Stephen Francis, PhD, MS
Associate Professor
Neurological Surgery
School of Medicine

Awards

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• Cancer Center Impact Award, UCSF, 2016
• Brain Tumor Epidemiology Assoc, Young Investigator Award, 2014

Education & Training

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• PhD Epidemiology University of California, Berkeley 2014

Websites

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• Francis Lab (francislab.ucsf.edu)

Grants and Projects

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• Discovering Infection-mediated Pathways of Glioma Etiology and Prognosis by Leveraging Multiplex Serology and Immunogenomics, NATIONAL CANCER INSTITUTE, 2022-2026
• 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, 2018-2021

Publications (68)

Top publication keywords:
Cytomegalovirus InfectionsGastroschisisEpidemiologic MethodsCentral Nervous System NeoplasmsHerpesvirus 3, HumanEpstein-Barr Virus InfectionsImmunoglobulin EAntineoplastic Agents, AlkylatingViridans StreptococciGliomaGerm-Line MutationBrain NeoplasmsPrecursor Cell Lymphoblastic Leukemia-LymphomaHerpesviridae InfectionsSpace-Time Clustering

• Dissecting the biology of gliomagenesis: Evaluating the interaction between IDH tumor mutation and germline variants.
  Neuro-oncology advances 2025 Kosel ML, Decker PA, Kollmeyer TM, Drucker KL, Shurtz AK, Molinaro AM, Conte GM, Moassefi M, Erickson BJ, Wiencke JK, Francis S, Burns TC, Vaubel RA, Wrensch M, Lachance DH, Tobin WO, Jenkins RB, …
• Functional germline variants in DNA damage repair pathways are associated with altered survival in adults with glioma treated with temozolomide.
  Neuro-oncology 2025 Guerra G, Wendt G, McCoy L, Hansen HM, Kachuri L, Molinaro AM, Rice T, Guan V, Capistrano L, Hsieh A, Kalsi V, Sallee J, Taylor JW, Clarke JL, Almaraz ER, Wiencke JK, Eckel-Passow JE, Jenkins RB, …
• Integration of MRI radiomics and germline genetics to predict the IDH mutation status of gliomas.
  NPJ precision oncology 2025 Nakase T, Henderson GA, Barba T, Bareja R, Guerra G, Zhao Q, Francis SS, Gevaert O, Kachuri L
• Association of immunoglobulin E levels with glioma risk and survival.
  Journal of the National Cancer Institute 2025 Guerra G, Nakase T, Kachuri L, McCoy L, Hansen HM, Rice T, Wiemels JL, Wiencke JK, Molinaro AM, Wrensch M, Francis SS
• Response to Lehrer and Rheinstein and to Alexiou, Zagorianakou, and Voulgaris.
  Journal of the National Cancer Institute 2025 Francis SS, Guerra G

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• Genome-Wide Association Analyses of HPV16 and HPV18 Seropositivity Identify Susceptibility Loci for Cervical Cancer.
  Journal of medical virology 2025 Beckhaus T, Kachuri L, Nakase T, Schürmann P, Eisenblätter R, Geerts M, Böhmer G, Strauß HG, Hirchenhain C, Schmidmayr M, Müller F, Fasching PA, Häfner N, Luyten A, Jentschke M, Hillemanns P, O'Mara …
• Longitudinal profiling of IDH-mutant astrocytomas reveals acquired RAS-MAPK pathway mutations associated with inferior survival.
  Neuro-oncology advances 2025 Rodriguez Almaraz E, Guerra GA, Al-Adli NN, Young JS, Dada A, Quintana D, Taylor JW, Oberheim Bush NA, Clarke JL, Butowski NA, de Groot J, Pekmezci M, Perry A, Bollen AW, Scheffler AW, Glidden DV, …
• Genetic predisposition to altered blood cell homeostasis is associated with glioma risk and survival.
  Nature communications 2025 Kachuri L, Guerra GA, Nakase T, Wendt GA, Hansen HM, Molinaro AM, Bracci P, McCoy L, Rice T, Wiencke JK, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS
• Functional germline variants in DNA damage repair pathways are associated with altered survival in adults with glioma treated with temozolomide.
  medRxiv : the preprint server for health sciences 2024 Guerra G, Wendt G, McCoy L, Hansen HM, Kachuri L, Molinaro AM, Rice T, Guan V, Capistrano L, Hsieh A, Kalsi V, Sallee J, Taylor JW, Clarke JL, Rodriguez Almaraz E, Wiencke JK, Eckel-Passow JE, Jenkins…
• Genome-wide polygenic risk scores predict risk of glioma and molecular subtypes.
  Neuro-oncology 2024 Nakase T, Guerra GA, Ostrom QT, Ge T, Melin BS, Wrensch M, Wiencke JK, Jenkins RB, Eckel-Passow JE, Glioma International Case-Control Study (GICC), Bondy ML, Francis SS, Kachuri L
• Association of immunoglobulin E levels with glioma risk and survival.
  medRxiv : the preprint server for health sciences 2024 Guerra G, Nakase T, Kachuri L, McCoy L, Hansen HM, Rice T, Wiemels JL, Wiencke JK, Molinaro AM, Wrensch M, Francis SS
• Oligodendroglioma patient survival is associated with circulating B-cells and age.
  Neuro-oncology advances 2024 Taylor JW, Warrier G, Hansen HM, McCoy L, Rice T, Guerra G, Francis SS, Clarke JL, Bracci PM, Hadad S, Kelsey KT, Wrensch M, Molinaro AM, Wiencke JK
• Genome-wide Polygenic Risk Scores Predict Risk of Glioma and Molecular Subtypes.
  medRxiv : the preprint server for health sciences 2024 Nakase T, Guerra G, Ostrom QT, Ge T, Melin B, Wrensch M, Wiencke JK, Jenkins RB, Eckel-Passow JE, Glioma International Case-Control Study (GICC), Bondy ML, Francis SS, Kachuri L
• Genetic determinants of IgG antibody response to COVID-19 vaccination.
  American journal of human genetics 2024 Bian S, Guo X, Yang X, Wei Y, Yang Z, Cheng S, Yan J, Chen Y, Chen GB, Du X, Francis SS, Shu Y, Liu S
• Genetic predisposition to altered blood cell homeostasis is associated with glioma risk and survival.
  medRxiv : the preprint server for health sciences 2023 Kachuri L, Guerra GA, Wendt GA, Hansen HM, Molinaro AM, Bracci P, McCoy L, Rice T, Wiencke JK, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS
• Inherited polymorphisms in the Human Leukocyte Antigen Region modify the association between varicella-zoster virus antibody reactivity and glioma prognosis.
  Neuro-oncology 2023 Francis SS, Guerra G, Hansen HM, Wendt G, Kachuri L, Wiencke JK, Wrensch M
• Antibodies to varicella-zoster virus and three other herpesviruses and survival in adults with glioma.
  Neuro-oncology 2023 Guerra G, McCoy L, Hansen HM, Rice T, Molinaro AM, Wiemels JL, Wiencke JK, Wrensch M, Francis SS
• Nivolumab combined with brentuximab vedotin for relapsed/refractory mediastinal gray zone lymphoma.
  Blood 2023 Santoro A, Moskowitz AJ, Ferrari S, Carlo-Stella C, Lisano J, Francis S, Wen R, Akyol A, Savage KJ
• Nivolumab and brentuximab vedotin with or without bendamustine for R/R Hodgkin lymphoma in children, adolescents, and young adults.
  Blood 2023 Harker-Murray P, Mauz-Körholz C, Leblanc T, Mascarin M, Michel G, Cooper S, Beishuizen A, Leger KJ, Amoroso L, Buffardi S, Rigaud C, Hoppe BS, Lisano J, Francis S, Sacchi M, Cole PD, Drachtman RA, …
• Pediatric brain tumors: Origins, epidemiology, and classification - The 2022 Brain Tumor Epidemiology Consortium meeting report.
  Clinical neuropathology 2023 Johnson KJ, Bauchet L, Francis SS, Hainfellner JA, Kruchko C, Lau CC, Ostrom QT, Scheurer ME, Yuan Y
• Accurate Identification of Mucinous Pancreatic Cystic Lesions Using Small-Volume Analytes.
  The Journal of surgical research 2022 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
• Pre-surgery immune profiles of adult glioma patients.
  Journal of neuro-oncology 2022 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
• The immunogenetics of viral antigen response is associated with subtype-specific glioma risk and survival.
  American journal of human genetics 2022 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
• Clinical characteristics of cytomegalovirus-positive pediatric acute lymphoblastic leukemia at diagnosis.
  American journal of hematology 2022 Gallant RE, Arroyo K, Bracci PM, Li S, Metayer C, Kogan SC, Wendt GA, Francis SS, de Smith AJ, Wiemels JL
• The Epidemiology of Central Nervous System Tumors.
  Hematology/oncology clinics of North America 2022 Francis SS, Ostrom QT, Cote DJ, Smith TR, Claus E, Barnholtz-Sloan JS
• Epidemiology of Brain and Other CNS Tumors.
  Current neurology and neuroscience reports 2021 Ostrom QT, Francis SS, Barnholtz-Sloan JS
• 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.
  Scientific reports 2021 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, …
• Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response.
  Scientific reports 2021 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, …
• Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C.
  Neuro-oncology 2020 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, …
• Socioeconomic status and childhood central nervous system tumors in California.
  Cancer causes & control : CCC 2020 Francis SS, Wang R, Enders C, Prado I, Wiemels JL, Ma X, Metayer C
• The landscape of host genetic factors involved in immune response to common viral infections.
  Genome medicine 2020 Kachuri L, Francis SS, Morrison ML, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS
• The landscape of host genetic factors involved in immune response to common viral infections.
  medRxiv : the preprint server for health sciences 2020 Kachuri L, Francis SS, Morrison M, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS
• Pediatric glioma and medulloblastoma risk and population demographics: a Poisson regression analysis.
  Neuro-oncology advances 2020 Muskens IS, Feng Q, Francis SS, Walsh KM, Mckean-Cowdin R, Gauderman WJ, de Smith AJ, Wiemels JL
• ClustR: A Space-Time Cluster Analysis R Package for Individual-level Data.
  Epidemiology (Cambridge, Mass.) 2020 Enders C, Hyde RJ, Selvin S, Metayer C, Francis SS
• Spatial-Temporal Cluster Analysis of Childhood Cancer in California.
  Epidemiology (Cambridge, Mass.) 2020 Francis SS, Enders C, Hyde R, Gao X, Wang R, Ma X, Wiemels JL, Selvin S, Metayer C
• Maternal Infection in Pregnancy and Childhood Leukemia: A Systematic Review and Meta-analysis.
  The Journal of pediatrics 2019 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, Linet MS, Dwyer T
• Nivolumab Combined With Brentuximab Vedotin for Relapsed/Refractory Primary Mediastinal Large B-Cell Lymphoma: Efficacy and Safety From the Phase II CheckMate 436 Study.
  Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2019 Zinzani PL, Santoro A, Gritti G, Brice P, Barr PM, Kuruvilla J, Cunningham D, Kline J, Johnson NA, Mehta-Shah N, Manley T, Francis S, Sharma M, Moskowitz AJ
• Heritable variation at the chromosome 21 gene ERG is associated with acute lymphoblastic leukemia risk in children with and without Down syndrome.
  Leukemia 2019 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, …
• Early Infection with Cytomegalovirus and Risk of Childhood Hematologic Malignancies.
  Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2019 Wiemels JL, Talbäck M, Francis S, Feychting M
• The Authors Respond.
  Epidemiology (Cambridge, Mass.) 2019 Francis SS, Shaw GM
• Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History.
  Cell 2018 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, …
• BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia.
  International journal of cancer 2018 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…
• To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes.
  Frontiers in genetics 2018 Wallace AD, Wendt GA, Barcellos LF, de Smith AJ, Walsh KM, Metayer C, Costello JF, Wiemels JL, Francis SS
• Allergies and Childhood Acute Lymphoblastic Leukemia: A Case-Control Study and Meta-analysis.
  Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2018 Wallace AD, Francis SS, Ma X, McKean-Cowdin R, Selvin S, Whitehead TP, Barcellos LF, Kang AY, Morimoto L, Moore TB, Wiemels JL, Metayer C
• Herpesvirus Infection in Infants with Gastroschisis.
  Epidemiology (Cambridge, Mass.) 2018 Francis SS, Wiemels JL, Yang W, Shaw GM
• GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21.
  Nature communications 2018 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
• A germ-line deletion of APOBEC3B does not contribute to subtype-specific childhood acute lymphoblastic leukemia etiology.
  Haematologica 2017 Wallace AD, Francis SS, Shao X, de Smith AJ, Walsh KM, Mckean-Cowdin R, Ma X, Dahl G, Barcellos LF, Wiemels JL, Metayer C
• Cesarean Section and Risk of Childhood Acute Lymphoblastic Leukemia in a Population-Based, Record-Linkage Study in California.
  American journal of epidemiology 2016 Wang R, Wiemels JL, Metayer C, Morimoto L, Francis SS, Kadan-Lottick N, DeWan AT, Zhang Y, Ma X
• In utero cytomegalovirus infection and development of childhood acute lymphoblastic leukemia.
  Blood 2016 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
• Clonal and microclonal mutational heterogeneity in high hyperdiploid acute lymphoblastic leukemia.
  Oncotarget 2016 de Smith AJ, Ojha J, Francis SS, Sanders E, Endicott AA, Hansen HM, Smirnov I, Termuhlen AM, Walsh KM, Metayer C, Wiemels JL
• Genotyping Oral Commensal Bacteria to Predict Social Contact and Structure.
  PloS one 2016 Francis SS, Plucinski MM, Wallace AD, Riley LW
• Phase II study of vemurafenib followed by ipilimumab in patients with previously untreated BRAF-mutated metastatic melanoma.
  Journal for immunotherapy of cancer 2016 Amin A, Lawson DH, Salama AK, Koon HB, Guthrie T, Thomas SS, O'Day SJ, Shaheen MF, Zhang B, Francis S, Hodi FS
• Common genetic variants associated with telomere length confer risk for neuroblastoma and other childhood cancers.
  Carcinogenesis 2016 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
• In vitro elimination of gaseous microemboli utilizing hypobaric oxygenation in the Terumo® FX15 oxygenator.
  Perfusion 2016 Clingan S, Schuldes M, Francis S, Hoerr H, Riley J
• Caesarean delivery and risk of childhood leukaemia: a pooled analysis from the Childhood Leukemia International Consortium (CLIC).
  The Lancet. Haematology 2016 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, …
• Bacterial microbiome of breast milk and child saliva from low-income Mexican-American women and children.
  Pediatric research 2016 Davé V, Street K, Francis S, Bradman A, Riley L, Eskenazi B, Holland N
• Longer genotypically-estimated leukocyte telomere length is associated with increased adult glioma risk.
  Oncotarget 2015 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, …
• Understanding inherited genetic risk of adult glioma - a review.
  Neuro-oncology practice 2015 Rice T, Lachance DH, Molinaro AM, Eckel-Passow JE, Walsh KM, Barnholtz-Sloan J, Ostrom QT, Francis SS, Wiemels J, Jenkins RB, Wiencke JK, Wrensch MR
• A real-time PCR signature to discriminate between tuberculosis and other pulmonary diseases.
  Tuberculosis (Edinburgh, Scotland) 2015 Laux da Costa L, Delcroix M, Dalla Costa ER, Prestes IV, Milano M, Francis SS, Unis G, Silva DR, Riley LW, Rossetti ML
• Metagenomic epidemiology: a new frontier.
  Journal of epidemiology and community health 2014 Francis SS, Riley LW
• Mode of delivery and risk of childhood leukemia.
  Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2014 Francis SS, Selvin S, Metayer C, Wallace AD, Crouse V, Moore TB, Wiemels JL, Buffler PA
• A hierarchy of signals regulates entry of membrane proteins into the ciliary membrane domain in epithelial cells.
  The Journal of cell biology 2011 Francis SS, Sfakianos J, Lo B, Mellman I
• Unusual space-time patterning of the Fallon, Nevada leukemia cluster: Evidence of an infectious etiology.
  Chemico-biological interactions 2011 Francis SS, Selvin S, Yang W, Buffler PA, Wiemels JL
• Intermittent target inhibition with dasatinib 100 mg once daily preserves efficacy and improves tolerability in imatinib-resistant and -intolerant chronic-phase chronic myeloid leukemia.
  Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2008 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, …
• Neoadjuvant treatment of postmenopausal breast cancer with anastrozole, tamoxifen, or both in combination: the Immediate Preoperative Anastrozole, Tamoxifen, or Combined with Tamoxifen (IMPACT) multicenter double-blind randomized trial.
  Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2005 Smith IE, Dowsett M, Ebbs SR, Dixon JM, Skene A, Blohmer JU, Ashley SE, Francis S, Boeddinghaus I, Walsh G, IMPACT Trialists Group
• Biomarker changes during neoadjuvant anastrozole, tamoxifen, or the combination: influence of hormonal status and HER-2 in breast cancer--a study from the IMPACT trialists.
  Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2005 Dowsett M, Ebbs SR, Dixon JM, Skene A, Griffith C, Boeddinghaus I, Salter J, Detre S, Hills M, Ashley S, Francis S, Walsh G, Smith IE
• Recycling endosomes can serve as intermediates during transport from the Golgi to the plasma membrane of MDCK cells.
  The Journal of cell biology 2004 Ang AL, Taguchi T, Francis S, Fölsch H, Murrells LJ, Pypaert M, Warren G, Mellman I
• Quality of life of postmenopausal women in the Arimidex, Tamoxifen, Alone or in Combination (ATAC) Adjuvant Breast Cancer Trial.
  Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2004 Fallowfield L, Cella D, Cuzick J, Francis S, Locker G, Howell A