Papers from the lab and with our collaborators

2026

• Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study

  Wolf J, Goggin KP, Inaba Y, Allison KJ, Ahmed AA, Maron G, … Thomas P, Ferrolino J, Lazure L, Kohler C, Brenner A, Sun Y, Tang L, Gonzalez-Pena V, Rubnitz JE, Gawad C, Margolis EB, Thomas P show all 17 authors

  Lancet Microbe2026
  PubMed DOI Free full text

2025

• Somatic mtDNA mutations at intermediate levels of heteroplasmy are a source of functional heterogeneity among primary leukemic cells

  McCastlain K, Welsh C, Ni Y, Ding L, Chang TC, Autry RJ, … Kundu M, Sejdiu BI, Pan Q, Franco M, Chen W, Wu H, Gonzalez-Pena V, Schreiner P, Arunachalam S, Joo JH, Brady S, Zhang J, Gawad C, Evans WE, Babu MM, Khrapko K, Yu J, Wu G, Pounds S, Kundu M show all 25 authors

  Sci Adv2025
  PubMed DOI Free full text

• Single-Cell Sequencing Reveals Extensive Genetic Diversity Underlying Pediatric ALL Treatment Complexity

  Pang Y, Prieto T, Gonzalez-Pena V, Aragon A, Xia Y, Kao S, … Gawad C, Rajagopalan S, Zinno J, Quentin J, Laval J, Yuan DJ, Omans ND, Potenski C, Klein D, MacKay M, De Vlaminck I, Easton J, Evans W, Landau DA, Gawad C show all 20 authors

  bioRxiv2025 Preprint
  PubMed bioRxiv DOI Free full text

2024

• Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution

  Schiffman JS, D'Avino AR, Prieto T, Pang Y, Fan Y, Rajagopalan S, … Landau DA, Potenski C, Hara T, Suvà ML, Gawad C, Landau DA show all 11 authors

  Nat Genet2024
  PubMed DOI Free full text

• scMicrobe PTA: near complete genomes from single bacterial cells

  Bowers RM, Gonzalez-Pena V, Wardhani K, Goudeau D, Blow MJ, Udwary D, … Gawad C, Klein D, Vill AC, Brito IL, Woyke T, Malmstrom RR, Gawad C show all 12 authors

  ISME Commun2024
  PubMed DOI Free full text

2023

• Single-cell RNA sequencing distinctly characterizes the wide heterogeneity in pediatric mixed phenotype acute leukemia

  Mumme HL, Raikar SS, Bhasin SS, Thomas BE, Lawrence T, Weinzierl EP, … Bhasin M, Pang Y, DeRyckere D, Gawad C, Wechsler DS, Porter CC, Castellino SM, Graham DK, Bhasin M show all 14 authors

  Genome Med2023
  PubMed DOI Free full text

2022

• Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia

  Pilheden M, Ahlgren L, Hyrenius-Wittsten A, Gonzalez-Pena V, Sturesson H, Hansen Marquart HV, … Hagström-Andersson AK, Lausen B, Castor A, Pronk CJ, Barbany G, Pokrovskaja Tamm K, Fogelstrand L, Lohi O, Norén-Nyström U, Asklin J, Chen Y, Song G, Walsh M, Ma J, Zhang J, Saal LH, Gawad C, Hagström-Andersson AK show all 23 authors

  Hemasphere2022
  PubMed DOI Free full text

• Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements

  Luquette LJ, Miller MB, Zhou Z, Bohrson CL, Zhao Y, Jin H, … Park PJ, Gulhan D, Ganz J, Bizzotto S, Kirkham S, Hochepied T, Libert C, Galor A, Kim J, Lodato MA, Garaycoechea JI, Gawad C, West J, Walsh CA, Park PJ show all 20 authors

  Nat Genet2022
  PubMed DOI Free full text

• Simultaneous monitoring of disease and microbe dynamics through plasma DNA sequencing in pediatric patients with acute lymphoblastic leukemia

  Barsan V, Xia Y, Klein D, Gonzalez-Pena V, Youssef S, Inaba Y, … Gawad C, Mahmud O, Natarajan S, Agarwal V, Pang Y, Autry R, Pui CH, Inaba H, Evans W, Gawad C show all 15 authors

  Sci Adv2022
  PubMed DOI Free full text

• Bringing precision oncology to cellular resolution with single-cell genomics

  Xia Y, Gawad C

  Clin Exp Metastasis2022
  PubMed DOI Free full text

2021

• Accurate genomic variant detection in single cells with primary template-directed amplification

  Gonzalez-Pena V, Natarajan S, Xia Y, Klein D, Carter R, Pang Y, … Gawad C, Shaner B, Annu K, Putnam D, Chen W, Connelly J, Pruett-Miller S, Chen X, Easton J, Gawad C show all 15 authors

  Proc Natl Acad Sci U S A2021
  PubMed DOI Free full text

2020

• Integrative genomic analyses reveal mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia

  Autry RJ, Paugh SW, Carter R, Shi L, Liu J, Ferguson DC, … Evans WE, Lau CE, Bonten EJ, Yang W, McCorkle JR, Beard JA, Panetta JC, Diedrich JD, Crews KR, Pei D, Coke CJ, Natarajan S, Khatamian A, Karol SE, Lopez-Lopez E, Diouf B, Smith C, Gocho Y, Hagiwara K, Roberts KG, Pounds S, Kornblau SM, Stock W, Paietta EM, Litzow MR, Inaba H, Mullighan CG, Jeha S, Pui CH, Cheng C, Savic D, Yu J, Gawad C, Relling MV, Yang JJ, Evans WE show all 41 authors

  Nat Cancer2020
  PubMed DOI Free full text

• Evaluation of Plasma Microbial Cell-Free DNA Sequencing to Predict Bloodstream Infection in Pediatric Patients With Relapsed or Refractory Cancer

  Goggin KP, Gonzalez-Pena V, Inaba Y, Allison KJ, Hong DK, Ahmed AA, … Gawad C, Hollemon D, Natarajan S, Mahmud O, Kuenzinger W, Youssef S, Brenner A, Maron G, Choi J, Rubnitz JE, Sun Y, Tang L, Wolf J, Gawad C show all 19 authors

  JAMA Oncol2020
  PubMed DOI Free full text

2019

• Resolving medulloblastoma cellular architecture by single-cell genomics

  Hovestadt V, Smith KS, Bihannic L, Filbin MG, Shaw ML, Baumgartner A, … Northcott PA, DeWitt JC, Groves A, Mayr L, Weisman HR, Richman AR, Shore ME, Goumnerova L, Rosencrance C, Carter RA, Phoenix TN, Hadley JL, Tong Y, Houston J, Ashmun RA, DeCuypere M, Sharma T, Flasch D, Silkov A, Ligon KL, Pomeroy SL, Rivera MN, Rozenblatt-Rosen O, Rusert JM, Wechsler-Reya RJ, Li XN, Peyrl A, Gojo J, Kirchhofer D, Lötsch D, Czech T, Dorfer C, Haberler C, Geyeregger R, Halfmann A, Gawad C, Easton J, Pfister SM, Regev A, Gajjar A, Orr BA, Slavc I, Robinson GW, Bernstein BE, Suvà ML, Northcott PA show all 51 authors

  Nature2019
  PubMed DOI Free full text

• Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells

  Zhao Y, Carter R, Natarajan S, Varn FS, Compton DA, Gawad C, Cheng C, Godek KM

  BMC Med Genomics2019
  PubMed DOI Free full text

• Sequencing the Genomes of Single Cells

  Gonzalez-Pena V, Gawad C

  Methods Mol Biol2019
  PubMed DOI

2018

• Murine hematopoietic stem cell activity is derived from pre-circulation embryos but not yolk sacs

  Ganuza M, Chabot A, Tang X, Bi W, Natarajan S, Carter R, Gawad C, Kang G, Cheng Y, McKinney-Freeman S

  Nat Commun2018
  PubMed DOI Free full text

• LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance

  Cunha LD, Yang M, Carter R, Guy C, Harris L, Crawford JC, … Green DR, Quarato G, Boada-Romero E, Kalkavan H, Johnson MDL, Natarajan S, Turnis ME, Finkelstein D, Opferman JT, Gawad C, Green DR show all 16 authors

  Cell2018
  PubMed DOI Free full text

• A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum

  Carter RA, Bihannic L, Rosencrance C, Hadley JL, Tong Y, Phoenix TN, Natarajan S, Easton J, Northcott PA, Gawad C

  Curr Biol2018
  PubMed DOI

• High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor

  Yamashita T, Zheng F, Finkelstein D, Kellard Z, Carter R, Rosencrance CD, Sugino K, Easton J, Gawad C, Zuo J

  PLoS Genet2018
  PubMed DOI Free full text

• Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours

  Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, … Zhang J, Zhou X, Li Y, Rusch MC, Easton J, Huether R, Gonzalez-Pena V, Wilkinson MR, Hermida LC, Davis S, Sioson E, Pounds S, Cao X, Ries RE, Wang Z, Chen X, Dong L, Diskin SJ, Smith MA, Guidry Auvil JM, Meltzer PS, Lau CC, Perlman EJ, Maris JM, Meshinchi S, Hunger SP, Gerhard DS, Zhang J show all 33 authors

  Nature2018
  PubMed DOI Free full text

• Measurable residual disease detection by high-throughput sequencing improves risk stratification for pediatric B-ALL

  Wood B, Wu D, Crossley B, Dai Y, Williamson D, Gawad C, … Kirsch I, Borowitz MJ, Devidas M, Maloney KW, Larsen E, Winick N, Raetz E, Carroll WL, Hunger SP, Loh ML, Robins H, Kirsch I show all 17 authors

  Blood2018
  PubMed DOI Free full text

2017

• Genome-wide segregation of single nucleotide and structural variants into single cancer cells

  Easton J, Gonzalez-Pena V, Yergeau D, Ma X, Gawad C

  BMC Genomics2017
  PubMed DOI Free full text

2016

• Dynamic ASXL1 Exon Skipping and Alternative Circular Splicing in Single Human Cells

  Koh W, Gonzalez V, Natarajan S, Carter R, Brown PO, Gawad C

  PLoS One2016
  PubMed DOI Free full text

• Early somatic mosaicism is a rare cause of long-QT syndrome

  Priest JR, Gawad C, Kahlig KM, Yu JK, O'Hara T, Boyle PM, … Ashley EA, Rajamani S, Clark MJ, Garcia ST, Ceresnak S, Harris J, Boyle S, Dewey FE, Malloy-Walton L, Dunn K, Grove M, Perez MV, Neff NF, Chen R, Maeda K, Dubin A, Belardinelli L, West J, Antolik C, Macaya D, Quertermous T, Trayanova NA, Quake SR, Ashley EA show all 29 authors

  Proc Natl Acad Sci U S A2016
  PubMed DOI Free full text

• Single-cell genome sequencing: current state of the science

  Gawad C, Koh W, Quake SR

  Nat Rev Genet2016
  PubMed DOI

2014

• Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics

  Gawad C, Koh W, Quake SR

  Proc Natl Acad Sci U S A2014
  PubMed DOI Free full text

• A quantitative comparison of single-cell whole genome amplification methods

  de Bourcy CF, De Vlaminck I, Kanbar JN, Wang J, Gawad C, Quake SR

  PLoS One2014
  PubMed DOI Free full text

• Noninvasive in vivo monitoring of tissue-specific global gene expression in humans

  Koh W, Pan W, Gawad C, Fan HC, Kerchner GA, Wyss-Coray T, Blumenfeld YJ, El-Sayed YY, Quake SR

  Proc Natl Acad Sci U S A2014
  PubMed DOI Free full text

2012

• Massive evolution of the immunoglobulin heavy chain locus in children with B precursor acute lymphoblastic leukemia

  Gawad C, Pepin F, Carlton VE, Klinger M, Logan AC, Miklos DB, Faham M, Dahl G, Lacayo N

  Blood2012
  PubMed DOI Free full text

• Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types

  Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO

  PLoS One2012
  PubMed DOI Free full text

2005

• Towards molecular medicine: a case for a biological periodic table

  Gawad C

  Am J Pharmacogenomics2005
  PubMed DOI