The Research Technologies Branch (RTB) Integrated Data Sciences Section (IDSS) provides scientific consultation, training and workshops, computational and data science support and collaboration on technology development projects. IDSS works with RTB technologies to develop a fully integrated resource for NIAID investigators that includes experimental design support through final data analysis and manuscript preparation. IDSS pipelines and software are available for use by NIAID investigators and staff along with focused workshops and training.
The IDSS collaborates with NIAID and NIH scientists to provide bioinformatics, data science, and computational biology expertise for genomics, proteomics, biostatistics, structural biology, image analysis and visualization (including 3D models and reconstructions), machine learning and AI, and molecular modeling (eg. AI applications for structure prediction, docking, complexes, etc.) and simulation. The IDSS brings together domain scientists with strong computational expertise to address complex scientific problems and leverages a shared team approach as projects often require expertise in multiple areas of data analysis and domain science that are beyond the expertise and capacity of a single analyst.
IDSS integrates resources from multiple NIH institutes including: National Institute of Allergy and Infectious Diseases (NIAID), National Heart Lung and Blood Institute (NHLBI), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), and National Cancer Institute (NCI). This allows IDSS to achieve an economy of scale and greater bandwidth to handle complex data analysis projects across a range of scientific domains.
Collaborative Technological Resources
IDSS offers collaborative technological resources such as structural biology; genomics, metagenomics, single cell, proteomics; machine learning/artificial intelligence (IA) image analysis; molecular modeling; clinical sequencing; experimental design; statistical analysis; and training classes.
Tools
IDSS pipelines and software are available for use by NIAID/NIH investigators and staff including focused workshops and training
Selected Publications
MoNuSAC2020: A Multi-Organ Nuclei Segmentation and Classification Challenge. IEEE Trans Med Imaging.
Verma R, Kumar N, Patil A, Kurian NC, Rane S, Graham S, Vu QD, Zwager M, Raza SEA, Rajpoot N, Wu X, Chen H, Huang Y, Wang L, Jung H, Brown GT, Liu Y, Liu S, Jahromi SAF, Khani AA, Montahaei E, Baghshah MS, Behroozi H, Semkin P, Rassadin A, Dutande P, Lodaya R, Baid U, Baheti B, Talbar S, Mahbod A, Ecker R, Ellinger I, Luo Z, Dong B, Xu Z, Yao Y, Lv S, Feng M, Xu K, Zunair H, Hamza AB, Smiley S, Yin TK, Fang QR, Srivastava S, Mahapatra D, Trnavska L, Zhang H, Narayanan PL, Law J, Yuan Y, Tejomay A, Mitkari A, Koka D, Ramachandra V, Kini L, Sethi A. 2021 Dec;40(12):3413-3423. doi: 10.1109/TMI.2021.3085712. Epub 2021 Nov 30. PMID: 34086562.
Immune responses to SARS-CoV2 mRNA vaccination in people with idiopathic CD4 lymphopenia.
Rocco JM, Boswell KL, Laidlaw E, Epling B, Anderson M, Serebryannyy L, Narpala S, O'Connell S, Kalish H, Kelly S, Porche S, Oguz C, McDermott A, Manion M, Koup RA, Lisco A, Sereti I. 2024 Feb; 153(2):503-512. https://doi.org/10.1016/j.jaci.2023.10.012.
TGFB prevents IgE-mediated allergic disease by restraining T follicular helper 2 differentiation.
Haque TT, Weissler KA, Schmiechen Z, Laky K, Schwartz DM, Li J, Locci M, Turfkruyer M, Yao C, Schaughency P, Leak L, Lack J, Kanno Y, O’Shea J, Frischmeyer-Guerrerio PA. 2024 Jan; eadg8691. doi:10.1126/sciimmunol.adg8691
Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19.
Sacco K, Castagnoli R, Vakkilainen S, Liu C, Delmonte OM, Oguz C, Kaplan IM, Alehashemi S, Burbelo PD, Bhuyan F, de Jesus AA, Dobbs K, Rosen LB, Cheng A, Shaw E, Vakkilainen MS, Pala F, Lack J, Zhang Y, Fink DL, Oikonomou V, Snow AL, Dalgard CL, Chen J, Sellers BA, Montealegre Sanchez GA, Barron K, Rey-Jurado E, Vial C, Poli MC, Licari A, Montagna D, Marseglia GL, Licciardi F, Ramenghi U, Discepolo V, Lo Vecchio A, Guarino A, Eisenstein EM, Imberti L, Sottini A, Biondi A, Mató S, Gerstbacher D, Truong M, Stack MA, Magliocco M, Bosticardo M, Kawai T, Danielson JJ, Hulett T, Askenazi M, Hu S; NIAID Immune Response to COVID Group; Chile MIS-C Group; Pavia Pediatric COVID-19 Group, Cohen JI, Su HC, Kuhns DB, Lionakis MS, Snyder TM, Holland SM, Goldbach-Mansky R, Tsang JS, Notarangelo LD. Nat Med. 2022 May;28(5):1050-1062. doi: 10.1038/s41591-022-01724-3. Epub 2022 Feb 17. PMID: 35177862; PMCID: PMC9119950.
OP059: Clinical Impact of a Targeted Pharmacogenomic Assessment Within a Cohort of Individuals with Suspected Inborn Errors of Immunity. Similuk, Morgan et al. Genetics in medicine 24.3 (2022): n. pag. Web.
Dromedary camel nanobodies broadly neutralize SARS-CoV-2 variants.
Hong J, Kwon HJ, Cachau R, Chen CZ, Butay KJ, Duan Z, Li D, Ren H, Liang T, Zhu J, Dandey VP, Martin NP, Esposito D, Ortega-Rodriguez U, Xu M, Borgnia MJ, Xie H, Ho M. Proc Natl Acad Sci U S A. 2022 May 3;119(18):e2201433119. doi: 10.1073/pnas.2201433119. Epub 2022 Apr 27. PMID: 35476528; PMCID: PMC9170159.
Combination anti-HIV antibodies provide sustained virological suppression.
Sneller MC, Blazkova J, Justement JS, Shi V, Kennedy BD, Gittens K, Tolstenko J, McCormack G, Whitehead EJ, Schneck RF, Proschan MA, Benko E, Kovacs C, Oguz C, Seaman MS, Caskey M, Nussenzweig MC, Fauci AS, Moir S, Chun TW. Nature. 2022 Jun;606(7913):375-381. doi: 10.1038/s41586-022-04797-9. Epub 2022 Jun 1. PMID: 35650437.
Clinical Exome Sequencing of 1000 Families with Complex Immune Phenotypes: Towards comprehensive genomic evaluations.
Similuk MN, Yan J, Ghosh R, Oler AJ, Franco LM, Setzer M, Kamen M, Jodarski C, DiMaggio T, Davis J, Gore R, Jamal L, Borges A, Gentile N, Niemela J, Lowe C, Jevtich K, Yu Y, Hullfish H, Hsu AP, Hong C, Littel P, Seifert BA, Milner J, Johnston JJ, Cheng X, Li Z, Veltri D, Huang K, Kaladi K, Barnett J, Zhang L, Vlasenko N, Fan Y, Karlins E, Ganakammal SR, Gilmore R, Tran E, Yun A, Mackey J, Yazhuk S, Lack J, Kuram V, Cao W, Huse S, Frank K, Fahle G, Rosenzweig S, Su Y, Hwang S, Bi W, Bennett J, Myles IA, De Ravin SS, Fussm I, Strober W, Bielekova B, Almeida de Jesus A, Goldbach-Mansky R, Williamson P, Kumar K, Dempsy C, Frischmeyer-Guerrerio P, Eisch R, Bolan H, Metcalfe DD, Komarow H, Carter M, Druey KM, Sereti I, Dropulic L, Klion AD, Khoury P, O' Connell EM, Holland-Thomas NC, Brown T, McDermott DH, Murphy PM, Bundy V, Keller MD, Peng C, Kim H, Norman S, Delmonte OM, Kang E, Su HC, Malech H, Freeman A, Zerbe C, Uzel G, Bergerson JRE, Rao VK, Olivier KN, Lyons JJ, Lisco A, Cohen JI, Lionakis MS, Biesecker LG, Xirasagar S, Notarangelo L, Holland SM, Walkiewicz MA. J Allergy Clin Immunol. 2022 Jun 23:S0091-6749(22)00839-9. doi: 10.1016/j.jaci.2022.06.009. Epub ahead of print. PMID: 35753512.
Access (Links may require NIH login)
To submit a project, go to the IDSS Bioinformatics submission portal.
Currently, collaborating with RTB is only available to federally funded institutions. Currently, collaborating with RTB is only available to federally funded institutions. Researchers may access all RTB support services by visiting RTB on Inside NIAID.
Leadership
Jack Collins, Ph.D.
Director, Integrated Data Science Section
Jack Collins, Ph.D.
Staff List
Jack R. Collins, Ph.D., Director, Integrated Data Science Section (IDSS)
Raul Cachau, Ph.D., Scientific Lead, Structural Biology, Molecular Modeling, Cheminformatics
Justin Lack, Ph.D., Scientific Lead, Bioinformatics
Yanling Liu, Ph.D., Scientific Lead, Image Analysis/AI
Randall Johnson, Ph.D., Scientific Lead, Statistics
BobbieJo McCord, Operations and Administration