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Items: 32

1.

Pre-existing Functional Heterogeneity of Tumorigenic Compartment as the Origin of Chemoresistance in Pancreatic Tumors.

Seth S, Li CY, Ho IL, Corti D, Loponte S, Sapio L, Del Poggetto E, Yen EY, Robinson FS, Peoples M, Karpinets T, Deem AK, Kumar T, Song X, Jiang S, Kang Y, Fleming J, Kim M, Zhang J, Maitra A, Heffernan TP, Giuliani V, Genovese G, Futreal A, Draetta GF, Carugo A, Viale A.

Cell Rep. 2019 Feb 5;26(6):1518-1532.e9. doi: 10.1016/j.celrep.2019.01.048.

2.

Prospective Analysis of Adoptive TIL Therapy in Patients with Metastatic Melanoma: Response, Impact of Anti-CTLA4, and Biomarkers to Predict Clinical Outcome.

Forget MA, Haymaker C, Hess KR, Meng YJ, Creasy C, Karpinets T, Fulbright OJ, Roszik J, Woodman SE, Kim YU, Sakellariou-Thompson D, Bhatta A, Wahl A, Flores E, Thorsen ST, Tavera RJ, Ramachandran R, Gonzalez AM, Toth CL, Wardell S, Mansaray R, Patel V, Carpio DJ, Vaughn C, Farinas CM, Velasquez PG, Hwu WJ, Patel SP, Davies MA, Diab A, Glitza IC, Tawbi H, Wong MK, Cain S, Ross MI, Lee JE, Gershenwald JE, Lucci A, Royal R, Cormier JN, Wargo JA, Radvanyi LG, Torres-Cabala CA, Beroukhim R, Hwu P, Amaria RN, Bernatchez C.

Clin Cancer Res. 2018 Sep 15;24(18):4416-4428. doi: 10.1158/1078-0432.CCR-17-3649. Epub 2018 May 30.

3.

Increased Tumor Glycolysis Characterizes Immune Resistance to Adoptive T Cell Therapy.

Cascone T, McKenzie JA, Mbofung RM, Punt S, Wang Z, Xu C, Williams LJ, Wang Z, Bristow CA, Carugo A, Peoples MD, Li L, Karpinets T, Huang L, Malu S, Creasy C, Leahey SE, Chen J, Chen Y, Pelicano H, Bernatchez C, Gopal YNV, Heffernan TP, Hu J, Wang J, Amaria RN, Garraway LA, Huang P, Yang P, Wistuba II, Woodman SE, Roszik J, Davis RE, Davies MA, Heymach JV, Hwu P, Peng W.

Cell Metab. 2018 May 1;27(5):977-987.e4. doi: 10.1016/j.cmet.2018.02.024. Epub 2018 Apr 5.

4.

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.

5.

The RNA-binding Protein MEX3B Mediates Resistance to Cancer Immunotherapy by Downregulating HLA-A Expression.

Huang L, Malu S, McKenzie JA, Andrews MC, Talukder AH, Tieu T, Karpinets T, Haymaker C, Forget MA, Williams LJ, Wang Z, Mbofung RM, Wang ZQ, Davis RE, Lo RS, Wargo JA, Davies MA, Bernatchez C, Heffernan T, Amaria RN, Korkut A, Peng W, Roszik J, Lizée G, Woodman SE, Hwu P.

Clin Cancer Res. 2018 Jul 15;24(14):3366-3376. doi: 10.1158/1078-0432.CCR-17-2483. Epub 2018 Mar 1.

6.

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.

7.

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.

8.

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.

9.

Insights from 20 years of bacterial genome sequencing.

Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW.

Funct Integr Genomics. 2015 Mar;15(2):141-61. doi: 10.1007/s10142-015-0433-4. Epub 2015 Feb 27. Review.

10.

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.

11.

Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8.

Deveau A, Gross H, Morin E, Karpinets T, Utturkar S, Mehnaz S, Martin F, Frey-Klett P, Labbé J.

Genome Announc. 2014 Jan 9;2(1). pii: e01152-13. doi: 10.1128/genomeA.01152-13.

12.

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.

13.

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.

14.

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.

15.

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.

16.

Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans--Ignicoccus hospitalis relationship.

Giannone RJ, Huber H, Karpinets T, Heimerl T, Küper U, Rachel R, Keller M, Hettich RL, Podar M.

PLoS One. 2011;6(8):e22942. doi: 10.1371/journal.pone.0022942. Epub 2011 Aug 3.

17.

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.

18.

Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types.

Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, Karpinets T, Uberbacher E, Tuskan GA, Vilgalys R, Doktycz MJ, Schadt CW.

Appl Environ Microbiol. 2011 Sep;77(17):5934-44. doi: 10.1128/AEM.05255-11. Epub 2011 Jul 15.

19.

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.

20.

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
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.
27.

From pull-down data to protein interaction networks and complexes with biological relevance.

Zhang B, Park BH, Karpinets T, Samatova NF.

Bioinformatics. 2008 Apr 1;24(7):979-86. doi: 10.1093/bioinformatics/btn036. Epub 2008 Feb 26.

PMID:
18304937
29.

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
30.
31.

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
32.

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