Federated learning enables big data for rare cancer boundary detection
Pati S, Baid U, Edwards B, Sheller M, Wang SH, Reina GA, Foley P, Gruzdev A, Karkada D, Davatzikos C, Sako C, Ghodasara S, Bilello M, Mohan S, Vollmuth P, Brugnara G, Preetha CJ ... Menze B, Barnholtz-Sloan JS, Martin J, Bakas S. Nat Commun. 2022 Dec 5;13(1):7346. doi: 10.1038/s41467-022-33407-5.
Assistant Professor of Pathology and Laboratory Medicine
Perelman School of Medicine at the University of Pennsylvania
Assistant Director, Immunogenetics Laboratory,
Children's Hospital of Philadelphia
Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes
Ko J, Wilkovitsch M, Oh J, Kohler RH, Bolli E, Pittet MJ, Vinegoni C, Sykes DB, Mikula H, Weissleder R, Carlson JCT. Nat Biotechnol. 2022 Jun 2. doi: 10.1038/s41587-022-01339-6. Online ahead of print.
Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types
Pahl MC, Le Coz C, Su C, Sharma P, Thomas RM, Pippin JA, Cruz Cabrera E, Johnson ME, Leonard ME, Lu S, Chesi A, Sullivan KE, Romberg N, Grant SFA, Wells AD. Genome Biol. 2022 Jun 3;23(1):125. doi: 10.1186/s13059-022-02691-1.
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease
Liu H, Doke T, Guo D, Sheng X, Ma Z, Park J, Vy HMT, Nadkarni GN, Abedini A, Miao Z, Palmer M, Voight BF, Li H, Brown CD, Ritchie MD, Shu Y, Susztak K. Nat Genet. 2022 Jun 16. doi: 10.1038/s41588-022-01097-w. Online ahead of print.
Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes
Fasolino M, Schwartz GW, Patil AR, Mongia A, Golson ML, Wang YJ, Morgan A, Liu C, Schug J, Liu J, Wu M, Traum D, Kondo A, May CL, Goldman N, Wang W, Feldman M, Moore JH, Japp AS, Betts MR, Faryabi RB, Naji A, Kaestner KH, Vahedi G. Nat Metab; 4, 284–299. Published online: 28 February 2022. doi: 10.1038/s42255-022-00531-x
Pyrimidine inhibitors synergize with nucleoside analogues to block SARS-CoV-2
Schultz DC, Johnson RM, Ayyanathan K, Miller J, Whig K, Kamalia B, Dittmar M, Weston S, Hammond HL, Dillen C, Ardanuy J, Taylor L, Lee JS, Li M, Lee E, Shoffler C, Petucci C, Constant S, Ferrer M, Thaiss CA, Frieman MB, Cherry S. Nature. 2022 Feb 7. doi: 10.1038/s41586-022-04482-x. Online ahead of print.
TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes
Schwartz GW, Zhou Y, Petrovic J, Pear WS, Faryabi RB. Cell Rep. 2021 Aug 24;36(8):109575. doi: 10.1016/j.celrep.2021.109575.
Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-Cov-2
Dittmar M, Lee JS, Whig K, Segrist E, Li M, Kamalia B, Castellana L, Ayyanathan K, Cardenas-Diaz FL, Morrisey EE, Truitt R, Yang W, Jurado K, Samby K, Ramage H, Schultz DC, Cherry S. Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-Cov-2. Cell Rep. 2021 Mar 23;108959. doi: 10.1016/j.celrep.2021.108959. Online ahead of print.
Federated learning in medicine: facilitating multi-institutional collaborations without sharing patient data
Sheller MJ, Edwards B, Reina GA, Martin J, Pati S, Kotrotsou A, Milchenko M, Xu W, Marcus D, Colen RR, Bakas S. Federated learning in medicine: facilitating multi-institutional collaborations without sharing patient data. Sci Rep. 2020 Jul 28;10(1):12598. doi: 10.1038/s41598-020-69250-1.
