Publications

RNA Sequencing in COVID-19 patients identifies neutrophil activation biomarkers as a promising diagnostic platform for infections.

Richard Wargodsky, Philip Dela Cruz, John LaFleur, David Yamane, Justin Sungmin Kim, Ivy Benjenk, Eric Heinz, Obinna Ome Irondi, Katherine Farrar, Ian Toma, Tristan Jordan, Jennifer Goldman, Timothy A. McCaffrey.

PLoS ONE 17(1): e0261679.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0261679

RNA sequencing of blood in coronary artery disease: involvement of regulatory T cell imbalance.

Timothy A. McCaffrey, Ian Toma, Zhaoquing Yang, Richard Katz, Jonathan Reiner,

Ramesh Mazhari, Palak Shah, Michael Tackett, Dan Jones, Tisha Jepson, Zachary Falk,

Richard Wargodsky, Dmitry Shtakalo, Denis Antonets, Justin Ertle, Ju H. Kim, Yinglei Lai, Zeynep Arslan,

Emily Aledort, Maha Alfaraidy, and Georges St. Laurent III

BMC Medical Genomics (2021) 14:216

https://doi.org/10.1186/s12920-021-01062-2

Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts.

McCaffrey TA, St Laurent G 3rd, Shtokalo D, Antonets D, Vyatkin Y, Jones D, Battison E, Nigg JT.

BMC Med Genomics. 2020 Oct 28;13(1):160. doi: 10.1186/s12920-020-00808-8.

PMID: 33115496.

RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model.

Georges St. Laurent III, Ian Toma, Bernd Seilheimer, Konstantin Cesnulevicius, Myron Schultz,

Michael Tackett, Jianhua Zhou, Maxim Ri, Dmitry Shtokalo, Denis Antonets, Tisha Jepson, and Timothy A. McCaffrey.

BMC Genomics (2021) 22:854.

https://doi.org/10.1186/s12864-021-08083-2

Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia.

Toma I, Siegel MO, Keiser J, Yakovleva A, Kim A, Davenport L, Devaney J, Hoffman EP, Alsubail R, Crandall KA, Castro-Nallar E, Pérez-Losada M, Hilton SK, Chawla LS, McCaffrey TA, Simon GL.

J Clin Microbiol. 2014 Nov;52(11):3913-21. doi: 10.1128/JCM.01678-14. Epub 2014 Aug 20.

PMID: 25143582

Predictors of high on-aspirin platelet reactivity in elderly patients with coronary artery disease.

Zhang JW, Liu WW, McCaffrey TA, He XQ, Liang WY, Chen XH, Feng XR, Fu SW, Liu ML.

Clin Interv Aging. 2017 Aug 10;12:1271-1279. doi: 10.2147/CIA.S138592. eCollection 2017.

PMID: 28848334

Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14.

St Laurent G 3rd, Seilheimer B, Tackett M, Zhou J, Shtokalo D, Vyatkin Y, Ri M, Toma I, Jones D, McCaffrey TA.

Front Mol Biosci. 2017 Aug 17;4:57. doi: 10.3389/fmolb.2017.00057. eCollection 2017.

PMID: 28879183

Concordant integrative gene set enrichment analysis of multiple large-scale two-sample expression data sets.

Lai Y, Zhang F, Nayak TK, Modarres R, Lee NH, McCaffrey TA.

BMC Genomics. 2014;15 Suppl 1:S6. doi: 10.1186/1471-2164-15-S1-S6. Epub 2014 Jan 24.

PMID: 24564564

VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer.

St Laurent G, Shtokalo D, Dong B, Tackett MR, Fan X, Lazorthes S, Nicolas E, Sang N, Triche TJ, McCaffrey TA, Xiao W, Kapranov P.

Genome Biol. 2013 Jul 22;14(7):R73. doi: 10.1186/gb-2013-14-7-r73.

PMID: 23876380

Aspirin exposure reveals novel genes associated with platelet function and cardiovascular events.

Voora D, Cyr D, Lucas J, Chi JT, Dungan J, McCaffrey TA, Katz R, Newby LK, Kraus WE, Becker RC, Ortel TL, Ginsburg GS.

J Am Coll Cardiol. 2013 Oct 1;62(14):1267-76. doi: 10.1016/j.jacc.2013.05.073. Epub 2013 Jul 3.

PMID: 23831034

Genomic profiling reveals the potential role of TCL1A and MDR1 deficiency in chemotherapy-induced cardiotoxicity.

McCaffrey TA, Tziros C, Lewis J, Katz R, Siegel R, Weglicki W, Kramer J, Mak IT, Toma I, Chen L, Benas E, Lowitt A, Rao S, Witkin L, Lian Y, Lai Y, Yang Z, Fu SW.

Int J Biol Sci. 2013 Apr 22;9(4):350-60. doi: 10.7150/ijbs.6058. Print 2013.

PMID: 23630447

On the importance of small changes in RNA expression.

St Laurent G, Shtokalo D, Tackett MR, Yang Z, Vyatkin Y, Milos PM, Seilheimer B, McCaffrey TA, Kapranov P.

Methods. 2013 Sep 1;63(1):18-24. doi: 10.1016/j.ymeth.2013.03.027. Epub 2013 Apr 4.

PMID: 23563143

Aspirin insensitive thrombophilia: transcript profiling of blood identifies platelet abnormalities and HLA restriction.

Fallahi P, Katz R, Toma I, Li R, Reiner J, VanHouten K, Carpio L, Marshall L, Lian Y, Bupp S, Fu SW, Rickles F, Leitenberg D, Lai Y, Weksler BB, Rebling F, Yang Z, McCaffrey TA.

Gene. 2013 May 15;520(2):131-8. doi: 10.1016/j.gene.2013.02.032. Epub 2013 Feb 27.

PMID: 23454623

Role of deregulated microRNAs in breast cancer progression using FFPE tissue.

Chen L, Li Y, Fu Y, Peng J, Mo MH, Stamatakos M, Teal CB, Brem RF, Stojadinovic A, Grinkemeyer M, McCaffrey TA, Man YG, Fu SW.

PLoS One. 2013;8(1):e54213. doi: 10.1371/journal.pone.0054213. Epub 2013 Jan 23.

PMID: 23372687

Cardiovascular pharmacogenomics: current status and future directions-report of a national heart, lung, and blood institute working group.

Musunuru K, Roden DM, Boineau R, Bristow MR, McCaffrey TA, Newton-Cheh C, Paltoo DN, Rosenberg Y, Wohlgemuth JG, Zineh I, Hasan AA.

J Am Heart Assoc. 2012 Apr;1(2):e000554. doi: 10.1161/JAHA.111.000554. Epub 2012 Apr 24. No abstract available.

PMID: 23130127

Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells.

St Laurent G, Shtokalo D, Tackett MR, Yang Z, Eremina T, Wahlestedt C, Urcuqui-Inchima S, Seilheimer B, McCaffrey TA, Kapranov P.

BMC Genomics. 2012 Sep 24;13:504. doi: 10.1186/1471-2164-13-504.

PMID: 23006825

Apolipoprotein L6, induced in atherosclerotic lesions, promotes apoptosis and blocks Beclin 1-dependent autophagy in atherosclerotic cells.

Zhaorigetu S, Yang Z, Toma I, McCaffrey TA, Hu CA.

J Biol Chem. 2011 Aug 5;286(31):27389-98. doi: 10.1074/jbc.M110.210245. Epub 2011 Jun 6.

PMID: 21646352