Stephen Francis, PhD, MS

Title(s)Associate Professor, Neurological Surgery
SchoolSchool of Medicine
Address1450 Third St, #483
San Francisco CA 94158
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    Other Positions
    Title(s)UCSF Weill Institute for Neurosciences


    Collapse Biography 
    Collapse Education and Training
    University of California, Berkeley PhD2014Epidemiology
    Collapse Awards and Honors
    UCSF2016Cancer Center Impact Award
    Young Investigator Award2014Brain Tumor Epidemiology Assoc

    Collapse Overview 
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    Collapse Research 
    Collapse Research Activities and Funding
    Discovering Infection-mediated Pathways of Glioma Etiology and Prognosis by Leveraging Multiplex Serology and Immunogenomics
    NATIONAL CANCER INSTITUTE 1R01CA266676Sep 1, 2022 - Aug 31, 2026
    Role: Principle Investigator
    Description: Glioma has been associated with a number of infections. We will examine antigen reactivity to all infections previously linked with glioma to assess the risk and survival associated with each of these infections and groups of co-infections. We will then sequence an area of the genome that controls immune response to determine which genetic alterations interact with infections, and how infections and genetics together alter risk and survival of glioma.
    HKLE-seq: an enrichment method for unbiased amplification and next-generation sequencing of all HERV-K and SVA (HKLE) insertion breakpoints genome-wide in human DNA samples
    NIH/NIGMS R15GM126562Feb 1, 2018 - Jan 31, 2021
    Role: Principal Investigator

    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. Pediatric brain tumors: Origins, epidemiology, and classification - The 2022 Brain Tumor Epidemiology Consortium meeting report. Clin Neuropathol. 2023 Mar-Apr; 42(2):74-80. Johnson KJ, Bauchet L, Francis SS, Hainfellner JA, Kruchko C, Lau CC, Ostrom QT, Scheurer ME, Yuan Y. PMID: 36633374.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    2. Antibodies to varicella-zoster virus and three other herpesviruses and survival in adults with glioma. Neuro Oncol. 2023 Jan 04. Guerra G, McCoy L, Hansen HM, Rice T, Molinaro AM, Wiemels JL, Wiemels JL, Wiencke JK, Wrensch M, Francis SS. PMID: 36610073.
      View in: PubMed   Mentions:    Fields:    
    3. Accurate Identification of Mucinous Pancreatic Cystic Lesions Using Small-Volume Analytes. J Surg Res. 2023 04; 284:322-331. Caiazza F, Conroy PC, Ivry SL, York T, Lin J, Hernandez S, Hoffmann TJ, Francis SS, Park WG, Yip-Schneider MT, Schmidt CM, Brand R, Craik CS, Kirkwood K. PMID: 36369049.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    4. Pre-surgery immune profiles of adult glioma patients. J Neurooncol. 2022 Aug; 159(1):103-115. Bracci PM, Rice T, Hansen HM, Francis SS, Lee S, McCoy LS, Shrestha PP, Warrier G, Clarke JL, Molinaro AM, Taylor JW, Wiencke JK, Wrensch MR. PMID: 35716311; PMCID: PMC9325836.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    5. The immunogenetics of viral antigen response is associated with subtype-specific glioma risk and survival. Am J Hum Genet. 2022 06 02; 109(6):1105-1116. Guerra G, Kachuri L, Wendt G, Hansen HM, Mack SJ, Molinaro AM, Rice T, Bracci P, Wiencke JK, Kasahara N, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS. PMID: 35550063; PMCID: PMC9247888.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. Clinical characteristics of cytomegalovirus-positive pediatric acute lymphoblastic leukemia at diagnosis. Am J Hematol. 2022 06 01; 97(6):E198-E201. Gallant RE, Arroyo K, Bracci PM, Li S, Metayer C, Kogan SC, Wendt GA, Francis SS, de Smith AJ, Wiemels JL, Wiemels JL. PMID: 35285969.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    7. The Epidemiology of Central Nervous System Tumors. Hematol Oncol Clin North Am. 2022 02; 36(1):23-42. Francis SS, Ostrom QT, Cote DJ, Smith TR, Claus E, Barnholtz-Sloan JS. PMID: 34801162.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    8. Epidemiology of Brain and Other CNS Tumors. Curr Neurol Neurosci Rep. 2021 11 24; 21(12):68. Ostrom QT, Francis SS, Barnholtz-Sloan JS. PMID: 34817716; PMCID: PMC8613072.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    9. Publisher Correction: Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response. Sci Rep. 2021 Sep 15; 11(1):18728. Liu R, Wu P, Ogrodzki P, Mahmoud S, Liang K, Liu P, Francis SS, Khalak H, Liu D, Li J, Ma T, Chen F, Liu W, Huang X, He W, Yuan Z, Qiao N, Meng X, Alqarni B, Quilez J, Kusuma V, Lin L, Jin X, Yang C, Anton X, Koshy A, Yang H, Xu X, Wang J, Xiao P, Al Kaabi N, Fasihuddin MS, Selvaraj FA, Weber S, Al Hosani FI, Liu S, Zaher WA. PMID: 34526633; PMCID: PMC8441957.
      View in: PubMed   Mentions:    Fields:    
    10. Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response. Sci Rep. 2021 07 07; 11(1):13971. Liu R, Wu P, Ogrodzki P, Mahmoud S, Liang K, Liu P, Francis SS, Khalak H, Liu D, Li J, Ma T, Chen F, Liu W, Huang X, He W, Yuan Z, Qiao N, Meng X, Alqarni B, Quilez J, Kusuma V, Lin L, Jin X, Yang C, Anton X, Koshy A, Yang H, Xu X, Wang J, Xiao P, Al Kaabi N, Fasihuddin MS, Selvaraj FA, Weber S, Al Hosani FI, Liu S, Zaher WA. PMID: 34234167; PMCID: PMC8263779.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    11. Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C. Neuro Oncol. 2020 11 26; 22(11):1602-1613. Eckel-Passow JE, Drucker KL, Kollmeyer TM, Kosel ML, Decker PA, Molinaro AM, Rice T, Praska CE, Clark L, Caron A, Abyzov A, Batzler A, Song JS, Pekmezci M, Hansen HM, McCoy LS, Bracci PM, Wiemels J, Wiemels J, Wiencke JK, Francis S, Burns TC, Giannini C, Lachance DH, Wrensch M, Jenkins RB. PMID: 32386320; PMCID: PMC7690366.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    12. Socioeconomic status and childhood central nervous system tumors in California. Cancer Causes Control. 2021 Jan; 32(1):27-39. Francis SS, Wang R, Enders C, Prado I, Wiemels JL, Wiemels JL, Ma X, Metayer C. PMID: 33113073.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    13. The landscape of host genetic factors involved in immune response to common viral infections. Genome Med. 2020 10 27; 12(1):93. Kachuri L, Francis SS, Morrison ML, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. PMID: 33109261; PMCID: PMC7590248.
      View in: PubMed   Mentions: 36     Fields:    Translation:Humans
    14. The landscape of host genetic factors involved in immune response to common viral infections. medRxiv. 2020 Sep 05. Kachuri L, Francis SS, Morrison M, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. PMID: 32511533; PMCID: PMC7273301.
      View in: PubMed   Mentions:
    15. Pediatric glioma and medulloblastoma risk and population demographics: a Poisson regression analysis. Neurooncol Adv. 2020 Jan-Dec; 2(1):vdaa089. Muskens IS, Feng Q, Francis SS, Walsh KM, Mckean-Cowdin R, Gauderman WJ, de Smith AJ, Wiemels JL, Wiemels JL. PMID: 32864610; PMCID: PMC7447139.
      View in: PubMed   Mentions: 2  
    16. ClustR: A Space-Time Cluster Analysis R Package for Individual-level Data. Epidemiology. 2020 03; 31(2):224-228. Enders C, Hyde RJ, Selvin S, Metayer C, Francis SS. PMID: 31596789.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansPHPublic Health
    17. Spatial-Temporal Cluster Analysis of Childhood Cancer in California. Epidemiology. 2020 03; 31(2):214-223. Francis SS, Enders C, Hyde R, Gao X, Wang R, Ma X, Wiemels JL, Wiemels JL, Selvin S, Metayer C. PMID: 31596791; PMCID: PMC9005107.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansPHPublic Health
    18. Maternal Infection in Pregnancy and Childhood Leukemia: A Systematic Review and Meta-analysis. J Pediatr. 2020 02; 217:98-109.e8. He JR, Ramakrishnan R, Hirst JE, Bonaventure A, Francis SS, Paltiel O, Håberg SE, Lemeshow S, Olsen S, Tikellis G, Magnus P, Murphy MFG, Wiemels JL, Wiemels JL, Linet MS, Dwyer T. PMID: 31810630; PMCID: PMC7605597.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    19. Heritable variation at the chromosome 21 gene ERG is associated with acute lymphoblastic leukemia risk in children with and without Down syndrome. Leukemia. 2019 11; 33(11):2746-2751. de Smith AJ, Walsh KM, Morimoto LM, Francis SS, Hansen HM, Jeon S, Gonseth S, Chen M, Sun H, Luna-Fineman S, Antillón F, Girón V, Kang AY, Smirnov I, Shao X, Whitehead TP, Barcellos LF, Jolly KW, Healy J, Laverdière C, Sinnett D, Taub JW, Birch JM, Thompson PD, Pombo-de-Oliveira MS, Spector LG, DeWan AT, Mueller BA, Chiang C, Metayer C, Ma X, Wiemels JL, Wiemels JL. PMID: 31296947; PMCID: PMC6858994.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    20. Early Infection with Cytomegalovirus and Risk of Childhood Hematologic Malignancies. Cancer Epidemiol Biomarkers Prev. 2019 06; 28(6):1024-1027. Wiemels JL, Wiemels JL, Talbäck M, Francis S, Feychting M. PMID: 30996022; PMCID: PMC7731595.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    21. The Authors Respond. Epidemiology. 2019 01; 30(1):e2-e3. Francis SS, Shaw GM. PMID: 30299403.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    22. Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. Cell. 2018 10 04; 175(2):347-359.e14. Liu S, Huang S, Chen F, Zhao L, Yuan Y, Francis SS, Fang L, Li Z, Lin L, Liu R, Zhang Y, Xu H, Li S, Zhou Y, Davies RW, Liu Q, Walters RG, Lin K, Ju J, Korneliussen T, Yang MA, Fu Q, Wang J, Zhou L, Krogh A, Zhang H, Wang W, Chen Z, Cai Z, Yin Y, Yang H, Mao M, Shendure J, Wang J, Albrechtsen A, Jin X, Nielsen R, Xu X. PMID: 30290141.
      View in: PubMed   Mentions: 74     Fields:    Translation:Humans
    23. BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia. Int J Cancer. 2018 12 01; 143(11):2647-2658. de Smith AJ, Walsh KM, Francis SS, Zhang C, Hansen HM, Smirnov I, Morimoto L, Whitehead TP, Kang A, Shao X, Barcellos LF, McKean-Cowdin R, Zhang L, Fu C, Wang R, Yu H, Hoh J, Dewan AT, Metayer C, Ma X, Wiemels JL, Wiemels JL. PMID: 29923177; PMCID: PMC6235695.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    24. To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes. Front Genet. 2018; 9:298. Wallace AD, Wendt GA, Barcellos LF, de Smith AJ, Walsh KM, Metayer C, Costello JF, Wiemels JL, Wiemels JL, Francis SS. PMID: 30154825; PMCID: PMC6102640.
      View in: PubMed   Mentions: 17  
    25. Allergies and Childhood Acute Lymphoblastic Leukemia: A Case-Control Study and Meta-analysis. Cancer Epidemiol Biomarkers Prev. 2018 10; 27(10):1142-1150. Wallace AD, Francis SS, Ma X, McKean-Cowdin R, Selvin S, Whitehead TP, Barcellos LF, Kang AY, Morimoto L, Moore TB, Wiemels JL, Wiemels JL, Metayer C. PMID: 30068517; PMCID: PMC6628274.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    26. Herpesvirus Infection in Infants with Gastroschisis. Epidemiology. 2018 07; 29(4):571-573. Francis SS, Wiemels JL, Wiemels JL, Yang W, Shaw GM. PMID: 29634591.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCellsPHPublic Health
    27. GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21. Nat Commun. 2018 01 18; 9(1):286. Wiemels JL, Wiemels JL, Walsh KM, de Smith AJ, Metayer C, Gonseth S, Hansen HM, Francis SS, Ojha J, Smirnov I, Barcellos L, Xiao X, Morimoto L, McKean-Cowdin R, Wang R, Yu H, Hoh J, DeWan AT, Ma X. PMID: 29348612; PMCID: PMC5773513.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    28. A germ-line deletion of APOBEC3B does not contribute to subtype-specific childhood acute lymphoblastic leukemia etiology. Haematologica. 2018 01; 103(1):e29-e31. Wallace AD, Francis SS, Shao X, de Smith AJ, Walsh KM, Mckean-Cowdin R, Ma X, Dahl G, Barcellos LF, Wiemels JL, Wiemels JL, Metayer C. PMID: 29025908; PMCID: PMC5777211.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    29. Cesarean Section and Risk of Childhood Acute Lymphoblastic Leukemia in a Population-Based, Record-Linkage Study in California. Am J Epidemiol. 2017 01 15; 185(2):96-105. Wang R, Wiemels JL, Wiemels JL, Metayer C, Morimoto L, Francis SS, Kadan-Lottick N, DeWan AT, Zhang Y, Ma X. PMID: 27986703; PMCID: PMC5253971.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    30. In utero cytomegalovirus infection and development of childhood acute lymphoblastic leukemia. Blood. 2017 03 23; 129(12):1680-1684. Francis SS, Wallace AD, Wendt GA, Li L, Liu F, Riley LW, Kogan S, Walsh KM, de Smith AJ, Dahl GV, Ma X, Delwart E, Metayer C, Wiemels JL, Wiemels JL. PMID: 27979823; PMCID: PMC5364339.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansPHPublic Health
    31. Clonal and microclonal mutational heterogeneity in high hyperdiploid acute lymphoblastic leukemia. Oncotarget. 2016 Nov 08; 7(45):72733-72745. de Smith AJ, Ojha J, Francis SS, Sanders E, Endicott AA, Hansen HM, Smirnov I, Termuhlen AM, Walsh KM, Metayer C, Wiemels JL, Wiemels JL. PMID: 27683039; PMCID: PMC5341940.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    32. Genotyping Oral Commensal Bacteria to Predict Social Contact and Structure. PLoS One. 2016; 11(9):e0160201. Francis SS, Plucinski MM, Wallace AD, Riley LW. PMID: 27684062; PMCID: PMC5042546.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    33. Common genetic variants associated with telomere length confer risk for neuroblastoma and other childhood cancers. Carcinogenesis. 2016 06; 37(6):576-582. Walsh KM, Whitehead TP, de Smith AJ, Smirnov IV, Park M, Endicott AA, Francis SS, Codd V, ENGAGE Consortium Telomere Group, Samani NJ, Metayer C, Wiemels JL, Wiemels JL. PMID: 27207662; PMCID: PMC4876988.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCells
    34. Caesarean delivery and risk of childhood leukaemia: a pooled analysis from the Childhood Leukemia International Consortium (CLIC). Lancet Haematol. 2016 Apr; 3(4):e176-85. Marcotte EL, Thomopoulos TP, Infante-Rivard C, Clavel J, Petridou ET, Schüz J, Ezzat S, Dockerty JD, Metayer C, Magnani C, Scheurer ME, Mueller BA, Mora AM, Wesseling C, Skalkidou A, Rashed WM, Francis SS, Ajrouche R, Erdmann F, Orsi L, Spector LG. PMID: 27063976; PMCID: PMC5283076.
      View in: PubMed   Mentions: 42     Fields:    Translation:Humans
    35. Bacterial microbiome of breast milk and child saliva from low-income Mexican-American women and children. Pediatr Res. 2016 06; 79(6):846-54. Davé V, Street K, Francis S, Bradman A, Riley L, Eskenazi B, Holland N. PMID: 26756784; PMCID: PMC4899194.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCellsPHPublic Health
    36. Longer genotypically-estimated leukocyte telomere length is associated with increased adult glioma risk. Oncotarget. 2015 Dec 15; 6(40):42468-77. Walsh KM, Codd V, Rice T, Nelson CP, Smirnov IV, McCoy LS, Hansen HM, Elhauge E, Ojha J, Francis SS, Madsen NR, Bracci PM, Pico AR, Molinaro AM, Tihan T, Berger MS, Chang SM, Prados MD, Jenkins RB, Wiemels JL, Wiemels JL, ENGAGE Consortium Telomere Group, Samani NJ, Wiencke JK, Wrensch MR. PMID: 26646793; PMCID: PMC4767445.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansCells
    37. Understanding inherited genetic risk of adult glioma - a review. Neurooncol Pract. 2016 Mar; 3(1):10-16. Rice T, Lachance DH, Molinaro AM, Eckel-Passow JE, Walsh KM, Barnholtz-Sloan J, Ostrom QT, Francis SS, Wiemels J, Wiemels J, Jenkins RB, Wiencke JK, Wrensch MR. PMID: 26941959; PMCID: PMC4774334.
      View in: PubMed   Mentions: 39  
    38. A real-time PCR signature to discriminate between tuberculosis and other pulmonary diseases. Tuberculosis (Edinb). 2015 Jul; 95(4):421-5. Laux da Costa L, Delcroix M, Dalla Costa ER, Prestes IV, Milano M, Francis SS, Unis G, Silva DR, Riley LW, Rossetti ML. PMID: 26025597; PMCID: PMC4475479.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    39. Metagenomic epidemiology: a new frontier. J Epidemiol Community Health. 2015 Apr; 69(4):306-8. Francis SS, Riley LW. PMID: 25248921.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    40. Mode of delivery and risk of childhood leukemia. Cancer Epidemiol Biomarkers Prev. 2014 May; 23(5):876-81. Francis SS, Selvin S, Metayer C, Wallace AD, Crouse V, Moore TB, Wiemels JL, Wiemels JL, Buffler PA. PMID: 24618997.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    41. A hierarchy of signals regulates entry of membrane proteins into the ciliary membrane domain in epithelial cells. J Cell Biol. 2011 Apr 04; 193(1):219-33. Francis SS, Sfakianos J, Lo B, Mellman I. PMID: 21444686; PMCID: PMC3082196.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansAnimalsCells
    42. Unusual space-time patterning of the Fallon, Nevada leukemia cluster: Evidence of an infectious etiology. Chem Biol Interact. 2012 Apr 05; 196(3):102-9. Francis SS, Selvin S, Yang W, Buffler PA, Wiemels JL, Wiemels JL. PMID: 21352818; PMCID: PMC3839794.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    43. Intermittent target inhibition with dasatinib 100 mg once daily preserves efficacy and improves tolerability in imatinib-resistant and -intolerant chronic-phase chronic myeloid leukemia. J Clin Oncol. 2008 Jul 01; 26(19):3204-12. Shah NP, Kantarjian HM, Kim DW, Réa D, Dorlhiac-Llacer PE, Milone JH, Vela-Ojeda J, Silver RT, Khoury HJ, Charbonnier A, Khoroshko N, Paquette RL, Deininger M, Collins RH, Otero I, Hughes T, Bleickardt E, Strauss L, Francis S, Hochhaus A. PMID: 18541900.
      View in: PubMed   Mentions: 165     Fields:    Translation:HumansCTClinical Trials
    44. Recycling endosomes can serve as intermediates during transport from the Golgi to the plasma membrane of MDCK cells. J Cell Biol. 2004 Nov 08; 167(3):531-43. Ang AL, Taguchi T, Francis S, Fölsch H, Murrells LJ, Pypaert M, Warren G, Mellman I. PMID: 15534004; PMCID: PMC2172492.
      View in: PubMed   Mentions: 192     Fields:    Translation:AnimalsCells
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