop: worldwide variation in the KIR loci and further evidence for the co-evolution of KIR and HLA. Tissue Antigens. 2010 Jul; 76(1):9-17. PMID: 20331834.
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    40. Thomson G, Marthandan N, Hollenbach JA, Mack SJ, Erlich HA, Single RM, Waller MJ, Marsh SG, Guidry PA, Karp DR, Scheuermann RH, Thompson SD, Glass DN, Helmberg W. Sequence feature variant type (SFVT) analysis of the HLA genetic association in juvenile idiopathic arthritis. Pac Symp Biocomput. 2010; 359-70. PMID: 19908388; PMCID: PMC2958177.
    41. Hollenbach JA, Ladner MB, Saeteurn K, Taylor KD, Mei L, Haritunians T, McGovern DP, Erlich HA, Rotter JI, Trachtenberg EA. Susceptibility to Crohn's disease is mediated by KIR2DL2/KIR2DL3 heterozygosity and the HLA-C ligand. Immunogenetics. 2009 Oct; 61(10):663-71. PMID: 19789864; PMCID: PMC2813946.
    42. Trachtenberg E, Vinson M, Hayes E, Hsu YM, Houtchens K, Erlich H, Klitz W, Hsia Y, Hollenbach J. HLA class I (A, B, C) and class II (DRB1, DQA1, DQB1, DPB1) alleles and haplotypes in the Han from southern China. Tissue Antigens. 2007 Dec; 70(6):455-63. PMID: 17900288.
      View in: PubMed
    43. Single RM, Meyer D, Hollenbach JA, Nelson MP, Noble JA, Erlich HA, Thomson G. Haplotype frequency estimation in patient populations: the effect of departures from Hardy-Weinberg proportions and collapsing over a locus in the HLA region. Genet Epidemiol. 2002 Feb; 22(2):186-95. PMID: 11788963.
      View in: PubMed
    44. Cao K, Hollenbach J, Shi X, Shi W, Chopek M, Fernández-Viña MA. Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations. Hum Immunol. 2001 Sep; 62(9):1009-30. PMID: 11543903.
      View in: PubMed
    45. Begovich AB, Moonsamy PV, Mack SJ, Barcellos LF, Steiner LL, Grams S, Suraj-Baker V, Hollenbach J, Trachtenberg E, Louie L, Zimmerman P, Hill AV, Stoneking M, Sasazuki T, Konenkov VI, Sartakova ML, Titanji VP, Rickards O, Klitz W. Genetic variability and linkage disequilibrium within the HLA-DP region: analysis of 15 different populations. Tissue Antigens. 2001 May; 57(5):424-39. PMID: 11556967.
      View in: PubMed
    46. Hollenbach JA, Thomson G, Cao K, Fernandez-Vina M, Erlich HA, Bugawan TL, Winkler C, Winter M, Klitz W. HLA diversity, differentiation, and haplotype evolution in Mesoamerican Natives. Hum Immunol. 2001 Apr; 62(4):378-90. PMID: 11295471.
      View in: PubMed
    47. Chen JJ, Hollenbach JA, Trachtenberg EA, Just JJ, Carrington M, Rønningen KS, Begovich A, King MC, McWeeney S, Mack SJ, Erlich HA, Thomson G. Hardy-Weinberg testing for HLA class II (DRB1, DQA1, DQB1, and DPB1) loci in 26 human ethnic groups. Tissue Antigens. 1999 Dec; 54(6):533-42. PMID: 10674966.
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