Thomas G. Brooks
- Research Associate
- ITMAT Bioinformatics Lab
- Institute for Translational Medicine and Therapeutics
- University of Pennsylvania
I'm a research associate at the ITMAT Bioinformatics lab. I study transcriptomics and RNA-seq methodology, circadian biology and diurnal rhythms. Previously, I studied Riemannian geometry.
Research Interests
- Transcriptomics, RNA-seq
- Diurnal rhythms
- Circadian biology
- Methods development and benchmarking
Education
- PostDoc in Bioinformatics, 2018-2023. University of Pennsylvania
- PhD in mathematics, 2013-2018. University of Pennsylvania
- BA in mathematics, 2009-2013. Cornell University
Projects
Temperature Rhythms
Skin temperature rhythms mark circadian rhythms in individuals, and are typically higher temperatures at night, opposite to the core body temperature rhythms. We use a measurement of wrist temperature that captures this variability in the UK Biobank cohort to show that individuals with poor rhythms end up with substantially worse health outcomes. View our results at the Temperature Biorhythm Atlas.
Nitecap - Circadian Omics Webapp
The transcriptome varies dramatically through the day. But these datasets are large and difficult to explore, so we made a web app that makes it easy to view, process, and share timeseries omics datasets. Try it out at nitecap.org.
RNA-Seq Simulation - BEERS 2
RNA-seq is a foundational technology in modern biology, but involves many subtleties that influence data processing. Reads do not correspond one-to-one to input RNA transcripts, but must be aligned, quantified, and normalized to generate results. Each of these steps involves difficulties. Through detailed simulation of the RNA-seq process, including library preparation, we can address these difficulties and benchmark the performance of analysis methods.
dependentsimr
R package to simulate omics data with realistic correlation. Mimics the top PCA components of a dataset and is almost as simple and fast as generating entirely independent data.
See more projects on my github page.
Publications
- BEERS2: RNA-Seq simulation through high fidelity in silico modeling Brooks TG, Lahens NF, Mrcela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. Briefings in Bioinformatics. 2024 April.
- Challenges and best practices in omics benchmarking Brooks TG, Lahens NF, Mrcela A, Grant GR. Nature Reviews Genetics. 2024 January. https://doi.org/10.1038/s41576-023-00679-6
- Prognostic utility of rhythmic components in 24-h ambulatory blood pressure monitoring for the risk stratification of chronic kidney disease patients with cardiovascular co-morbidity El Jamal N, Brooks TG, Cohen J, Townsend RR, Rodriguez de Sosa G, Shah V, Chronic Renal Insufficiency Cohort Study (CRIC) Consortium, Nelson RG, Drawz PE, Rao P, Bhat Z, Chang A, Yang W, FitzGerald GA, Skarke C. Journal of Human Hypertension. 2024 January. https://doi.org/10.1038/s41371-023-00884-0
- Deep Phenotyping of the Lipidomic Response in COVID-19 and non-COVID-19 Sepsis. Meng H, Sengupta A, Ricciotti E, Mrcela A, Mathew D, Mazaleuskaya LL, Ghosh S, Brooks TG, Turner AP, Schanoski AS, Lahens NF, Tan AW, Woolfork A, Grant GR, Susztak K, Letizia AG, Sealfon SC, Wherry EJ, Laudanski K, Weljie AM, Meyer NJ, FitzGerald GA. Clinical and Translational Medicine. 2023 November. DOI: 10.1002/ctm2.1440
- Diurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank Brooks TG, Lahens NF, Grant GR, Sheline YI, FitzGerald GA, Skarke C. Nat Commun. 2023 August
- Circadian regulation of lung repair and regeneration Naik A, Forrest KM, Paul O, Issah Y, Valekunja UK, Tang SY, Akhilesh RB, Hennessy EJ, Brooks TG, Chaudhry F, Babu A, Morley M, Zepp JA, Grant GR, FitzGerald GA, Sehgal A, Worthen GS, Frank DB, Morrisey EE, Sengupta S. JCI Insight. 2023 July
- Meta-analysis of diurnal transcriptomics in mouse liver reveals low repeatability of rhythm analyses Brooks TG, Manjrekar A, Mrcela A, Grant GR. J Biol Rhythms. 2023 June
- Sexual dimorphism in the response to chronic circadian misalignment on a high fat diet. Anderson ST, Meng H, Brooks TG, et al. Sci Transl Med. 2023 May DOI: 10.1126/scitranslmed.abo2022
- No increase in inflammation in late-life major depression screened to exclude physical illness. Luning Prak ET, Brooks TG, Makhoul W, Beer JC, Zhao L, Girelli T, Skarke C, Sheline YI. Transl Psychiatry. 2022 Mar 12(1):118. doi: 10.1038/s41398-022-01883-4. PubMed PMID: 35332134.
- Nitecap: An Exploratory Circadian Analysis Web Application. Brooks TG, Mrcela A, Lahens NF, Paschos GK, Grosser T, Skarke CC, FitzGerald GA, Grant GR. J Biol Rhythms. 2022 Feb 37(1):43-52. doi: 10.1177/07487304211054408. Epub 2021 Nov 2. PubMed PMID: 34724846.
- CAMPAREE: a robust and configurable RNA expression simulator. Lahens* NF, Brooks* TG, Sarantopoulou D, Nayak S, Lawrence C, Mrcela A, Srinivasan A, Schug J, Hogenesch JB, Barash Y, Grant GR. BMC Genomics. 2021 Sep 22(1):692. doi: 10.1186/s12864-021-07934-2. PubMed PMID: 34563123; PubMed Central PMCID: PMC8467241.
- Comparative evaluation of full-length isoform quantification from RNA-Seq. Sarantopoulou* D, Brooks* TG, Nayak S, Mrcela A, Lahens NF, Grant GR. BMC Bioinformatics. 2021 May 22(1):266. PubMed PMID: 34034652.
- Loss of circadian protection against influenza infection in adult mice exposed to hyperoxia as neonates. Issah Y, Naik A, Tang SY, Forrest K, Brooks TG, Lahens N, Theken KN, Mermigos M, Sehgal A, Worthen GS, FitzGerald GA, Sengupta S. Elife. 2021 Mar 10. doi: 10.7554/eLife.61241. PubMed PMID: 33650487.
- Accounting for Time: Circadian Rhythms in the Time of COVID-19. Sengupta S, Brooks TG, Grant GR, FitzGerald GA. J Biol Rhythms. 2021 Feb 36(1):4-8. doi: 10.1177/0748730420953335. Epub 2020 Sep 2. Review. PubMed PMID: 32875944.
- Nonnegative curvature and conullity of the curvature tensor. Brooks TG. Annals of Global Analysis and Geometry. 2019 August. doi: https://doi.org/10.1007/s10455-019-09678-5.
- Targeting MRTF/SRF in CAP2-dependent dilated cardiomyopathy delays disease onset. Xiong Y, Bedi K, Berritt S, Attipoe BK, Brooks TG, Wang K, Margulies KB, Field J. JCI Insight. 2019 Mar 21 4(6). doi: 10.1172/jci.insight.124629. eCollection 2019 Mar 21. PubMed PMID: 30762586.
* indicates equal contributions
Pre-prints
- 3-Manifolds with Constant Ricci Eigenvalues (λ, λ, 0). Brooks TG. arXiv. November 2021. doi: 10.48550/arXiv.2111.15499