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Nicholas F. Lahens, Ph.D. - Publications

Affiliations: 
Genomics and Computational Biology University of Pennsylvania, Philadelphia, PA, United States 
Area:
Circadian Rhythms, Functional Genomics
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25/43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity modeling. Biorxiv : the Preprint Server For Biology. PMID 37162982 DOI: 10.1101/2023.04.21.537847  0.315
2023 Vaquero-Garcia J, Aicher JK, Jewell S, Gazzara MR, Radens CM, Jha A, Norton SS, Lahens NF, Grant GR, Barash Y. RNA splicing analysis using heterogeneous and large RNA-seq datasets. Nature Communications. 14: 1230. PMID 36869033 DOI: 10.1038/s41467-023-36585-y  0.324
2021 Lahens NF, Brooks TG, Sarantopoulou D, Nayak S, Lawrence C, Mrčela A, Srinivasan A, Schug J, Hogenesch JB, Barash Y, Grant GR. CAMPAREE: a robust and configurable RNA expression simulator. Bmc Genomics. 22: 692. PMID 34563123 DOI: 10.1186/s12864-021-07934-2  0.562
2021 Slaff B, Radens CM, Jewell P, Jha A, Lahens NF, Grant GR, Thomas-Tikhonenko A, Lynch KW, Barash Y. MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis. Nature Communications. 12: 3353. PMID 34099673 DOI: 10.1038/s41467-021-23608-9  0.41
2021 Sarantopoulou D, Brooks TG, Nayak S, Mrčela A, Lahens NF, Grant GR. Comparative evaluation of full-length isoform quantification from RNA-Seq. Bmc Bioinformatics. 22: 266. PMID 34034652 DOI: 10.1186/s12859-021-04198-1  0.33
2021 Lee Y, Fong SY, Shon J, Zhang SL, Brooks R, Lahens NF, Chen D, Dang CV, Field JM, Sehgal A. Time-of-day specificity of anticancer drugs may be mediated by circadian regulation of the cell cycle. Science Advances. 7. PMID 33579708 DOI: 10.1126/sciadv.abd2645  0.687
2019 Sarantopoulou D, Tang SY, Ricciotti E, Lahens NF, Lekkas D, Schug J, Guo XS, Paschos GK, FitzGerald GA, Pack AI, Grant GR. Comparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input. Scientific Reports. 9: 13477. PMID 31530843 DOI: 10.1038/S41598-019-49889-1  0.463
2019 Lee Y, Lahens NF, Zhang S, Bedont J, Field JM, Sehgal A. G1/S cell cycle regulators mediate effects of circadian dysregulation on tumor growth and provide targets for timed anticancer treatment. Plos Biology. 17: e3000228. PMID 31039152 DOI: 10.1371/Journal.Pbio.3000228  0.694
2018 Terry EE, Zhang X, Hoffmann C, Hughes LD, Lewis SA, Li J, Wallace MJ, Riley L, Douglas CM, Gutierrez-Montreal MA, Lahens NF, Gong MC, Andrade F, Esser KA, Hughes ME. Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues. Elife. 7. PMID 29809149 DOI: 10.7554/Elife.34613  0.502
2018 Terry EE, Zhang X, Hoffmann C, Hughes LD, Lewis SA, Li J, Wallace MJ, Riley LA, Douglas CM, Gutierrez-Monreal MA, Lahens NF, Gong MC, Andrade F, Esser KA, Hughes ME. Author response: Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues Elife. DOI: 10.7554/Elife.34613.040  0.497
2017 Norton S, Vaquero-Garcia J, Lahens NF, Grant GR, Barash Y. Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. Bioinformatics (Oxford, England). PMID 29236961 DOI: 10.1093/Bioinformatics/Btx790  0.385
2017 Skarke C, Lahens NF, Rhoades SD, Campbell A, Bittinger K, Bailey A, Hoffmann C, Olson RS, Chen L, Yang G, Price TS, Moore JH, Bushman FD, Greene CS, Grant GR, et al. A Pilot Characterization of the Human Chronobiome. Scientific Reports. 7: 17141. PMID 29215023 DOI: 10.1038/S41598-017-17362-6  0.324
2017 Lahens NF, Ricciotti E, Smirnova O, Toorens E, Kim EJ, Baruzzo G, Hayer KE, Ganguly T, Schug J, Grant GR. A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression. Bmc Genomics. 18: 602. PMID 28797240 DOI: 10.1186/S12864-017-4011-0  0.427
2017 Babb PL, Lahens NF, Correa-Garhwal SM, Nicholson DN, Kim EJ, Hogenesch JB, Kuntner M, Higgins L, Hayashi CY, Agnarsson I, Voight BF. The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression. Nature Genetics. PMID 28459453 DOI: 10.1038/Ng.3852  0.597
2016 Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y. A new view of transcriptome complexity and regulation through the lens of local splicing variations. Elife. 5. PMID 26829591 DOI: 10.7554/Elife.11752  0.595
2016 Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y. Author response: A new view of transcriptome complexity and regulation through the lens of local splicing variations Elife. DOI: 10.7554/Elife.11752.080  0.54
2016 Kim EJ, Lahens N, Ricciotti E, Manduchi E, Grosser T, Fitzgerald G, Hogenesch J, Grant G. Resampling-based read-level normalization of RNA-Seq for differential expression analysis F1000research. 5. DOI: 10.7490/F1000Research.1112772.1  0.616
2016 Lahens N, Ricciotti E, Smirnova O, Torrens E, Kim EJ, Baruzzo G, Hayer K, Ganguly T, Schug J, Grant G. A comparison of Illumina and Ion Torrent platforms in a study of differential gene expression F1000research. 5. DOI: 10.7490/F1000Research.1112705.1  0.328
2015 Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR. Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Bioinformatics (Oxford, England). 31: 3938-45. PMID 26338770 DOI: 10.1093/Bioinformatics/Btv488  0.626
2015 Jang C, Lahens NF, Hogenesch JB, Sehgal A. Ribosome profiling reveals an important role for translational control in circadian gene expression. Genome Research. 25: 1836-47. PMID 26338483 DOI: 10.1101/Gr.191296.115  0.648
2014 Toung JM, Lahens N, Hogenesch JB, Grant G. Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing. Plos One. 9: e112040. PMID 25396741 DOI: 10.1371/Journal.Pone.0112040  0.606
2014 Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB. A circadian gene expression atlas in mammals: implications for biology and medicine. Proceedings of the National Academy of Sciences of the United States of America. 111: 16219-24. PMID 25349387 DOI: 10.1073/Pnas.1408886111  0.656
2014 Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA sequencing. Genome Biology. 15: R86. PMID 24981968 DOI: 10.1186/Gb-2014-15-6-R86  0.709
2013 Pizarro A, Hayer K, Lahens NF, Hogenesch JB. CircaDB: a database of mammalian circadian gene expression profiles. Nucleic Acids Research. 41: D1009-13. PMID 23180795 DOI: 10.1093/Nar/Gks1161  0.599
2011 Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics (Oxford, England). 27: 2518-28. PMID 21775302 DOI: 10.1093/Bioinformatics/Btr427  0.613
Low-probability matches (unlikely to be authored by this person)
2023 Schwarz JE, Mrčela A, Lahens NF, Li Y, Hsu CT, Grant G, Skarke C, Zhang SL, Sehgal A. Evidence for a role of human blood-borne factors in mediating age-associated changes in molecular circadian rhythms. Biorxiv : the Preprint Server For Biology. PMID 37808824 DOI: 10.1101/2023.04.19.537477  0.282
2022 Babb PL, Gregorič M, Lahens NF, Nicholson DN, Hayashi CY, Higgins L, Kuntner M, Agnarsson I, Voight BF. Characterization of the genome and silk-gland transcriptomes of Darwin's bark spider (Caerostris darwini). Plos One. 17: e0268660. PMID 35666730 DOI: 10.1371/journal.pone.0268660  0.281
2019 Theken KN, Hersh EV, Lahens NF, Lee HM, Li X, Granquist EJ, Giannakopoulos H, Levin LM, Secreto SA, Grant GR, Detre JA, FitzGerald GA, Grosser T, Farrar JT. Variability in the Analgesic Response to Ibuprofen is Associated with Cyclooxygenase Activation in Inflammatory Pain. Clinical Pharmacology and Therapeutics. PMID 30929268 DOI: 10.1002/Cpt.1446  0.277
2018 Manners MT, Yohn NL, Lahens NF, Grant GR, Bartolomei MS, Blendy JA. Transgenerational inheritance of chronic adolescent stress: Effects of stress response and the amygdala transcriptome. Genes, Brain, and Behavior. e12493. PMID 29896789 DOI: 10.1111/Gbb.12493  0.275
2021 Zhang SL, Lahens NF, Yue Z, Arnold DM, Pakstis PP, Schwarz JE, Sehgal A. A circadian clock regulates efflux by the blood-brain barrier in mice and human cells. Nature Communications. 12: 617. PMID 33504784 DOI: 10.1038/s41467-020-20795-9  0.249
2021 Brooks TG, Mrčela A, Lahens NF, Paschos GK, Grosser T, Skarke C, FitzGerald GA, Grant GR. Nitecap: An Exploratory Circadian Analysis Web Application. Journal of Biological Rhythms. 7487304211054408. PMID 34724846 DOI: 10.1177/07487304211054408  0.238
2018 Ricciotti E, Castro C, Tang SY, Briggs WTE, West JA, Malik D, Rhoades SD, Meng H, Li X, Lahens NF, Sparks JA, Karlson EW, Weljie AM, Griffin JL, FitzGerald GA. Cyclooxygenase-2, Asymmetric Dimethylarginine and the Cardiovascular Hazard from NSAIDs. Circulation. PMID 29930022 DOI: 10.1161/Circulationaha.118.033540  0.232
2018 Perron IJ, Keenan BT, Chellappa K, Lahens NF, Yohn NL, Shockley KR, Pack AI, Veasey SC. Dietary challenges differentially affect activity and sleep/wake behavior in mus musculus: Isolating independent associations with diet/energy balance and body weight. Plos One. 13: e0196743. PMID 29746501 DOI: 10.1371/Journal.Pone.0196743  0.208
2024 Brooks TG, Lahens NF, Mrčela A, Grant GR. Challenges and best practices in omics benchmarking. Nature Reviews. Genetics. PMID 38216661 DOI: 10.1038/s41576-023-00679-6  0.15
2021 Issah Y, Naik A, Tang SY, Forrest K, Brooks TG, Lahens N, Theken KN, Mermigos M, Sehgal A, Worthen GS, FitzGerald GA, Sengupta S. Loss of circadian protection against influenza infection in adult mice exposed to hyperoxia as neonates. Elife. 10. PMID 33650487 DOI: 10.7554/eLife.61241  0.144
2023 Anderson ST, Meng H, Brooks TG, Tang SY, Lordan R, Sengupta A, Nayak S, Mřela A, Sarantopoulou D, Lahens NF, Weljie A, Grant GR, Bushman FD, FitzGerald GA. Sexual dimorphism in the response to chronic circadian misalignment on a high-fat diet. Science Translational Medicine. 15: eabo2022. PMID 37196066 DOI: 10.1126/scitranslmed.abo2022  0.122
2023 Skarke C, Brooks T, Lahens N, Grant G, Sheline Y, FitzGerald G. Diurnal rhythmicity of wearable device-measured wrist temperature predicts future disease incidence in the UK Biobank. Research Square. PMID 36824952 DOI: 10.21203/rs.3.rs-2535978/v1  0.105
2023 Brooks TG, Lahens NF, Grant GR, Sheline YI, FitzGerald GA, Skarke C. Diurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank. Nature Communications. 14: 5172. PMID 37620332 DOI: 10.1038/s41467-023-40977-5  0.091
2023 Meng H, Sengupta A, Ricciotti E, Mrčela A, Mathew D, Mazaleuskaya LL, Ghosh S, Brooks TG, Turner AP, Schanoski AS, Lahens NF, Tan AW, Woolfork A, Grant G, Susztak K, et al. Deep Phenotyping of the Lipidomic Response in COVID and non-COVID Sepsis. Biorxiv : the Preprint Server For Biology. PMID 37398323 DOI: 10.1101/2023.06.02.543298  0.08
2022 Lahens NF, Rahman M, Cohen JB, Cohen DL, Chen J, Weir MR, Feldman HI, Grant GR, Townsend RR, Skarke C, Study Investigators ATC. Time-specific associations of wearable sensor-based cardiovascular and behavioral readouts with disease phenotypes in the outpatient setting of the Chronic Renal Insufficiency Cohort. Digital Health. 8: 20552076221107903. PMID 35746950 DOI: 10.1177/20552076221107903  0.075
2021 Tang SY, Meng H, Anderson ST, Sarantopoulou D, Ghosh S, Lahens NF, Theken KN, Ricciotti E, Hennessy EJ, Tu V, Bittinger K, Weljie AM, Grant GR, FitzGerald GA. Sex-dependent compensatory mechanisms preserve blood pressure homeostasis in prostacyclin receptor deficient mice. The Journal of Clinical Investigation. PMID 34101620 DOI: 10.1172/JCI136310  0.073
2023 Skarke C, Lordan R, Barekat K, Naik A, Mathew D, Ohtani T, Greenplate AR, Grant GR, Lahens NF, Gouma S, Troisi E, Sengupta A, Weljie AM, Meng W, Luning Prak ET, et al. . The Journal of Pharmacology and Experimental Therapeutics. PMID 37105582 DOI: 10.1124/jpet.122.001415  0.056
2023 Meng H, Sengupta A, Ricciotti E, Mrčela A, Mathew D, Mazaleuskaya LL, Ghosh S, Brooks TG, Turner AP, Schanoski AS, Lahens NF, Tan AW, Woolfork A, Grant G, Susztak K, et al. Deep phenotyping of the lipidomic response in COVID-19 and non-COVID-19 sepsis. Clinical and Translational Medicine. 13: e1440. PMID 37948331 DOI: 10.1002/ctm2.1440  0.043
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