Search Results - "Brooks, Thomas G."

Comparative evaluation of full-length isoform quantification from RNA-Seq by Sarantopoulou, Dimitra, Brooks, Thomas G, Nayak, Soumyashant, Mrcela, Antonijo, Lahens, Nicholas F, Grant, Gregory R

“…Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The…”
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Diurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank by Brooks, Thomas G., Lahens, Nicholas F., Grant, Gregory R., Sheline, Yvette I., FitzGerald, Garret A., Skarke, Carsten

“…Many chronic disease symptomatologies involve desynchronized sleep-wake cycles, indicative of disrupted biorhythms. This can be interrogated using body…”
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Accounting for Time: Circadian Rhythms in the Time of COVID-19 by Sengupta, Shaon, Brooks, Thomas G., Grant, Gregory R., FitzGerald, Garret A.

“…The COVID-19 pandemic has necessitated novel approaches and collaborative efforts across multiple disciplines. It is known that various aspects of our…”
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CAMPAREE: a robust and configurable RNA expression simulator by Lahens, Nicholas F, Brooks, Thomas G, Sarantopoulou, Dimitra, Nayak, Soumyashant, Lawrence, Cris, Mrčela, Antonijo, Srinivasan, Anand, Schug, Jonathan, Hogenesch, John B, Barash, Yoseph, Grant, Gregory R

“…The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms…”
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Loss of circadian protection against influenza infection in adult mice exposed to hyperoxia as neonates by Issah, Yasmine, Naik, Amruta, Tang, Soon Y, Forrest, Kaitlyn, Brooks, Thomas G, Lahens, Nicholas, Theken, Katherine N, Mermigos, Mara, Sehgal, Amita, Worthen, George S, FitzGerald, Garret A, Sengupta, Shaon

“…Adverse early-life exposures have a lasting negative impact on health. Neonatal hyperoxia that is a risk factor for bronchopulmonary dysplasia confers…”
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Deep phenotyping of the lipidomic response in COVID‐19 and non‐COVID‐19 sepsis by Meng, Hu, Sengupta, Arjun, Ricciotti, Emanuela, Mrčela, Antonijo, Mathew, Divij, Mazaleuskaya, Liudmila L., Ghosh, Soumita, Brooks, Thomas G., Turner, Alexandra P., Schanoski, Alessa Soares, Lahens, Nicholas F., Tan, Ai Wen, Woolfork, Ashley, Grant, Greg, Susztak, Katalin, Letizia, Andrew G., Sealfon, Stuart C., Wherry, E. John, Laudanski, Krzysztof, Weljie, Aalim M., Meyer, Nuala J., FitzGerald, Garret A.

“…Background Lipids may influence cellular penetrance by viral pathogens and the immune response that they evoke. We deeply phenotyped the lipidomic response to…”
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Circadian regulation of lung repair and regeneration by Naik, Amruta, Forrest, Kaitlyn M, Paul, Oindrila, Issah, Yasmine, Valekunja, Utham K, Tang, Soon Y, Reddy, Akhilesh B, Hennessy, Elizabeth J, Brooks, Thomas G, Chaudhry, Fatima, Babu, Apoorva, Morley, Michael, Zepp, Jarod A, Grant, Gregory R, FitzGerald, Garret A, Sehgal, Amita, Worthen, G Scott, Frank, David B, Morrisey, Edward E, Sengupta, Shaon

“…Optimal lung repair and regeneration are essential for recovery from viral infections, including influenza A virus (IAV). We have previously demonstrated that…”
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Challenges and best practices in omics benchmarking by Brooks, Thomas G., Lahens, Nicholas F., Mrčela, Antonijo, Grant, Gregory R.

“…Technological advances enabling massively parallel measurement of biological features — such as microarrays, high-throughput sequencing and mass spectrometry —…”
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Meta-analysis of Diurnal Transcriptomics in Mouse Liver Reveals Low Repeatability of Rhythm Analyses by Brooks, Thomas G., Manjrekar, Aditi, Mrcˇela, Antonijo, Grant, Gregory R.

“…To assess the consistency of biological rhythms across studies, 57 public mouse liver tissue timeseries totaling 1096 RNA-seq samples were obtained and…”
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Nonnegative curvature and conullity of the curvature tensor by Brooks, Thomas G.

“…The conullity of a curvature tensor is the codimension of its kernel. We consider the cases of conullity two in any dimension and conullity 3 in dimension…”
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Sexual dimorphism in the response to chronic circadian misalignment on a high-fat diet by Anderson, Seán T, Meng, Hu, Brooks, Thomas G, Tang, Soon Yew, Lordan, Ronan, Sengupta, Arjun, Nayak, Soumyashant, Mřela, Antonijo, Sarantopoulou, Dimitra, Lahens, Nicholas F, Weljie, Aalim, Grant, Gregory R, Bushman, Frederic D, FitzGerald, Garret A

“…Longitudinal studies associate shiftwork with cardiometabolic disorders but do not establish causation or elucidate mechanisms of disease. We developed a mouse…”
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BEERS2: RNA-Seq simulation through high fidelity in silico modeling by Brooks, Thomas G, Lahens, Nicholas F, Mrčela, Antonijo, Sarantopoulou, Dimitra, Nayak, Soumyashant, Naik, Amruta, Sengupta, Shaon, Choi, Peter S, Grant, Gregory R

“…Abstract Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq…”
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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 by El Jamal, Nadim, Brooks, Thomas G., Cohen, Jordana, Townsend, Raymond R., Sosa, Giselle Rodriguez de, Shah, Vallabh, Nelson, Robert G., Drawz, Paul E., Rao, Panduranga, Bhat, Zeenat, Chang, Alexander, Yang, Wei, FitzGerald, Garret A., Skarke, Carsten

“…Chronic kidney disease (CKD) represents a significant global burden. Hypertension is a modifiable risk factor for rapid progression of CKD. We extend the risk…”
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Nitecap: An Exploratory Circadian Analysis Web Application by Brooks, Thomas G., Mrčela, Antonijo, Lahens, Nicholas F., Paschos, Georgios K., Grosser, Tilo, Skarke, Carsten, FitzGerald, Garret A., Grant, Gregory R.

“…Circadian omics analyses present investigators with large amounts of data to consider and many choices for methods of analysis. Visualization is crucial as…”
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Targeting MRTF/SRF in CAP2-dependent dilated cardiomyopathy delays disease onset by Xiong, Yao, Bedi, Kenneth, Berritt, Simon, Attipoe, Bennette K, Brooks, Thomas G, Wang, Kevin, Margulies, Kenneth B, Field, Jeffrey

“…About one-third of dilated cardiomyopathy (DCM) cases are caused by mutations in sarcomere or cytoskeletal proteins. However, treating the cytoskeleton…”
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Circadian regulation of lung repair and regeneration by Naik, Amruta, Forrest, Kaitlyn M, Paul, Oindrila, Issah, Yasmine, Valekunja, Utham K, Tang, Soon Y, Reddy, Akhilesh B, Hennessy, Elizabeth J, Brooks, Thomas G, Chaudhry, Fatima, Babu, Apoorva, Morley, Michael, Zepp, Jarod A, Grant, Gregory R, FitzGerald, Garret A, Sehgal, Amita, Worthen, G Scott, Frank, David B, Morrisey, Edward E, Sengupta, Shaon

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Genetic variants associated with chronic fatigue syndrome predict population-level fatigue severity and actigraphic measurements by Liu, Patrick Z, Raizen, David M, Skarke, Carsten, Brooks, Thomas G, Anafi, Ron C

“…The diagnosis of myalgic encephalomyelitis/chronic fatigue syndrome (CFS) is based on a constellation of symptoms which center around fatigue. However, fatigue…”
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A novel electrical method to measure wire tensions for time projection chambers by Garcia-Gamez, Diego, Basque, Vincent, Brooks, Thomas G., Evans, Justin J., Perry, Michael, Söldner-Rembold, Stefan, Spagliardi, Fabio, Szelc, Andrzej M.

“…We present a novel electrical technique to measure the tension of wires in multi-wire drift chambers. We create alternating electric fields by biasing adjacent…”
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Sampling Spiked Wishart Eigenvalues by Brooks, Thomas G

“…Efficient schemes for sampling from the eigenvalues of the Wishart distribution have recently been described for both the uncorrelated central case (where the…”
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Generating Sets of Mathieu Groups by Brooks, Thomas G

“…Julius Whiston calculated the maximum size of an irredundant generating set for $S_n$ and $A_n$ by examination of maximal subgroups. Using analogous…”
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