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Items: 23

1.

Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks.

Karpinets TV, Gopalakrishnan V, Wargo J, Futreal AP, Schadt CW, Zhang J.

Front Microbiol. 2018 Mar 7;9:297. doi: 10.3389/fmicb.2018.00297. eCollection 2018.

2.

Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients.

Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, Prieto PA, Vicente D, Hoffman K, Wei SC, Cogdill AP, Zhao L, Hudgens CW, Hutchinson DS, Manzo T, Petaccia de Macedo M, Cotechini T, Kumar T, Chen WS, Reddy SM, Szczepaniak Sloane R, Galloway-Pena J, Jiang H, Chen PL, Shpall EJ, Rezvani K, Alousi AM, Chemaly RF, Shelburne S, Vence LM, Okhuysen PC, Jensen VB, Swennes AG, McAllister F, Marcelo Riquelme Sanchez E, Zhang Y, Le Chatelier E, Zitvogel L, Pons N, Austin-Breneman JL, Haydu LE, Burton EM, Gardner JM, Sirmans E, Hu J, Lazar AJ, Tsujikawa T, Diab A, Tawbi H, Glitza IC, Hwu WJ, Patel SP, Woodman SE, Amaria RN, Davies MA, Gershenwald JE, Hwu P, Lee JE, Zhang J, Coussens LM, Cooper ZA, Futreal PA, Daniel CR, Ajami NJ, Petrosino JF, Tetzlaff MT, Sharma P, Allison JP, Jenq RR, Wargo JA.

Science. 2018 Jan 5;359(6371):97-103. doi: 10.1126/science.aan4236. Epub 2017 Nov 2.

3.

Oncogenic Kras drives invasion and maintains metastases in colorectal cancer.

Boutin AT, Liao WT, Wang M, Hwang SS, Karpinets TV, Cheung H, Chu GC, Jiang S, Hu J, Chang K, Vilar E, Song X, Zhang J, Kopetz S, Futreal A, Wang YA, Kwong LN, DePinho RA.

Genes Dev. 2017 Feb 15;31(4):370-382. doi: 10.1101/gad.293449.116. Epub 2017 Mar 13.

4.

Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set.

Roszik J, Haydu LE, Hess KR, Oba J, Joon AY, Siroy AE, Karpinets TV, Stingo FC, Baladandayuthapani V, Tetzlaff MT, Wargo JA, Chen K, Forget MA, Haymaker CL, Chen JQ, Meric-Bernstam F, Eterovic AK, Shaw KR, Mills GB, Gershenwald JE, Radvanyi LG, Hwu P, Futreal PA, Gibbons DL, Lazar AJ, Bernatchez C, Davies MA, Woodman SE.

BMC Med. 2016 Oct 25;14(1):168.

5.

Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants.

Karpinets TV, Park BH, Syed MH, Klotz MG, Uberbacher EC.

Mol Plant Microbe Interact. 2014 Jul;27(7):664-77. doi: 10.1094/MPMI-12-13-0368-R.

6.

Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA.

Leuze MR, Karpinets TV, Syed MH, Beliaev AS, Uberbacher EC.

Gene Regul Syst Bio. 2012;6:93-107. doi: 10.4137/GRSB.S9357. Epub 2012 May 30.

7.

Analyzing large biological datasets with association networks.

Karpinets TV, Park BH, Uberbacher EC.

Nucleic Acids Res. 2012 Sep 1;40(17):e131. Epub 2012 May 25.

8.

Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa.

Nag A, Karpinets TV, Chang CH, Bar-Peled M.

Database (Oxford). 2012 Mar 31;2012:bas013. doi: 10.1093/database/bas013. Print 2012.

9.

BESC knowledgebase public portal.

Syed MH, Karpinets TV, Parang M, Leuze MR, Park BH, Hyatt D, Brown SD, Moulton S, Galloway MD, Uberbacher EC.

Bioinformatics. 2012 Mar 1;28(5):750-1. doi: 10.1093/bioinformatics/bts016. Epub 2012 Jan 11.

10.

Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum.

Brown SD, Guss AM, Karpinets TV, Parks JM, Smolin N, Yang S, Land ML, Klingeman DM, Bhandiwad A, Rodriguez M Jr, Raman B, Shao X, Mielenz JR, Smith JC, Keller M, Lynd LR.

Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13752-7. doi: 10.1073/pnas.1102444108. Epub 2011 Aug 8.

11.

Draft genome sequence of the polycyclic aromatic hydrocarbon-degrading, genetically engineered bioluminescent bioreporter Pseudomonas fluorescens HK44.

Chauhan A, Layton AC, Williams DE, Smartt AE, Ripp S, Karpinets TV, Brown SD, Sayler GS.

J Bacteriol. 2011 Sep;193(18):5009-10. doi: 10.1128/JB.05530-11. Epub 2011 Jul 8.

12.

CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.

Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC.

Glycobiology. 2010 Dec;20(12):1574-84. doi: 10.1093/glycob/cwq106. Epub 2010 Aug 9.

PMID:
20696711
13.

Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions.

Karpinets TV, Romine MF, Schmoyer DD, Kora GH, Syed MH, Leuze MR, Serres MH, Park BH, Samatova NF, Uberbacher EC.

Database (Oxford). 2010 Jul 6;2010:baq012. doi: 10.1093/database/baq012.

14.

Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes.

Karpinets TV, Obraztsova AY, Wang Y, Schmoyer DD, Kora GH, Park BH, Serres MH, Romine MF, Land ML, Kothe TB, Fredrickson JK, Nealson KH, Uberbacher EC.

Funct Integr Genomics. 2010 Mar;10(1):97-110. doi: 10.1007/s10142-009-0142-y. Epub 2009 Oct 3.

15.

Phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris.

Karpinets TV, Pelletier DA, Pan C, Uberbacher EC, Melnichenko GV, Hettich RL, Samatova NF.

PLoS One. 2009;4(2):e4615. doi: 10.1371/journal.pone.0004615. Epub 2009 Feb 26.

16.

Shewregdb: database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1.

Syed MH, Karpinets TV, Leuze MR, Kora GH, Romine MR, Uberbacher EC.

Bioinformation. 2009 Oct 15;4(4):169-72.

17.

A unifying concept for the dependence of whole-crop N : P ratio on biomass: theory and experiment.

Greenwood DJ, Karpinets TV, Zhang K, Bosh-Serra A, Boldrini A, Karawulova L.

Ann Bot. 2008 Dec;102(6):967-77. doi: 10.1093/aob/mcn188. Epub 2008 Oct 7.

18.
20.

Histone H3 lysine 9 and H4 lysine 20 trimethylation and the expression of Suv4-20h2 and Suv-39h1 histone methyltransferases in hepatocarcinogenesis induced by methyl deficiency in rats.

Pogribny IP, Ross SA, Tryndyak VP, Pogribna M, Poirier LA, Karpinets TV.

Carcinogenesis. 2006 Jun;27(6):1180-6. Epub 2006 Feb 23.

PMID:
16497704
21.
22.

Tailored gene array databases: applications in mechanistic toxicology.

Karpinets TV, Foy BD, Frazier JM.

Bioinformatics. 2004 Mar 1;20(4):507-17. Epub 2004 Jan 22.

PMID:
14990446
23.

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