Computational methods for analysis of multimodal single cell
dataNormalizing and denoising protein expression data from
droplet-based single cell profiling Mulè MP#, Martins AJ#,
Tsang JS Nature Communications (2022)
Identifying multicellular molecular immune networks that predict
responses to vaccination, cancer immunotherapy, and infectionIntegrating population and single-cell variations in vaccine
responses identifies a naturally adjuvanted human immune
setpoint. Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers
BA, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL,
Tsang JS. Immunity (2024) PMID: 38697118
Contrasting autoimmune and
treatment effects reveals baseline set points of immune toxicity
following checkpoint inhibitor treatment Mulè MP#, Zhao
C#, Martins AJ, Pinal-Fernandez I, Donahue RN, Chen J, Schlom J, Gulley
JL, Mammen A, Tsang JS, Rajan A bioRxiv (2022) PDF
Iron dysregulation and inflammatory stress erythropoiesis
associates with long-term outcome of COVID-19 Hanson AL,
Mulè MP, Ruffieux H, Mescia F, Bergamaschi L, Pelly VS, Turner L,
Kotagiri P; CITIID–NIHR, COVID BioResource Collaboration; Göttgens B,
Hess C, Gleadall N, Bradley JR, Nathan JA, Lyons PA, Drakesmith H, Smith
KGC. Nature Immunology (2024) PMID: 38429458
Broad immune activation
underlies shared set point signatures for vaccine responsiveness in
healthy individuals and disease activity in patients with
lupus. Kotliarov Y#, Sparks R#, (#equal contribution)
Martins AJ+, Mulè MP+, Lu Y+, (+equal contribution), Goswami M, Kardava
L, Banchereau R, Pascual V, Biancotto A, Chen J, Schwartzberg PL, Bansal
N, Liu CC, Cheung F, Moir S, Tsang JS. Nature Medicine
(2020) PMID: 32094927
Time-resolved systems
immunology reveals a late juncture linked to fatal COVID-19 Liu C, Martins AJ, Lau WW, Rachmaninoff N, Chen J, Imberti L,
Mostaghimi D, Fink DL, Burbelo PD, Dobbs K, Delmonte OM, Bansal N,
Failla L, Sottini A, Quiros-Roldan E, Han KL, Sellers BA, Cheung F,
Sparks R, Chun TW, Moir S, Lionakis MS; NIAID COVID Consortium; COVID
Clinicians; Rossi C, Su HC, Kuhns DB, Cohen JI, Notarangelo LD, Tsang
JS. Cell (2021) PMID: 33713619
Comparative systems immunology
studies of vaccination response and vaccine engineeringTranscriptional atlas of the human immune response to 13
vaccines reveals a common predictor of vaccine-induced antibody
responses. Hagan T, Gerritsen B, Tomalin LE, Fourati S,
Mulè MP, Chawla DG, Rychkov D, Henrich E, Miller HER, Diray-Arce J, Dunn
P, Lee A; Human Immunology Project Consortium (HIPC); Levy O, Gottardo
R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Sékaly RP, Kleinstein SH,
Pulendran B. Nature Immunology (2022) PMID: 36316475
Pan-vaccine analysis reveals
innate immune endotypes predictive of antibody responses to
vaccination. Fourati S, Tomalin LE, Mulè MP, Chawla DG,
Gerritsen B, Rychkov D, Henrich E, Miller HER, Hagan T, Diray-Arce J,
Dunn P; Human Immunology Project Consortium (HIPC); Levy O, Gottardo R,
Sarwal MM, Tsang JS, Suárez-Fariñas M, Pulendran B, Kleinstein SH,
Sékaly RP. Nature Immunology PMID: 36316476 (2022)
The Immune Signatures data
resource, a compendium of systems vaccinology datasets.
Diray-Arce J, Miller HER, Henrich E, Gerritsen B, Mulè MP, Fourati S,
Gygi J, Hagan T, Tomalin L, Rychkov D, Kazmin D, Chawla DG, Meng H, Dunn
P, Campbell J; Human Immunology Project Consortium (HIPC); Sarwal M,
Tsang JS, Levy O, Pulendran B, Sekaly R, Floratos A, Gottardo R,
Kleinstein SH, Suárez-Fariñas M. Scientific Data (2022)
PMID: 36266291
Clinical molecular diagnostics and pathology in
hematologic malignancies and immune-mediated diseaseMultigene Measurable Residual Disease Assessment Improves Acute
Myeloid Leukemia Relapse Risk Stratification in Autologous Hematopoietic
Cell Transplantation Mulé MP, Mannis GN, Wood BL, Radich
JP, Hwang J, Ramos NR, Andreadis C, Damon L, Logan AC, Martin TG,
Hourigan CS. Biology of Blood and Marrow Transplantation
(2016) PMID: 27544285
Advancing the Minimal
Residual Disease Concept in Acute Myeloid Leukemia Hokland
P, Ommen HB, Mulé MP, Hourigan CS. Seminars in Hematology
(2015) PMID: 26111465
MDS-associated mutations in
germline GATA2 mutated patients with hematologic
manifestations McReynolds LJ, Yang Y, Yuen Wong H, Tang J,
Zhang Y, Mulé MP, Daub J, Palmer C, Foruraghi L, Liu Q, Zhu J, Wang W,
West RR, Yohe ME, Hsu AP, Hickstein DD, Townsley DM, Holland SM, Calvo
KR, Hourigan CS. Leukemia Research (2019) PMID: 30578959
Rapid progression to AML in a patient with germline GATA2
mutation and acquired NRAS Q61K mutation. McReynolds LJ,
Zhang Y, Yang Y, Tang J, Mulé M, Hsu AP, Townsley DM, West RR, Zhu J,
Hickstein DD, Holland SM, Calvo KR, Hourigan CS. Leukemia
Research Reports (2019) PMID: 31245276
Molecular Measurable Residual Disease Testing of Blood
During AML Cytotoxic Therapy for Early Prediction of Clinical
Response Wong HY, Sung AD, Lindblad KE, Sheela S, Roloff
GW, Rizzieri D, Goswami M, Mulé MP, Ramos NR, Tang J, Thompson J,
DeStefano CB, Romero K, Dillon LW, Kim DY, Lai C, Hourigan CS. Frontiers in Oncology (2019) PMID: 30697529
Bacterial transcriptional dynamics in infection
The core promoter of the capsule operon of Streptococcus
pneumoniae is necessary and sufficient for colonization and invasive
disease. Shainheit MG, Mulé M, Camilli A. Infection
and Immunity (2014) PMID: 24478084
Iron- dependent gene
expression in Actinomyces oris Mulè MP, Giacalone D,
Lawlor K, Golden A, Cook C, Lott T, Aksten E, O’Toole GA, Bergeron, LJ
Journal of Oral Microbiology (2015 )PMID: 26685151