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ResearcherID: K-3728-2016
Scopus Author ID: 55644101100

Keywords

Computational Biology, Bioinformatics, Genomics, Computer Science, Web Development

Countries

United States

Biography

Kamil Slowikowski is a computational biologist working as a postdoc in the Center for Immunology and Inflammatory Diseases at Massachusetts General Hospital under the mentorship of Dr. Alexandra-Chloé Villani. He completed a PhD in Bioinformatics and Integrative Genomics at Harvard under the mentorship of Dr. Soumya Raychaudhuri at the Department of Biomedical Informatics and in close collaboration with Dr. Michael B. Brenner at the Brigham and Women's Hospital. He develops open-source computational software packages for single cell RNA-seq data and genetics data, and makes interactive web apps to help researchers interpret the primary data from biomedical studies.

Activities

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Employment (1)

Massachusetts General Hospital: Charlestown, MA, US

2019-08 to present | Postdoctoral Associate (Center for Immunology and Inflammatory Diseases)
Employment
Source: Self-asserted source
Kamil Slowikowski

Education and qualifications (1)

Harvard University: Boston, MA, US

2012-08-22 to 2019-04-16 | PhD (Bioinformatics and Integrative Genomics)
Education
Source: Self-asserted source
Kamil Slowikowski

Funding (2)

Transcriptomics in synoviocytes defines pathogenesis of rheumatoid arthritis

2016-09-01 to 2018-08-31 | Grant
National Institute of Arthritis and Musculoskeletal and Skin Diseases (n/a, US)
URL: https://grants.uberresearch.com/100000069/F31AR070582/Transcriptomics-in-synoviocytes-defines-pathogenesis-of-rheumatoid-arthritis
GRANT_NUMBER: grant.F31AR070582
Source: Self-asserted source
Kamil Slowikowski via DimensionsWizard

Training in Bioinformatics and Integrative Genomics

2000-07-01 to 2018-08-31 | Grant
National Human Genome Research Institute (Bethesda, US)
GRANT_NUMBER: 2T32HG002295-11
GRANT_NUMBER: 2T32HG002295-11
Source: Self-asserted source
Kamil Slowikowski via DimensionsWizard

Works (29)

Single-cell transcriptomics in cancer: computational challenges and opportunities

Experimental & Molecular Medicine
2020-09-15 | Journal article
DOI: 10.1038/s12276-020-0422-0
Contributors: Jean Fan; Kamil Slowikowski; Fan Zhang
Source: check_circle
Crossref

Synoviocyte-targeted therapy synergizes with TNF inhibition in arthritis reversal

Science Advances
2020-06 | Journal article
DOI: 10.1126/sciadv.aba4353
Part of ISSN: 2375-2548
Contributors: Mattias N. D. Svensson; Martina Zoccheddu; Shen Yang; Gyrid Nygaard; Christian Secchi; Karen M. Doody; Kamil Slowikowski; Fumitaka Mizoguchi; Frances Humby; Rebecca Hands et al.
Source: Self-asserted source
Kamil Slowikowski via Crossref Metadata Search

A positively selected FBN1 missense variant reduces height in Peruvian individuals

Nature
2020-06-11 | Journal article
DOI: 10.1038/s41586-020-2302-0
Contributors: Samira Asgari; Yang Luo; Ali Akbari; Gillian M. Belbin; Xinyi Li; Daniel N. Harris; Martin Selig; Eric Bartell; Roger Calderon; Kamil Slowikowski et al.
Source: check_circle
Crossref

Using genetics to prioritize diagnoses for rheumatology outpatients with inflammatory arthritis

Science Translational Medicine
2020-05-27 | Journal article
DOI: 10.1126/scitranslmed.aay1548
Contributors: Rachel Knevel; Saskia le Cessie; Chikashi C. Terao; Kamil Slowikowski; Jing Cui; Tom W. J. Huizinga; Karen H. Costenbader; Katherine P. Liao; Elizabeth W. Karlson; Soumya Raychaudhuri
Source: check_circle
Crossref

CUX1 and IκBζ (NFKBIZ) mediate the synergistic inflammatory response to TNF and IL-17A in stromal fibroblasts

Proceedings of the National Academy of Sciences
2020-03-10 | Journal article
DOI: 10.1073/pnas.1912702117
Contributors: Kamil Slowikowski; Hung N. Nguyen; Erika H. Noss; Daimon P. Simmons; Fumitaka Mizoguchi; Gerald F. M. Watts; Michael F. Gurish; Michael B. Brenner; Soumya Raychaudhuri
Source: check_circle
Crossref

Fast, sensitive and accurate integration of single-cell data with Harmony

Nature Methods
2019-11-18 | Journal article
DOI: 10.1038/s41592-019-0619-0
Part of ISSN: 1548-7091
Part of ISSN: 1548-7105
Source: Self-asserted source
Kamil Slowikowski

Using genetics to differentiate patients with similar symptoms: application to inflammatory arthritis in the rheumatology outpatient clinic

2019-10-22 | Other
DOI: 10.1101/813220
Contributors: Rachel Knevel; Saskia le Cessie; Chikashi C. Terao; Kamil Slowikowski; Jing Cui; Tom W.J. Huizinga; Karen H. Costenbader; Katherine P. Liao; Elizabeth W. Karlson; Soumya Raychaudhuri
Source: check_circle
Crossref

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

Nature Immunology
2019-05-06 | Journal article
DOI: 10.1038/s41590-019-0378-1
Part of ISSN: 1529-2908
Part of ISSN: 1529-2916
Source: Self-asserted source
Kamil Slowikowski

CUX1 and IκBζ mediate the synergistic inflammatory response to TNF and IL-17A in stromal fibroblasts

2019-03-11 | Other
DOI: 10.1101/571315
Contributors: Kamil Slowikowski; Hung N. Nguyen; Erika H. Noss; Daimon P. Simmons; Fumitaka Mizoguchi; Gerald F.M. Watts; Michael F. Gurish; Michael B. Brenner; Soumya Raychaudhuri
Source: check_circle
Crossref

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions

Nature Communications
2019-02-08 | Journal article
DOI: 10.1038/s41467-019-08604-4
Contributors: Maria Gutierrez-Arcelus; Nikola Teslovich; Alex R. Mola; Rafael B. Polidoro; Aparna Nathan; Hyun Kim; Susan Hannes; Kamil Slowikowski; Gerald F. M. Watts; Ilya Korsunsky et al.
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Functional genomics of stromal cells in chronic inflammatory diseases

Current Opinion in Rheumatology
2018 | Journal article
DOI: 10.1097/BOR.0000000000000455
EID:

2-s2.0-85036555141
Contributors: Slowikowski, K.; Wei, K.; Brenner, M.B.; Raychaudhuri, S.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier
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Methods for high-dimensonal analysis of cells dissociated from cyropreserved synovial tissue

Arthritis Research and Therapy
2018 | Journal article
DOI: 10.1186/s13075-018-1631-y
EID:

2-s2.0-85050025146
Contributors: Donlin, L.T.; Rao, D.A.; Wei, K.; Slowikowski, K.; McGeachy, M.J.; Turner, J.D.; Meednu, N.; Mizoguchi, F.; Gutierrez-Arcelus, M.; Lieb, D.J. et al.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier

Fast, sensitive, and accurate integration of single cell data with Harmony

2018-11-04 | Other
DOI: 10.1101/461954
Contributors: Ilya Korsunsky; Jean Fan; Kamil Slowikowski; Fan Zhang; Kevin Wei; Yuriy Baglaenko; Michael Brenner; Po-Ru Loh; Soumya Raychaudhuri
Source: check_circle
Crossref

Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial

Genome Biology
2018-10 | Journal article
DOI: 10.1186/s13059-018-1560-8
Version of DOI: 10.1101/118703
Part of ISSN: 1474-760X
Source: Self-asserted source
Kamil Slowikowski
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Mixed-effects association of single cells identifies an expanded effector CD4 + T cell subset in rheumatoid arthritis

Science Translational Medicine
2018-10-17 | Journal article
DOI: 10.1126/scitranslmed.aaq0305
Contributors: Chamith Y. Fonseka; Deepak A. Rao; Nikola C. Teslovich; Ilya Korsunsky; Susan K. Hannes; Kamil Slowikowski; Michael F. Gurish; Laura T. Donlin; James A. Lederer; Michael E. Weinblatt et al.
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Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

Nature Genetics
2018-04 | Journal article
DOI: 10.1038/s41588-018-0081-4
Contributors: Hilary K. Finucane; Yakir A. Reshef; Verneri Anttila; Kamil Slowikowski; Alexander Gusev; Andrea Byrnes; Steven Gazal; Po-Ru Loh; Caleb Lareau; Noam Shoresh et al.
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Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis

Nature Communications
2018-02-23 | Journal article
DOI: 10.1038/s41467-018-02892-y
Contributors: Fumitaka Mizoguchi; Kamil Slowikowski; Kevin Wei; Jennifer L. Marshall; Deepak A. Rao; Sook Kyung Chang; Hung N. Nguyen; Erika H. Noss; Jason D. Turner; Brandon E. Earp et al.
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Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis

Nature
2017 | Journal article
DOI: 10.1038/nature20810
EID:

2-s2.0-85011994125
Contributors: Rao, D.A.; Gurish, M.F.; Marshall, J.L.; Slowikowski, K.; Fonseka, C.Y.; Liu, Y.; Donlin, L.T.; Henderson, L.A.; Wei, K.; Mizoguchi, F. et al.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier

Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples

Nature Genetics
2017 | Journal article
DOI: 10.1038/ng.3789
EID:

2-s2.0-85012277777
Contributors: Kosmicki, J.A.; Samocha, K.E.; Howrigan, D.P.; Sanders, S.J.; Slowikowski, K.; Lek, M.; Karczewski, K.J.; Cutler, D.J.; Devlin, B.; Roeder, K. et al.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier

Mixed Effects Association of Single Cells Identifies an Expanded Th1-Skewed Cytotoxic Effector CD4+ T Cell Subset in Rheumatoid Arthritis

2017-08-04 | Preprint
DOI: 10.1101/172403
Contributors: Chamith Y. Fonseka; Deepak A. Rao; Nikola C. Teslovich; Susan K. Hannes; Kamil Slowikowsi; Michael F. Gurish; Laura T. Donlin; Michael E. Weinblatt; Elena M. Massarotti; Jonathan S. Coblyn et al.
Source: check_circle
Crossref

UBiT2: a client-side web-application for gene expression data analysis

2017-03-22 | Other
DOI: 10.1101/118992
Contributors: Jean Fan; David Fan; Kamil Slowikowski; Nils Gehlenborg; Peter Kharchenko
Source: check_circle
Crossref

52 Genetic Loci Influencing Myocardial Mass

Journal of the American College of Cardiology
2016 | Journal article
DOI: 10.1016/j.jacc.2016.07.729
EID:

2-s2.0-84990929556
Contributors: van der Harst, P.; van Setten, J.; Verweij, N.; Vogler, G.; Franke, L.; Maurano, M.T.; Wang, X.; Mateo Leach, I.; Eijgelsheim, M.; Sotoodehnia, N. et al.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier

A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases

Nature Genetics
2016 | Journal article
DOI: 10.1038/ng.3572
EID:

2-s2.0-84968627067
Contributors: Han, B.; Pouget, J.G.; Slowikowski, K.; Stahl, E.; Lee, C.H.; Diogo, D.; Hu, X.; Park, Y.R.; Kim, E.; Gregersen, P.K. et al.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci

American Journal of Human Genetics
2015 | Journal article
DOI: 10.1016/j.ajhg.2015.05.016
EID:

2-s2.0-84937424402
Contributors: Trynka, G.; Westra, H.-J.; Slowikowski, K.; Hu, X.; Xu, H.; Stranger, B.E.; Klein, R.J.; Han, B.; Raychaudhuri, S.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier

Common genetic variants modulate pathogen-sensing responses in human dendritic cells

Science
2014 | Journal article
DOI: 10.1126/science.1246980
EID:

2-s2.0-84896759364
Contributors: Lee, M.N.; Ye, C.; Villani, A.-C.; Raj, T.; Li, W.; Eisenhaure, T.M.; Imboywa, S.H.; Chipendo, P.I.; Ran, F.A.; Slowikowski, K. et al.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization

Nature Genetics
2014 | Journal article
DOI: 10.1038/ng.3014
EID:

2-s2.0-84905594041
Contributors: Arking, D.E.; Pulit, S.L.; Crotti, L.; Van Der Harst, P.; Munroe, P.B.; Koopmann, T.T.; Sotoodehnia, N.; Rossin, E.J.; Morley, M.; Wang, X. et al.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier

Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4<sup>+</sup> Effector Memory T Cells

PLoS Genetics
2014 | Journal article
DOI: 10.1371/journal.pgen.1004404
EID:

2-s2.0-84903457544
Contributors: Hu, X.; Kim, H.; Raj, T.; Brennan, P.J.; Trynka, G.; Teslovich, N.; Slowikowski, K.; Chen, W.-M.; Onengut, S.; Baecher-Allan, C. et al.
Source: Self-asserted source
Kamil Slowikowski via Scopus - Elsevier

SNPsea: an algorithm to identify cell types, tissues, and pathways affected by risk loci

Bioinformatics
2014-05-10 | Journal article
DOI: 10.1093/bioinformatics/btu326
Part of ISSN: 1367-4803
Contributors: K. Slowikowski; X. Hu; S. Raychaudhuri
Source: Self-asserted source
Kamil Slowikowski via Crossref Metadata Search
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Computational and experimental analyses of retrotransposon-associated minisatellite DNAs in the soybean genome

BMC Bioinformatics
2012 | Journal article
DOI: 10.1186/1471-2105-13-s2-s13
Part of ISSN: 1471-2105
Contributors: Lauren S Mogil; Kamil Slowikowski; Howard M Laten
Source: Self-asserted source
Kamil Slowikowski via Crossref Metadata Search
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