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Richard H. Scheuermann is adjunct faculty at the J. Craig Venter Institute. After completing his doctoral research, he accepted an independent research position at the Basel Institute for Immunology in Basel, Switzerland. In 1992, he joined the faculty in the Department of Pathology at the University of Texas Southwestern Medical Center in Dallas where he rose to the rank of Professor with tenure. In 2001, he made a career shift into the discipline of bioinformatics, initiated with a sabbatical year at the San Diego Supercomputer Center. In 2012, Dr. Scheuermann moved to San Diego to become the Director of Informatics at JCVI, and in 2016 was promoted to Director of the La Jolla Campus.
Dr. Scheuermann has applied his deep knowledge in molecular immunology and infectious disease toward the development of novel computational data mining methods and knowledge representation approaches, including the development of biomedical ontologies and their use in data mining, novel methods for the analysis of gene expression, protein network and flow cytometry data, and novel comparative genomics methods. These computational methods have been made available through several public database and analysis resources, including the Influenza Research Database (IRD), the Virus Pathogen Resource (ViPR), and the Immunology Database and Analysis Portal (ImmPort) supported by the U.S. National Institutes of Health.
He received a BS in Life Sciences from the Massachusetts Institute of Technology, and a PhD in Molecular Biology from the University of California, Berkeley.
Research Priorities
Informatics database resources and knowledge representation standards
- Principle investigator on the Influenza Research Database (IRD), the Virus Pathogen Resource (ViPR) and the Immunology Database and Analysis Portal (ImmPort) development projects.
- Development of biomedical ontologies and other knowledge representation standards through the Open Biomedical Ontology (OBO) Foundry, including the Cell Ontology (CL), the Ontology for General Medical Sciences (OGMS), the Ontology for Biomedical Investigations (OBI), and the Minimum Information about a Flow Cytometry Experiment (MIFlowCyt).
Flow cytometry analysis methods
- Development of a suite of cytometry data processing and analysis methods, including FLOCK, FlowMap-FR, FCSTrans, and DAFi.
- Co-founder of the FlowCAP Consortium for the critical evaluation of cytometry analysis methods using benchmark datasets and objective performance metrics.
- Development of the FlowGate resource for user-friendly access to cytometry analysis methods.
- Application of computational cytometry analysis methods to study immunological responses to vaccination, respiratory pathogen infection, autoimmunity, and leukemia and lymphoma.
Systems biology analysis methods
- Identification of functional modules within gene/protein networks based on their topological properties using MoNet and dMoNet.
- Dissemination of systems biology of infectious diseases data through the IRD and ViPR resources.
Transcriptomics and single cell genomics
- Development of a suite of gene expression microarray analysis methods, including DFW, DFCM, CLASSIFI, and GO-Bayes.
- Use of single cell RNA sequencing (scRNAseq) to study the cellular complexity of the human cerebral cortex, vaccine responses, and the development of multiple sclerosis.
- Application of machine learning methods for scRNAseq analysis, including quality control procedures and marker gene feature selection.
Publications
Journal of neuroinflammation. 2024-06-24; 21.1: 161.
Astrocytic stress response is induced by exposure to astrocyte-binding antibodies expressed by plasmablasts from pediatric patients with acute transverse myelitis
Smith C, Telesford KM, Piccirillo SGM, Licon-Munoz Y, Zhang W, Tse KM, Rivas JR, Joshi C, Shah DS, Wu AX, Trivedi R, Christley S, Qian Y, Cowell LG, Scheuermann RH, Stowe AM, Nguyen L, Greenberg BM, Monson NL
PMID: 38915059
BMC medical genomics. 2024-06-19; 17.1: 165.
Association of disease severity and genetic variation during primary Respiratory Syncytial Virus infections
Bender W, Zhang Y, Corbett A, Chu C, Grier A, Wang L, Qiu X, McCall MN, Topham DJ, Walsh EE, Mariani TJ, Scheuermann R, Caserta MT, Anderson CS
PMID: 38898440
The Journal of investigative dermatology. 2024-02-01; 144.2: 252-262.e4.
Cross-Comparison of Inflammatory Skin Disease Transcriptomics Identifies PTEN as a Pathogenic Disease Classifier in Cutaneous Lupus Erythematosus
Aevermann BD, Di Domizio J, Olah P, Saidoune F, Armstrong JM, Bachelez H, Barker J, Haniffa M, Julia V, Juul K, Krishnaswamy JK, Litman T, Parsons I, Sarin KY, Schmuth M, Sierra M, Simpson M, Homey B, Griffiths CEM, Scheuermann RH, Gilliet M
PMID: 37598867
PloS one. 2024-01-18; 19.1: e0285093.
Coordinating virus research: The Virus Infectious Disease Ontology
Beverley J, Babcock S, Carvalho G, Cowell LG, Duesing S, He Y, Hurley R, Merrell E, Scheuermann RH, Smith B
PMID: 38236918
Nature genetics. 2023-12-01; 55.12: 2189-2199.
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma
Chapman OS, Luebeck J, Sridhar S, Wong IT, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L
PMID: 37945900
Frontiers in cellular neuroscience. 2023-11-29; 17.1256619.
Cochlear transcriptome analysis of an outbred mouse population (CFW)
Boussaty EC, Tedeschi N, Novotny M, Ninoyu Y, Du E, Draf C, Zhang Y, Manor U, Scheuermann RH, Friedman R
PMID: 38094513
Cell. 2023-10-26; 186.22: 4818-4833.e25.
Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8
Zimmerman O, Zimmerman MI, Raju S, Nelson CA, Errico JM, Madden EA, Holmes AC, Hassan AO, VanBlargan LA, Kim AS, Adams LJ, Basore K, Whitener BM, Palakurty S, Davis-Adams HG, Sun C, Gilliland T, Earnest JT, Ma H, Ebel GD, Zmasek C, Scheuermann RH, Klimstra WB, Fremont DH, Diamond MS
PMID: 37804831
Bioinformatics (Oxford, England). 2023-10-03; 39.10:
A cell-level discriminative neural network model for diagnosis of blood cancers
Robles EE, Jin Y, Smyth P, Scheuermann RH, Bui JD, Wang HY, Oak J, Qian Y
PMID: 37756695
Nature immunology. 2023-10-01; 24.10: 1616-1627.
SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)
Proal AD, VanElzakker MB, Aleman S, Bach K, Boribong BP, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Eimer W, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Iwasaki A, Izquierdo-Garcia D, Locci M, Mehandru S, Painter MM, Peluso MJ, Pretorius E, Price DA, Putrino D, Scheuermann RH, Tan GS, Tanzi RE, VanBrocklin HF, Yonker LM, Wherry EJ
PMID: 37667052
Nature immunology. 2023-10-01; 24.10: 1778.
Author Correction: SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)
Proal AD, VanElzakker MB, Aleman S, Bach K, Boribong BP, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Eimer W, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Iwasaki A, Izquierdo-Garcia D, Locci M, Mehandru S, Painter MM, Peluso MJ, Pretorius E, Price DA, Putrino D, Scheuermann RH, Tan GS, Tanzi RE, VanBrocklin HF, Yonker LM, Wherry EJ
PMID: 37723351
PLoS biology. 2023-06-30; 21.6: e3002133.
A guide to the BRAIN Initiative Cell Census Network data ecosystem
Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B
PMID: 37390046
Cell reports. Medicine. 2023-06-20; 4.6: 101088.
Targets and cross-reactivity of human T cell recognition of common cold coronaviruses
Tarke A, Zhang Y, Methot N, Narowski TM, Phillips E, Mallal S, Frazier A, Filaci G, Weiskopf D, Dan JM, Premkumar L, Scheuermann RH, Sette A, Grifoni A
PMID: 37295422
Scientific reports. 2023-06-13; 13.1: 9567.
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain
Zhang Y, Miller JA, Park J, Lelieveldt BP, Long B, Abdelaal T, Aevermann BD, Biancalani T, Comiter C, Dzyubachyk O, Eggermont J, Langseth CM, Petukhov V, Scalia G, Vaishnav ED, Zhao Y, Lein ES, Scheuermann RH
PMID: 37311768
Vaccine. 2023-05-11; 41.20: 3171-3177.
Monkeypox (Mpox) requires continued surveillance, vaccines, therapeutics and mitigating strategies
Roper RL, Garzino-Demo A, Del Rio C, Bréchot C, Gallo R, Hall W, Esparza J, Reitz M, Schinazi RF, Parrington M, Tartaglia J, Koopmans M, Osorio J, Nitsche A, Huan TB, LeDuc J, Gessain A, Weaver S, Mahalingam S, Abimiku A, Vahlne A, Segales J, Wang L, Isaacs SN, Osterhaus A, Scheuermann RH, McFadden G
PMID: 37088603
Emerging infectious diseases. 2023-05-01; 29.5:
US National Institutes of Health Prioritization of SARS-CoV-2 Variants
Turner S, Alisoltani A, Bratt D, Cohen-Lavi L, Dearlove BL, Drosten C, Fischer WM, Fouchier RAM, Gonzalez-Reiche AS, Jaroszewski L, Khalil Z, LeGresley E, Johnson M, Jones TC, Mühlemann B, O'Connor D, Sedova M, Shukla M, Theiler J, Wallace ZS, Yoon H, Zhang Y, van Bakel H, DeGrace MM, Ghedin E, Godzik A, Hertz T, Korber B, Lemieux J, Niewiadomska AM, Post DJ, Rolland M, Scheuermann R, Smith DJ
PMID: 37054986
Scientific data. 2023-04-28; 10.1: 246.
Author Correction: Brain Data Standards - A method for building data-driven cell-type ontologies
Tan SZK, Kir H, Aevermann BD, Gillespie T, Harris N, Hawrylycz MJ, Jorstad NL, Lein ES, Matentzoglu N, Miller JA, Mollenkopf TS, Mungall CJ, Ray PL, Sanchez REA, Staats B, Vermillion J, Yadav A, Zhang Y, Scheuermann RH, Osumi-Sutherland D
PMID: 37117232
Scientific data. 2023-01-24; 10.1: 50.
Brain Data Standards - A method for building data-driven cell-type ontologies
Tan SZK, Kir H, Aevermann BD, Gillespie T, Harris N, Hawrylycz MJ, Jorstad NL, Lein ES, Matentzoglu N, Miller JA, Mollenkopf TS, Mungall CJ, Ray PL, Sanchez REA, Staats B, Vermillion J, Yadav A, Zhang Y, Scheuermann RH, Osumi-Sutherland D
PMID: 36693887
Nucleic acids research. 2023-01-06; 51.D1: D678-D689.
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR
Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Kenyon RW, Kuscuoglu M, Lefkowitz EJ, Lu J, Machi D, Macken C, Mao C, Niewiadomska A, Nguyen M, Olsen GJ, Overbeek JC, Parrello B, Parrello V, Porter JS, Pusch GD, Shukla M, Singh I, Stewart L, Tan G, Thomas C, VanOeffelen M, Vonstein V, Wallace ZS, Warren AS, Wattam AR, Xia F, Yoo H, Zhang Y, Zmasek CM, Scheuermann RH, Stevens RL
PMID: 36350631
Cell host & microbe. 2022-12-14; 30.12: 1662-1670.e4.
Defining antigen targets to dissect vaccinia virus and monkeypox virus-specific T cell responses in humans
Grifoni A, Zhang Y, Tarke A, Sidney J, Rubiro P, Reina-Campos M, Filaci G, Dan JM, Scheuermann RH, Sette A
PMID: 36463861
Frontiers in bioinformatics. 2022-10-24; 2.1020189.
Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation
Wallace ZS, Davis J, Niewiadomska AM, Olson RD, Shukla M, Stevens R, Zhang Y, Zmasek CM, Scheuermann RH
PMID: 36353215
Bioinformatics (Oxford, England). 2022-10-14; 38.20: 4735-4744.
FastMix: a versatile data integration pipeline for cell type-specific biomarker inference
Zhang Y, Sun H, Mandava A, Aevermann BD, Kollmann TR, Scheuermann RH, Qiu X, Qian Y
PMID: 36018232
Scientific reports. 2022-10-06; 12.1: 16731.
A novel vaccine based on SARS-CoV-2 CD4+ and CD8+ T cell conserved epitopes from variants Alpha to Omicron
Palatnik-de-Sousa I, Wallace ZS, Cavalcante SC, Ribeiro MPF, Silva JABM, Cavalcante RC, Scheuermann RH, Palatnik-de-Sousa CB
PMID: 36202985
PloS one. 2022-09-23; 17.9: e0275070.
Machine learning for cell type classification from single nucleus RNA sequencing data
Le H, Peng B, Uy J, Carrillo D, Zhang Y, Aevermann BD, Scheuermann RH
PMID: 36149937
Journal of virology. 2022-08-10; 96.15: e0083322.
Animal Models of Enterovirus D68 Infection and Disease
Vermillion MS, Dearing J, Zhang Y, Adney DR, Scheuermann RH, Pekosz A, Tarbet EB
PMID: 35852353
Scientific reports. 2022-06-15; 12.1: 9996.
Cell type matching in single-cell RNA-sequencing data using FR-Match
Zhang Y, Aevermann B, Gala R, Scheuermann RH
PMID: 35705694
Virology. 2022-05-01; 570.123-133.
Genomic evolution of the Coronaviridae family
Zmasek CM, Lefkowitz EJ, Niewiadomska A, Scheuermann RH
PMID: 35398776
Nature. 2022-05-01; 605.7911: 640-652.
Defining the risk of SARS-CoV-2 variants on immune protection
DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Florence WC, Fischer WM, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli S, Turner SA, Vakaki MA, van Bakel H, VanBlargan LA, Vincent LR, Wallace ZS, Wang L, Wang M, Wang P, Wang W, Weaver SC, Webby RJ, Weiss CD, Wentworth DE, Weston SM, Whelan SPJ, Whitener BM, Wilks SH, Xie X, Ying B, Yoon H, Zhou B, Hertz T, Smith DJ, Diamond MS, Post DJ, Suthar MS
PMID: 35361968
Nature. 2022-04-01; 604.7904: E8.
Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse
Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preiss S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES
PMID: 35319013
Science translational medicine. 2022-03-02; 14.634: eabn7842.
Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses
Sievers BL, Chakraborty S, Xue Y, Gelbart T, Gonzalez JC, Cassidy AG, Golan Y, Prahl M, Gaw SL, Arunachalam PS, Blish CA, Boyd SD, Davis MM, Jagannathan P, Nadeau KC, Pulendran B, Singh U, Scheuermann RH, Frieman MB, Vashee S, Wang TT, Tan GS
PMID: 35025672
Plant physiology. 2022-02-04; 188.2: 879-897.
The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness
Abramson BW, Novotny M, Hartwick NT, Colt K, Aevermann BD, Scheuermann RH, Michael TP
PMID: 34893913
Journal of leukocyte biology. 2021-12-01; 110.6: 1225-1239.
Corticosteroid treatment in COVID-19 modulates host inflammatory responses and transcriptional signatures of immune dysregulation
Pinski AN, Steffen TL, Zulu MZ, George SL, Dickson A, Tifrea D, Maroney KJ, Tedeschi N, Zhang Y, Scheuermann RH, Pinto AK, Brien JD, Messaoudi I
PMID: 34730254
Frontiers in immunology. 2021-10-29; 12.690470.
Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response
Aevermann BD, Shannon CP, Novotny M, Ben-Othman R, Cai B, Zhang Y, Ye JC, Kobor MS, Gladish N, Lee AH, Blimkie TM, Hancock RE, Llibre A, Duffy D, Koff WC, Sadarangani M, Tebbutt SJ, Kollmann TR, Scheuermann RH
PMID: 34777332
Nature. 2021-10-06; 598.7879: 111-119.
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES
PMID: 34616062
Genome research. 2021-10-01; 31.10: 1767-1780.
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing
Aevermann BD, Aevermann B, Zhang Y, Novotny M, Keshk M, Bakken TE, Bakken T, Miller JA, Miller J, Hodge RD, Hodge R, Lelieveldt B, Lein ES, Lein E, Scheuermann RH
PMID: 34088715
Cell reports. Medicine. 2021-07-20; 2.7: 100355.
Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals
Tarke A, Sidney J, Methot N, Yu ED, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, Wang E, Frazier A, Ramirez SI, Rawlings SA, Smith DM, da Silva Antunes R, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A
PMID: 34230917
Briefings in bioinformatics. 2021-07-20; 22.4:
FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test
Zhang Y, Aevermann BD, Bakken TE, Miller JA, Hodge RD, Lein ES, Scheuermann RH
PMID: 33249453
Database : the journal of biological databases and curation. 2021-07-09; 2021.
Standardization of assay representation in the Ontology for Biomedical Investigations
Vita R, Zheng J, Jackson R, Dooley D, Overton JA, Miller MA, Berrios DC, Scheuermann RH, He Y, McGinty HK, Brochhausen M, Lin AY, Jain SB, Chibucos MC, Judkins J, Giglio MG, Feng IY, Burns G, Brush MH, Peters B, Stoeckert CJ
PMID: 34244718
Nature medicine. 2021-05-01; 27.5: 892-903.
SARS-CoV-2 infection of the oral cavity and saliva
Huang N, Pérez P, Kato T, Mikami Y, Okuda K, Gilmore RC, Conde CD, Gasmi B, Stein S, Beach M, Pelayo E, Maldonado JO, Lafont BA, Jang SI, Nasir N, Padilla RJ, Murrah VA, Maile R, Lovell W, Wallet SM, Bowman NM, Meinig SL, Wolfgang MC, Choudhury SN, Novotny M, Aevermann BD, Scheuermann RH, Cannon G, Anderson CW, Lee RE, Marchesan JT, Bush M, Freire M, Kimple AJ, Herr DL, Rabin J, Grazioli A, Das S, French BN, Pranzatelli T, Chiorini JA, Kleiner DE, Pittaluga S, Hewitt SM, Burbelo PD, Chertow D, NIH COVID-19 Autopsy Consortium, HCA Oral and Craniofacial Biological Network, Frank K, Lee J, Boucher RC, Teichmann SA, Warner BM, Byrd KM
PMID: 33767405
JCI insight. 2021-04-08; 6.7:
A system-view of Bordetella pertussis booster vaccine responses in adults primed with whole-cell versus acellular vaccine in infancy
da Silva Antunes R, Soldevila F, Pomaznoy M, Babor M, Bennett J, Tian Y, Khalil N, Khalil NN, Qian Y, Mandava A, Scheuermann RH, Cortese M, Pulendran B, Petro CD, Gilkes AP, Purcell LA, Sette A, Peters B
PMID: 33690224
Nature neuroscience. 2021-04-01; 24.4: 613.
Publisher Correction: A community-based transcriptomics classification and nomenclature of neocortical cell types
Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, Arnedillo RA, Ascoli GA, Bielza C, Bokharaie V, Bergmann TB, Bystron I, Capogna M, Chang Y, Clemens A, de Kock CPJ, DeFelipe J, Dos Santos SE, Dunville K, Feldmeyer D, Fiáth R, Fishell GJ, Foggetti A, Gao X, Ghaderi P, Goriounova NA, Güntürkün O, Hagihara K, Hall VJ, Helmstaedter M, Herculano S, Hilscher MM, Hirase H, Hjerling-Leffler J, Hodge R, Huang J, Huda R, Khodosevich K, Kiehn O, Koch H, Kuebler ES, Kühnemund M, Larrañaga P, Lelieveldt B, Louth EL, Lui JH, Mansvelder HD, Marin O, Martinez-Trujillo J, Moradi Chameh H, Nath A, Nedergaard M, Němec P, Ofer N, Pfisterer UG, Pontes S, Redmond W, Rossier J, Sanes JR, Scheuermann R, Serrano-Saiz E, Steiger JF, Somogyi P, Tamás G, Tolias AS, Tosches MA, García MT, Vieira HM, Wozny C, Wuttke TV, Yong L, Yuan J, Zeng H, Lein E
PMID: 33277642
Nature neuroscience. 2021-04-01; 24.4: 612.
Author Correction: A community-based transcriptomics classification and nomenclature of neocortical cell types
Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, Armañanzas R, Ascoli GA, Bielza C, Bokharaie V, Bergmann TB, Bystron I, Capogna M, Chang Y, Clemens A, de Kock CPJ, DeFelipe J, Dos Santos SE, Dunville K, Feldmeyer D, Fiáth R, Fishell GJ, Foggetti A, Gao X, Ghaderi P, Goriounova NA, Güntürkün O, Hagihara K, Hall VJ, Helmstaedter M, Herculano-Houzel S, Hilscher MM, Hirase H, Hjerling-Leffler J, Hodge R, Huang J, Huda R, Khodosevich K, Kiehn O, Koch H, Kuebler ES, Kühnemund M, Larrañaga P, Lelieveldt B, Louth EL, Lui JH, Mansvelder HD, Marin O, Martinez-Trujillo J, Chameh HM, Mohapatra AN, Munguba H, Nedergaard M, Němec P, Ofer N, Pfisterer UG, Pontes S, Redmond W, Rossier J, Sanes JR, Scheuermann RH, Serrano-Saiz E, Staiger JF, Somogyi P, Tamás G, Tolias AS, Tosches MA, García MT, Wozny C, Wuttke TV, Liu Y, Yuan J, Zeng H, Lein E
PMID: 33742182
bioRxiv : the preprint server for biology. 2021-03-01;
Negligible impact of SARS-CoV-2 variants on CD4 + and CD8 + T cell reactivity in COVID-19 exposed donors and vaccinees
Tarke A, Sidney J, Methot N, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, da Silva Antunes R, Frazier A, Rawlings SA, Smith DM, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A
PMID: 33688655
Lancet (London, England). 2021-01-23; 397.10271: 334-346.
Acute flaccid myelitis: cause, diagnosis, and management
Murphy OC, Messacar K, Benson L, Bove R, Carpenter JL, Crawford T, Dean J, DeBiasi R, Desai J, Elrick MJ, Farias-Moeller R, Gombolay GY, Greenberg B, Harmelink M, Hong S, Hopkins SE, Oleszek J, Otten C, Sadowsky CL, Schreiner TL, Thakur KT, Van Haren K, Carballo CM, Chong PF, Fall A, Gowda VK, Helfferich J, Kira R, Lim M, Lopez EL, Wells EM, Yeh EA, Pardo CA, AFM working group
PMID: 33357469
Nature biotechnology. 2020-12-01; 38.12: 1384-1386.
Guidelines for reporting single-cell RNA-seq experiments
Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N, Scheuermann RH, Taylor D, Vasilevsky N, Clarke L, Gehlenborg N, Kent J, Marioni J, Teichmann S, Brazma A, Papatheodorou I
PMID: 33188371
Nature neuroscience. 2020-12-01; 23.12: 1456-1468.
A community-based transcriptomics classification and nomenclature of neocortical cell types
Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, Armañanzas R, Arnedillo RA, Ascoli GA, Bielza C, Bokharaie V, Bergmann TB, Bystron I, Capogna M, Chang Y, Clemens A, de Kock CPJ, DeFelipe J, Dos Santos SE, Dunville K, Feldmeyer D, Fiáth R, Fishell GJ, Foggetti A, Gao X, Ghaderi P, Goriounova NA, Güntürkün O, Hagihara K, Hall VJ, Helmstaedter M, Herculano S, Herculano-Houzel S, Hilscher MM, Hirase H, Hjerling-Leffler J, Hodge R, Huang J, Huda R, Khodosevich K, Kiehn O, Koch H, Kuebler ES, Kühnemund M, Larrañaga P, Lelieveldt B, Louth EL, Lui JH, Mansvelder HD, Marin O, Martinez-Trujillo J, Moradi Chameh H, Chameh HM, Nath A, Mohapatra AN, Munguba H, Nedergaard M, Němec P, Ofer N, Pfisterer UG, Pontes S, Redmond W, Rossier J, Sanes JR, Scheuermann R, Scheuermann RH, Serrano-Saiz E, Steiger JF, Staiger JF, Somogyi P, Tamás G, Tolias AS, Tosches MA, García MT, Vieira HM, Wozny C, Wuttke TV, Yong L, Liu Y, Yuan J, Zeng H, Lein E
PMID: 32839617
Frontiers in immunology. 2020-11-30; 11.578801.
Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort
Shannon CP, Blimkie TM, Ben-Othman R, Gladish N, Amenyogbe N, Drissler S, Edgar RD, Chan Q, Krajden M, Foster LJ, Kobor MS, Mohn WW, Brinkman RR, Le Cao KA, Scheuermann RH, Tebbutt SJ, Hancock REW, Koff WC, Kollmann TR, Sadarangani M, Lee AH
PMID: 33329547
Microorganisms. 2020-11-25; 8.12:
Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses
Brown DM, Zhang Y, Scheuermann RH
PMID: 33255654
Frontiers in immunology. 2020-11-04; 11.580373.
Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Ben-Othman R, Cai B, Liu AC, Varankovich N, He D, Blimkie TM, Lee AH, Gill EE, Novotny M, Aevermann B, Drissler S, Shannon CP, McCann S, Marty K, Bjornson G, Edgar RD, Lin DTS, Gladish N, Maclsaac J, Amenyogbe N, Chan Q, Llibre A, Collin J, Landais E, Le K, Reiss SM, Koff WC, Havenar-Daughton C, Heran M, Sangha B, Walt D, Krajden M, Crotty S, Sok D, Briney B, Burton DR, Duffy D, Foster LJ, Mohn WW, Kobor MS, Tebbutt SJ, Brinkman RR, Scheuermann RH, Hancock REW, Kollmann TR, Sadarangani M
PMID: 33250895
medRxiv : the preprint server for health sciences. 2020-10-27;
Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis
Huang N, Perez P, Kato T, Mikami Y, Okuda K, Gilmore RC, Domínguez Conde C, Gasmi B, Stein S, Beach M, Pelayo E, Maldonado J, LaFont B, Padilla R, Murrah V, Maile R, Lovell W, Wallet S, Bowman NM, Meinig SL, Wolfgang MC, Choudhury SN, Novotny M, Aevermann BD, Scheuermann R, Cannon G, Anderson C, Marchesan J, Bush M, Freire M, Kimple A, Herr DL, Rabin J, Grazioli A, French BN, Pranzatelli T, Chiorini JA, Kleiner DE, Pittaluga S, Hewitt S, Burbelo PD, Chertow D, Frank K, Lee J, Boucher RC, Teichmann SA, Warner BM, Byrd KM
PMID: 33140061
Vaccine: X. 2020-08-07; 5.100065.
Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein
Thakar J, Qian Y, Benoodt L, Roumanes D, Qiu X, Laniewski N, Chu C, Slaunwhite C, Wang L, Mandava A, Chang I, Falsey AR, Caserta MT, Mariani TJ, Scheuermann RH, Walsh EE, Topham DJ
PMID: 32529184
Proceedings of the National Academy of Sciences of the United States of America. 2020-06-09; 117.23: 12522-12523.
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M
PMID: 32381734
Cell host & microbe. 2020-04-08; 27.4: 671-680.e2.
A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2
Grifoni A, Sidney J, Zhang Y, Scheuermann RH, Peters B, Sette A
PMID: 32183941
Nature communications. 2020-03-03; 11.1: 1172.
Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons
Hodge RD, Miller JA, Novotny M, Kalmbach BE, Ting JT, Bakken TE, Aevermann BD, Barkan ER, Berkowitz-Cerasano ML, Cobbs C, Diez-Fuertes F, Ding SL, McCorrison J, Schork NJ, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Yanny AM, Steemers FJ, Phillips JW, Bernard A, Koch C, Lasken RS, Scheuermann RH, Lein ES
PMID: 32127543
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2020-03-01; 97.3: 296-307.
Machine Learning of Discriminative Gate Locations for Clinical Diagnosis
Ji D, Putzel P, Qian Y, Chang I, Mandava A, Scheuermann RH, Bui JD, Wang HY, Smyth P
PMID: 31691488
Human immunology. 2019-11-01; 80.11: 923-929.
A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis
Grifoni A, Mahajan S, Sidney J, Martini S, Scheuermann RH, Peters B, Sette A
PMID: 31451291
Nature. 2019-09-01; 573.7772: 61-68.
Conserved cell types with divergent features in human versus mouse cortex
Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES
PMID: 31435019
JCI insight. 2019-05-02; 4.9:
Differential transcriptome and development of human peripheral plasma cell subsets
Garimilla S, Garimalla S, Nguyen DC, Halliley JL, Tipton C, Rosenberg AF, Fucile CF, Saney CL, Kyu S, Kaminski D, Qian Y, Scheuermann RH, Gibson G, Sanz I, Lee FE
PMID: 31045577
Virology. 2019-03-01; 529.29-42.
Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO)
Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH
PMID: 30660046
Methods in molecular biology (Clifton, N.J.). 2019-01-01; 1911.47-69.
Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR)
Zhang Y, Zmasek C, Sun G, Larsen CN, Scheuermann RH
PMID: 30593617
PloS one. 2018-12-26; 13.12: e0209648.
Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B
PMID: 30586455
mBio. 2018-10-16; 9.5:
Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells
Brown DM, Hixon AM, Oldfield LM, Zhang Y, Novotny M, Wang W, Das SR, Shabman RS, Tyler KL, Scheuermann RH
PMID: 30327438
Blood advances. 2018-10-09; 2.19: 2419-2429.
Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant
Wang W, Huang H, Halagan M, Vierra-Green C, Heuer M, Brelsford JE, Haagenson M, Scheuermann RH, Telenti A, Biggs W, Pearson NM, Udell J, Spellman S, Maiers M, Kennedy CJ
PMID: 30262602
Nature neuroscience. 2018-09-01; 21.9: 1185-1195.
Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type
Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Close JL, Diez-Fuertes F, Ding SL, Faragó N, Kocsis ÁK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G
PMID: 30150662
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2018-06-01; 93.6: 597-610.
DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data
Lee AJ, Chang I, Burel JG, Lindestam Arlehamn CS, Mandava A, Weiskopf D, Peters B, Sette A, Scheuermann RH, Qian Y
PMID: 29665244
Viruses. 2018-05-14; 10.5:
Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting
Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M
PMID: 29757994
Frontiers in immunology. 2018-05-08; 9.976.
VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements
Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT, Fonner JM, Levin MK, Kim M, Mock SA, Jordan C, Ostmeyer J, Buntzman A, Rubelt F, Davila ML, Monson NL, Scheuermann RH, Cowell LG
PMID: 29867956
Human molecular genetics. 2018-05-01; 27.R1: R40-R47.
Cell type discovery using single-cell transcriptomics: implications for ontological representation
Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH
PMID: 29590361
The Journal of allergy and clinical immunology. 2018-02-01; 141.2: 775-777.e6.
Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells
Schulten V, Tripple V, Seumois G, Qian Y, Scheuermann RH, Fu Z, Locci M, Rosales S, Vijayanand P, Sette A, Alam R, Crotty S, Peters B
PMID: 28506846
BMC bioinformatics. 2017-12-21; 18.Suppl 17: 559.
Cell type discovery and representation in the era of high-content single cell phenotyping
Bakken T, Cowell L, Aevermann BD, Novotny M, Hodge R, Miller JA, Lee A, Chang I, McCorrison J, Pulendran B, Qian Y, Schork NJ, Lasken RS, Lein ES, Scheuermann RH
PMID: 29322913
Clinics in laboratory medicine. 2017-12-01; 37.4: 931-944.
Automated Analysis of Clinical Flow Cytometry Data: A Chronic Lymphocytic Leukemia Illustration
Scheuermann RH, Bui J, Wang HY, Qian Y
PMID: 29128077
BMC bioinformatics. 2017-10-11; 18.1: 448.
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data
Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG
PMID: 29020925
Proceedings of the National Academy of Sciences of the United States of America. 2017-07-25; 114.30: 8059-8064.
Fast and accurate HLA typing from short-read next-generation sequence data with xHLA
Xie C, Yeo ZX, Wong M, Piper J, Long T, Kirkness EF, Biggs WH, Bloom K, Spellman S, Vierra-Green C, Brady C, Scheuermann RH, Telenti A, Howard S, Brewerton S, Turpaz Y, Venter JC
PMID: 28674023
Nucleic acids research. 2017-01-04; 45.D1: D466-D474.
Influenza Research Database: An integrated bioinformatics resource for influenza virus research
Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH
PMID: 27679478
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2017-01-01; 22.564-575.
PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX
Aevermann B, McCorrison J, Venepally P, Hodge R, Bakken T, Miller J, Novotny M, Tran DN, Diezfuertes F, Christiansen L, Zhang F, Steemers F, Lasken RS, Lein ED, Schork N, Scheuermann RH
PMID: 27897007
Virus evolution. 2016-06-15; 2.1: vew015.
Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak
Zhang Y, Cao J, Zhang S, Lee AJ, Sun G, Larsen CN, Zhao H, Gu Z, He S, Klem EB, Scheuermann RH
PMID: 28512577
PloS one. 2016-04-29; 11.4: e0154556.
The Ontology for Biomedical Investigations
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J
PMID: 27128319
Nature protocols. 2016-03-01; 11.3: 499-524.
Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons
Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS
PMID: 26890679
Scientific reports. 2016-02-10; 6.20686.
Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium
Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, Pontikos N, Diaz A, Heck S, Villanova F, Terrazzini N, Kern F, Qian Y, Stanton R, Wang K, Brandes A, Ramey J, Aghaeepour N, Mosmann T, Scheuermann RH, Reed E, Palucka K, Pascual V, Blomberg BB, Nestle F, Nussenblatt RB, Brinkman RR, Gottardo R, Maecker H, McCoy JP
PMID: 26861911
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2016-01-01; 89.1: 71-88.
Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure
Hsiao C, Liu M, Stanton R, McGee M, Qian Y, Scheuermann RH
PMID: 26274018
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2016-01-01; 89.1: 16-21.
A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes
Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR
PMID: 26447924
Vaccine. 2015-08-26; 33.36: 4368-82.
Strengthening the influenza vaccine virus selection and development process: Report of the 3rd WHO Informal Consultation for Improving Influenza Vaccine Virus Selection held at WHO headquarters, Geneva, Switzerland, 1-3 April 2014
Sanouri TA, Alexander B, Alhammad BA, Alonso W, Ampofo WK, Azziz-Baumgartner E, Barakat A, Baric R, Barnes JR, Bashir U, Baumeister E, Hutchinson F, Belmont JW, Bogner P, Bruno A, Bucher D, Daniels P, Oliviera Rd, Donis R, Santos GD, Engelhardt OG, Garten R, Giovanni M, Guriev V, Gysin R, Huang S, Hungnes O, Jackson S, Kang C, Khramstov N, Lal R, Lassig M, Le QM, Le VP, Li Y, Liu MT, Martinez IL, McCauley J, Miyaki C, Paget J, Precioso A, Rydland KM, Sasono PM, Schweiger B, Shinde V, Siqueira M, Stevens J, Su IJ, Swayne DE, Thompson C, Waddell AL, Wang D, Wentworth D, Wildner O, Xiyan X, Xuemei Z, Ziegler T, Barr I, Bedford T, Blum M, Boschetti N, Bright H, Chadha M, Chen Y, Chen Z, Cox N, Di Francesco V, Dinarvand R, Donabedian A, Eichelberger M, Enouf V, Evseenko V, Fasce R, Fries LF, Gerentes L, Guan Y, Guillebaud J, Hay A, Hirve S, Hongje Y, Jernigan D, Katz J, Waiboci L, Wairagkar N, Walaza S, Wan XF, Webby R, Weir J, Wood J, Yamashita M, Yingyong T, Zambon M, Zhiping Y, Kazanji M, Laurie K, Luksza M, Mbayame N, Mironenko A, Mokhtari-Azad T, Mol E, Neumeier E, Njoum R, Penttinen P, Prosenc K, Rahman M, Rambaut A, Raw I, Sawanpanyalert P, Scheuermann R, Setiawaty V, Shu Y, Smith D, Spinu I, Spiro D, Tashiro M, Taylor B, Treurnicht F, Villanueva J
PMID: 26148877
Immunity. 2015-04-21; 42.4: 591-2.
Thinking outside the gate: single-cell assessments in multiple dimensions
Kvistborg P, Gouttefangeas C, Aghaeepour N, Cazaly A, Chattopadhyay PK, Chan C, Eckl J, Finak G, Hadrup SR, Maecker HT, Maurer D, Mosmann T, Qiu P, Scheuermann RH, Welters MJ, Ferrari G, Brinkman RR, Britten CM
PMID: 25902473
Evolutionary bioinformatics online. 2015-03-16; 11.43-8.
A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA
PMID: 25861210
Scientific data. 2014-10-14; 1.140033.
A comprehensive collection of systems biology data characterizing the host response to viral infection
Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH
PMID: 25977790
Nature methods. 2013-03-01; 10.3: 228-38.
Critical assessment of automated flow cytometry data analysis techniques
Aghaeepour N, Finak G, FlowCAP Consortium, DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH
PMID: 23396282
AMIA ... Annual Symposium proceedings. AMIA Symposium. 2012-11-03; 2012.779-88.
A machine learning approach for identifying anatomical locations of actionable findings in radiology reports
Roberts K, Rink B, Harabagiu SM, Scheuermann RH, Toomay S, Browning T, Bosler T, Peshock R
PMID: 23304352
Nucleic acids research. 2012-01-01; 40.Database issue: D593-8.
ViPR: an open bioinformatics database and analysis resource for virology research
Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, Liu M, Kumar S, Zaremba S, Gu Z, Zhou L, Larson CN, Dietrich J, Klem EB, Scheuermann RH
PMID: 22006842
Journal of biomedical informatics. 2011-02-01; 44.1: 3-7.
Ontologies for clinical and translational research: Introduction
Smith B, Scheuermann RH
PMID: 21241822
Viruses. 2010-10-13; 2.10: 2258-2268.
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop
Brister JR, Bao Y, Kuiken C, Lefkowitz EJ, Mercier PL, Le Mercier P, Leplae R, Madupu R, Scheuermann RH, Schobel S, Seto D, Shrivastava S, Sterk P, Zeng Q, Klimke W, Tatusova T
PMID: 21994619
Cytometry. Part B, Clinical cytometry. 2010-01-01; 78 Suppl 1.S69-82.
Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data
Qian Y, Wei C, Eun-Hyung Lee F, Campbell J, Halliley J, Lee JA, Cai J, Kong YM, Sadat E, Thomson E, Dunn P, Seegmiller AC, Karandikar NJ, Tipton CM, Mosmann T, Sanz I, Scheuermann RH
PMID: 20839340
Summit on translational bioinformatics. 2009-03-01; 2009.116-20.
Toward an ontological treatment of disease and diagnosis
Scheuermann RH, Ceusters W, Smith B
PMID: 21347182
BMC bioinformatics. 2009-02-25; 10.70.
An improved ontological representation of dendritic cells as a paradigm for all cell types
Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG
PMID: 19243617
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2008-10-01; 73.10: 926-30.
MIFlowCyt: the minimum information about a Flow Cytometry Experiment
Lee JA, Spidlen J, Boyce K, Cai J, Crosbie N, Dalphin M, Furlong J, Gasparetto M, Goldberg M, Goralczyk EM, Hyun B, Jansen K, Kollmann T, Kong M, Leif R, McWeeney S, Moloshok TD, Moore W, Nolan G, Nolan J, Nikolich-Zugich J, Parrish D, Purcell B, Qian Y, Selvaraj B, Smith C, Tchuvatkina O, Wertheimer A, Wilkinson P, Wilson C, Wood J, Zigon R, International Society for Advancement of Cytometry Data Standards Task Force, Scheuermann RH, Brinkman RR
PMID: 18752282
Coronavirus Research
Overview of various projects related to the novel coronavirus pandemic.Discriminative Machine Learning for Blood Cancer Precision Diagnostics
Our goal is to improve and utilize machine intelligence for elucidating cancer heterogeneity and disease endotypes for supporting cancer precision medicine.
05-Sep-2023
National Library of Medicine
NLM Selects Dr. Richard H. Scheuermann as Scientific Director for the National Library of Medicine
04-Sep-2023
Collaborator Release
PolyBio Research Foundation Consortium & colleagues publishes Nature position paper on SARS-CoV-2 reservoir in Long COVID/PASC
18-Jul-2023
Collaborator Release
Using AI to speed up vaccine development against Disease X
01-Jun-2023
Collaborator Release
Family resemblance: How T cells could fight many coronaviruses at once
LJI researchers work to head off future pandemics by uncovering key similarities between SARS-CoV-2 and common cold coronaviruses
29-Mar-2023
Collaborator Release
Scientists aim to develop vaccine against all deadly coronaviruses
$8 million NIH grant supports effort to avert next pandemic
08-Sep-2022
Reuters
Top scientists join forces to study leading theory behind long COVID
Several JCVI scientists will be contributing to the newly launched Long Covid Research Initiative — a collaboration of researchers, clinicians, and patients working to rapidly study and treat long Covid.
03-Mar-2021
Blog
SARS-CoV-2 Mutation Tracking
24-Dec-2020
The San Diego Union Tribune
Scientists rush to determine if mutant strain of coronavirus will deepen pandemic
U.S. researchers have been slow to perform the genetic sequencing that will help clarify the situation
17-Mar-2020
Blog
Coronavirus Pandemic: Putting Comprehensive Genomic Data in the Hands of Frontline Researchers Worldwide is Paramount
12-Mar-2020
Collaborator Release
LJI Scientists Identify Potential Targets for Immune Responses to Novel Coronavirus
The research, which includes comparative genomics analysis by JCVI scientists Yun Zhang and Richard Scheuermann, provides essential information about the human immune response to coronavirus infection that will guide the design and evaluation of diagnostics and vaccine candidates
01-Jun-2019
Asia Times
How AI can help us decode immunity
Artificial intelligence and machine learning will be the keys to unraveling how the human immune system prevents and controls disease
05-Nov-2018
Blog
Fighting Back Against Flu
11-Sep-2018
Blog
Newly Discovered Human Brain Cell: Rosehip Neurons
27-Aug-2018
Collaborator Release
Scientists identify a new kind of human brain cell
‘Rosehip’ neurons not found in rodents, may be involved in fine-level control between regions of the human brain
26-Jun-2018
Collaborator Release
S2 Genomics Awarded $280,000 Phase I STTR Grant from the National Institutes of Health
S2 Genomics will develop the Singulator™ system for automated preparation of single cells or nuclei from solid tissue samples
19-Apr-2018
Blog
JCVI to Receive Grant from Chan Zuckerberg Initiative to Define the Language of Human Cell Classification
08-Feb-2018
Blog