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Decoding systems biology of plant stress for sustainable agriculture development and optimized food production.

Shameer K, Naika MBN, Shafi KM, Sowdhamini R.

Prog Biophys Mol Biol. 2018 Dec 15. pii: S0079-6107(17)30089-5. doi: 10.1016/j.pbiomolbio.2018.12.002. [Epub ahead of print] Review.


CANDI: an R package and Shiny app for annotating radiographs and evaluating Computer-Aided Diagnosis.

Badgeley MA, Liu M, Glicksberg BS, Shervey M, Zech J, Shameer K, Lehar J, Oermann EK, McConnell MV, Snyder TM, Dudley JT.

Bioinformatics. 2018 Oct 10. doi: 10.1093/bioinformatics/bty855. [Epub ahead of print]


Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining.

Shameer K, Perez-Rodriguez MM, Bachar R, Li L, Johnson A, Johnson KW, Glicksberg BS, Smith MR, Readhead B, Scarpa J, Jebakaran J, Kovatch P, Lim S, Goodman W, Reich DL, Kasarskis A, Tatonetti NP, Dudley JT.

BMC Med Inform Decis Mak. 2018 Sep 14;18(Suppl 3):79. doi: 10.1186/s12911-018-0653-3.


Correction: Population Distribution Analyses Reveal a Hierarchy of Molecular Players Underlying Parallel Endocytic Pathways.

Gupta GD, Dey G, Mg S, Ramalingam B, Shameer K, Thottacherry JJ, Kalappurakkal JM, Howes MT, Chandran R, Das A, Menon S, Parton RG, Sowdhamini R, Thattai M, Mayor S.

PLoS One. 2018 Sep 21;13(9):e0204770. doi: 10.1371/journal.pone.0204770. eCollection 2018.


The whole is greater than the sum of its parts: combining classical statistical and machine intelligence methods in medicine.

Shameer K, Johnson KW, Glicksberg BS, Dudley JT, Sengupta PP.

Heart. 2018 Jul;104(14):1228. doi: 10.1136/heartjnl-2018-313377. No abstract available.


A Network-Biology Informed Computational Drug Repositioning Strategy to Target Disease Risk Trajectories and Comorbidities of Peripheral Artery Disease.

Shameer K, Dow G, Glicksberg BS, Johnson KW, Ze Y, Tomlinson MS, Readhead B, Dudley JT, Kullo IJ.

AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:108-117. eCollection 2018.


Artificial Intelligence in Cardiology.

Johnson KW, Torres Soto J, Glicksberg BS, Shameer K, Miotto R, Ali M, Ashley E, Dudley JT.

J Am Coll Cardiol. 2018 Jun 12;71(23):2668-2679. doi: 10.1016/j.jacc.2018.03.521. Review.


Direct and indirect influences of intercrops on the coconut defoliator Opisina arenosella.

Shameer KS, Nasser M, Mohan C, Hardy ICW.

J Pest Sci (2004). 2018;91(1):259-275. doi: 10.1007/s10340-017-0904-6. Epub 2017 Aug 9.


Machine learning in cardiovascular medicine: are we there yet?

Shameer K, Johnson KW, Glicksberg BS, Dudley JT, Sengupta PP.

Heart. 2018 Jul;104(14):1156-1164. doi: 10.1136/heartjnl-2017-311198. Epub 2018 Jan 19. Review.


Causal inference on electronic health records to assess blood pressure treatment targets: an application of the parametric g formula.

Johnson KW, Glicksberg BS, Hodos RA, Shameer K, Dudley JT.

Pac Symp Biocomput. 2018;23:180-191.


Automated disease cohort selection using word embeddings from Electronic Health Records.

Glicksberg BS, Miotto R, Johnson KW, Shameer K, Li L, Chen R, Dudley JT.

Pac Symp Biocomput. 2018;23:145-156.


Editorial: Improving Neuropharmacology using Big Data, Machine Learning and Computational Algorithms.

Shameer K, Nayarisseri A, Romero Duran FX, Gonzalez-Diaz H.

Curr Neuropharmacol. 2017 Nov 14;15(8):1058-1061. doi: 10.2174/1570159X1508171114113425. No abstract available.


A functional genomics predictive network model identifies regulators of inflammatory bowel disease.

Peters LA, Perrigoue J, Mortha A, Iuga A, Song WM, Neiman EM, Llewellyn SR, Di Narzo A, Kidd BA, Telesco SE, Zhao Y, Stojmirovic A, Sendecki J, Shameer K, Miotto R, Losic B, Shah H, Lee E, Wang M, Faith JJ, Kasarskis A, Brodmerkel C, Curran M, Das A, Friedman JR, Fukui Y, Humphrey MB, Iritani BM, Sibinga N, Tarrant TK, Argmann C, Hao K, Roussos P, Zhu J, Zhang B, Dobrin R, Mayer LF, Schadt EE.

Nat Genet. 2017 Oct;49(10):1437-1449. doi: 10.1038/ng.3947. Epub 2017 Sep 11.


Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes.

Chamaria S, Johnson KW, Vengrenyuk Y, Baber U, Shameer K, Divaraniya AA, Glicksberg BS, Li L, Bhatheja S, Moreno P, Maehara A, Mehran R, Dudley JT, Narula J, Sharma SK, Kini AS.

Sci Rep. 2017 Aug 1;7(1):7001. doi: 10.1038/s41598-017-07029-7.


Artificial Intelligence-Based Assessment of Left Ventricular Filling Pressures From 2-Dimensional Cardiac Ultrasound Images.

Salem Omar AM, Shameer K, Narula S, Abdel Rahman MA, Rifaie O, Narula J, Dudley JT, Sengupta PP.

JACC Cardiovasc Imaging. 2018 Mar;11(3):509-510. doi: 10.1016/j.jcmg.2017.05.003. Epub 2017 Jul 19. No abstract available.


Enabling Precision Cardiology Through Multiscale Biology and Systems Medicine.

Johnson KW, Shameer K, Glicksberg BS, Readhead B, Sengupta PP, Björkegren JLM, Kovacic JC, Dudley JT.

JACC Basic Transl Sci. 2017 Jun 26;2(3):311-327. doi: 10.1016/j.jacbts.2016.11.010. eCollection 2017 Jun. Review.


Reply: Deep Learning With Unsupervised Feature in Echocardiographic Imaging.

Narula S, Shameer K, Salem Omar AM, Dudley JT, Sengupta PP.

J Am Coll Cardiol. 2017 Apr 25;69(16):2101-2102. doi: 10.1016/j.jacc.2017.01.062. No abstract available.


Accelerators: Sparking Innovation and Transdisciplinary Team Science in Disparities Research.

Horowitz CR, Shameer K, Gabrilove J, Atreja A, Shepard P, Goytia CN, Smith GW, Dudley J, Manning R, Bickell NA, Galvez MP.

Int J Environ Res Public Health. 2017 Feb 23;14(3). pii: E225. doi: 10.3390/ijerph14030225.


Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.

Shameer K, Glicksberg BS, Hodos R, Johnson KW, Badgeley MA, Readhead B, Tomlinson MS, O'Connor T, Miotto R, Kidd BA, Chen R, Ma'ayan A, Dudley JT.

Brief Bioinform. 2018 Jul 20;19(4):656-678. doi: 10.1093/bib/bbw136.


Shared decision-making following disclosure of coronary heart disease genetic risk: results from a randomized clinical trial.

Jouni H, Haddad RA, Marroush TS, Brown SA, Kruisselbrink TM, Austin EE, Shameer K, Behnken EM, Chaudhry R, Montori VM, Kullo IJ.

J Investig Med. 2017 Mar;65(3):681-688. doi: 10.1136/jim-2016-000318. Epub 2016 Dec 19.


Intracoronary Imaging, Cholesterol Efflux, and Transcriptomes After Intensive Statin Treatment: The YELLOW II Study.

Kini AS, Vengrenyuk Y, Shameer K, Maehara A, Purushothaman M, Yoshimura T, Matsumura M, Aquino M, Haider N, Johnson KW, Readhead B, Kidd BA, Feig JE, Krishnan P, Sweeny J, Milind M, Moreno P, Mehran R, Kovacic JC, Baber U, Dudley JT, Narula J, Sharma S.

J Am Coll Cardiol. 2017 Feb 14;69(6):628-640. doi: 10.1016/j.jacc.2016.10.029. Epub 2016 Oct 29.



Shameer K, Johnson KW, Yahi A, Miotto R, Li LI, Ricks D, Jebakaran J, Kovatch P, Sengupta PP, Gelijns S, Moskovitz A, Darrow B, David DL, Kasarskis A, Tatonetti NP, Pinney S, Dudley JT.

Pac Symp Biocomput. 2017;22:276-287. doi: 10.1142/9789813207813_0027.


Machine-Learning Algorithms to Automate Morphological and Functional Assessments in 2D Echocardiography.

Narula S, Shameer K, Salem Omar AM, Dudley JT, Sengupta PP.

J Am Coll Cardiol. 2016 Nov 29;68(21):2287-2295. doi: 10.1016/j.jacc.2016.08.062.


Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth.

Saha S, Xiong X, Chakraborty PK, Shameer K, Arvizo RR, Kudgus RA, Dwivedi SK, Hossen MN, Gillies EM, Robertson JD, Dudley JT, Urrutia RA, Postier RG, Bhattacharya R, Mukherjee P.

ACS Nano. 2016 Dec 27;10(12):10636-10651. doi: 10.1021/acsnano.6b02231. Epub 2016 Oct 19.


Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.

Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, Dudley JT.

Bioinformatics. 2016 Jun 15;32(12):i101-i110. doi: 10.1093/bioinformatics/btw282.


Cognitive Machine-Learning Algorithm for Cardiac Imaging: A Pilot Study for Differentiating Constrictive Pericarditis From Restrictive Cardiomyopathy.

Sengupta PP, Huang YM, Bansal M, Ashrafi A, Fisher M, Shameer K, Gall W, Dudley JT.

Circ Cardiovasc Imaging. 2016 Jun;9(6). pii: e004330. doi: 10.1161/CIRCIMAGING.115.004330.


Systems Medicine Approaches to Improving Understanding, Treatment, and Clinical Management of Neuroendocrine Prostate Cancer.

Yadav KK, Shameer K, Readhead B, Yadav SS, Li L, Kasarskis A, Tewari AK, Dudley JT.

Curr Pharm Des. 2016;22(34):5234-5248. Review.


In silico methods for drug repurposing and pharmacology.

Hodos RA, Kidd BA, Shameer K, Readhead BP, Dudley JT.

Wiley Interdiscip Rev Syst Biol Med. 2016 May;8(3):186-210. doi: 10.1002/wsbm.1337. Epub 2016 Apr 15. Review.


EHDViz: clinical dashboard development using open-source technologies.

Badgeley MA, Shameer K, Glicksberg BS, Tomlinson MS, Levin MA, McCormick PJ, Kasarskis A, Reich DL, Dudley JT.

BMJ Open. 2016 Mar 24;6(3):e010579. doi: 10.1136/bmjopen-2015-010579.


Incorporating a Genetic Risk Score Into Coronary Heart Disease Risk Estimates: Effect on Low-Density Lipoprotein Cholesterol Levels (the MI-GENES Clinical Trial).

Kullo IJ, Jouni H, Austin EE, Brown SA, Kruisselbrink TM, Isseh IN, Haddad RA, Marroush TS, Shameer K, Olson JE, Broeckel U, Green RC, Schaid DJ, Montori VM, Bailey KR.

Circulation. 2016 Mar 22;133(12):1181-8. doi: 10.1161/CIRCULATIONAHA.115.020109. Epub 2016 Feb 25.


Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams.

Shameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JT.

Brief Bioinform. 2017 Jan;18(1):105-124. doi: 10.1093/bib/bbv118. Epub 2016 Feb 14.


Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses.

Barah P, B N MN, Jayavelu ND, Sowdhamini R, Shameer K, Bones AM.

Nucleic Acids Res. 2016 Apr 20;44(7):3147-64. doi: 10.1093/nar/gkv1463. Epub 2015 Dec 17.


Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

Shameer K, Tripathi LP, Kalari KR, Dudley JT, Sowdhamini R.

Brief Bioinform. 2016 Sep;17(5):841-62. doi: 10.1093/bib/bbv084. Epub 2015 Oct 22. Review.


Cardiomyopathy and Worsened Ischemic Heart Failure in SM22-α Cre-Mediated Neuropilin-1 Null Mice: Dysregulation of PGC1α and Mitochondrial Homeostasis.

Wang Y, Cao Y, Yamada S, Thirunavukkarasu M, Nin V, Joshi M, Rishi MT, Bhattacharya S, Camacho-Pereira J, Sharma AK, Shameer K, Kocher JP, Sanchez JA, Wang E, Hoeppner LH, Dutta SK, Leof EB, Shah V, Claffey KP, Chini EN, Simons M, Terzic A, Maulik N, Mukhopadhyay D.

Arterioscler Thromb Vasc Biol. 2015 Jun;35(6):1401-12. doi: 10.1161/ATVBAHA.115.305566. Epub 2015 Apr 16.


An integrative pipeline for multi-modal discovery of disease relationships.

Glicksberg BS, Li L, Cheng WY, Shameer K, Hakenberg J, Castellanos R, Ma M, Shi L, Shah H, Dudley JT, Chen R.

Pac Symp Biocomput. 2015:407-18.


Computational and experimental advances in drug repositioning for accelerated therapeutic stratification.

Shameer K, Readhead B, Dudley JT.

Curr Top Med Chem. 2015;15(1):5-20. Review.


POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.

Shameer K, Naika MB, Mathew OK, Sowdhamini R.

Bioinform Biol Insights. 2014 Dec 21;8:209-14. doi: 10.4137/BBI.S19057. eCollection 2014.


The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.

Tang X, Baheti S, Shameer K, Thompson KJ, Wills Q, Niu N, Holcomb IN, Boutet SC, Ramakrishnan R, Kachergus JM, Kocher JP, Weinshilboum RM, Wang L, Thompson EA, Kalari KR.

Nucleic Acids Res. 2014 Dec 16;42(22):e172. doi: 10.1093/nar/gku1005. Epub 2014 Oct 28.


Clinical Correlates of Autosomal Chromosomal Abnormalities in an Electronic Medical Record-Linked Genome-Wide Association Study: A Case Series.

Jouni H, Shameer K, Asmann YW, Hazin R, de Andrade M, Kullo IJ.

J Investig Med. 2013 Oct;1(4). pii: 2324709613508932.


Whole exome sequencing implicates an INO80D mutation in a syndrome of aortic hypoplasia, premature atherosclerosis, and arterial stiffness.

Shameer K, Klee EW, Dalenberg AK, Kullo IJ.

Circ Cardiovasc Genet. 2014 Oct;7(5):607-14. doi: 10.1161/CIRCGENETICS.113.000233. Epub 2014 Aug 13.


The ATXN2-SH2B3 locus is associated with peripheral arterial disease: an electronic medical record-based genome-wide association study.

Kullo IJ, Shameer K, Jouni H, Lesnick TG, Pathak J, Chute CG, de Andrade M.

Front Genet. 2014 Jun 25;5:166. doi: 10.3389/fgene.2014.00166. eCollection 2014.


Population distribution analyses reveal a hierarchy of molecular players underlying parallel endocytic pathways.

Gupta GD, Dey G, Swetha MG, Ramalingam B, Shameer K, Thottacherry JJ, Kalappurakkal JM, Howes MT, Chandran R, Das A, Menon S, Parton RG, Sowdhamini R, Thattai M, Mayor S.

PLoS One. 2014 Jun 27;9(6):e100554. doi: 10.1371/journal.pone.0100554. eCollection 2014. Erratum in: PLoS One. 2018 Sep 21;13(9):e0204770.


Understanding protein-nanoparticle interaction: a new gateway to disease therapeutics.

Giri K, Shameer K, Zimmermann MT, Saha S, Chakraborty PK, Sharma A, Arvizo RR, Madden BJ, Mccormick DJ, Kocher JP, Bhattacharya R, Mukherjee P.

Bioconjug Chem. 2014 Jun 18;25(6):1078-90. doi: 10.1021/bc500084f. Epub 2014 May 22.


Clinical Correlates of Autosomal Chromosomal Abnormalities in an Electronic Medical Record-Linked Genome-Wide Association Study: A Case Series.

Jouni H, Shameer K, Asmann YW, Hazin R, de Andrade M, Kullo IJ.

J Investig Med High Impact Case Rep. 2013 Oct 18;1(4):2324709613508932. doi: 10.1177/2324709613508932. eCollection 2013 Oct-Dec.


A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.

Shameer K, Denny JC, Ding K, Jouni H, Crosslin DR, de Andrade M, Chute CG, Peissig P, Pacheco JA, Li R, Bastarache L, Kho AN, Ritchie MD, Masys DR, Chisholm RL, Larson EB, McCarty CA, Roden DM, Jarvik GP, Kullo IJ.

Hum Genet. 2014 Jan;133(1):95-109. doi: 10.1007/s00439-013-1355-7. Epub 2013 Sep 12.


An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles.

Kotaru AR, Shameer K, Sundaramurthy P, Joshi RC.

Bioinformation. 2013 Apr 13;9(7):368-74. doi: 10.6026/97320630009368. Print 2013.


Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics.

Naika M, Shameer K, Sowdhamini R.

Mol Biosyst. 2013 Jul;9(7):1888-908. doi: 10.1039/c3mb70072k. Epub 2013 May 3.


Genetic Loci implicated in erythroid differentiation and cell cycle regulation are associated with red blood cell traits.

Ding K, Shameer K, Jouni H, Masys DR, Jarvik GP, Kho AN, Ritchie MD, McCarty CA, Chute CG, Manolio TA, Kullo IJ.

Mayo Clin Proc. 2012 May;87(5):461-74. doi: 10.1016/j.mayocp.2012.01.016.


Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome.

Shameer K, Sowdhamini R.

J Clin Bioinforma. 2012 Apr 3;2(1):8. doi: 10.1186/2043-9113-2-8.

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