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Analyzing large biological datasets with association networks.
Published in:
Nucleic Acids Research, 2012, v. 40, n. 17, p. e131, doi. 10.1093/nar/gks403
By:
- Karpinets, Tatiana V.;
- Park, Byung H.;
- Uberbacher, Edward C.
Publication type:
Article
Phenotype Fingerprinting Suggests the Involvement of Single-Genotype Consortia in Degradation of Aromatic Compounds by Rhodopseudomonas palustris.
Published in:
PLoS ONE, 2009, v. 4, n. 2, p. 1, doi. 10.1371/journal.pone.0004615
By:
- Karpinets, Tatiana V.;
- Pelletier, Dale A.;
- Chongle Pan;
- Uberbacher, Edward C.;
- Melnichenko, Galina V.;
- Hettich, Robert L.;
- Samatova, Nagiza F.
Publication type:
Article
Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes.
Published in:
Functional & Integrative Genomics, 2010, v. 10, n. 1, p. 97, doi. 10.1007/s10142-009-0142-y
By:
- Karpinets, Tatiana V.;
- Obraztsova, Anna Y.;
- Wang, Yanbing;
- Schmoyer, Denise D.;
- Kora, Guruprasad H.;
- Park, Byung H.;
- Serres, Margrethe H.;
- Romine, Margaret F.;
- Land, Miriam L.;
- Kothe, Terence B.;
- Fredrickson, Jim K.;
- Nealson, Kenneth H.;
- Uberbacher, Edward C.
Publication type:
Article
Intratumoral microbiome of adenoid cystic carcinomas and comparison with other head and neck cancers.
Published in:
Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-65939-9
By:
- Karpinets, Tatiana V.;
- Mitani, Yoshitsugu;
- Chang, Chia-Chi;
- Wu, Xiaogang;
- Song, Xingzhi;
- Flores, Ivonne I.;
- McDaniel, Lauren K.;
- Hoballah, Yasmine M.;
- Veguilla, Fabiana J.;
- Ferrarotto, Renata;
- Colbert, Lauren E.;
- Ajami, Nadim J.;
- Jenq, Robert R.;
- Zhang, Jianhua;
- Futreal, Andrew P.;
- El-Naggar, Adel K.
Publication type:
Article
Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa.
Published in:
Database: The Journal of Biological Databases & Curation, 2012, v. 2012, p. 1, doi. 10.1093/database/bas013
By:
- Nag, Ambarish;
- Karpinets, Tatiana V.;
- Chang, Christopher H.;
- Bar-Peled, Maor
Publication type:
Article
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions.
Published in:
Database: The Journal of Biological Databases & Curation, 2010, v. 2010, p. 1, doi. 10.1093/database/baq012
By:
- Karpinets, Tatiana V.;
- Romine, Margaret F.;
- Schmoyer, Denise D.;
- Kora, Guruprasad H.;
- Syed, Mustafa H.;
- Leuze, Michael R.;
- Serres, Margrethe H.;
- Park, Byung H.;
- Samatova, Nagiza F.;
- Uberbacher, Edward C.
Publication type:
Article
A prospective study of the adaptive changes in the gut microbiome during standard-of-care chemoradiotherapy for gynecologic cancers.
Published in:
PLoS ONE, 2021, v. 16, n. 3, p. 1, doi. 10.1371/journal.pone.0247905
By:
- El Alam, Molly B.;
- Sims, Travis T.;
- Kouzy, Ramez;
- Biegert, Greyson W. G.;
- Jaoude, Joseph A. B. I.;
- Karpinets, Tatiana V.;
- Yoshida-Court, Kyoko;
- Wu, Xiaogang;
- Delgado-Medrano, Andrea Y.;
- Mezzari, Melissa P.;
- Ajami, Nadim J.;
- Solley, Travis;
- Ahmed-Kaddar, Mustapha;
- Lin, Lilie L.;
- Ramondetta, Lois;
- Jazaeri, Amir;
- Jhingran, Anuja;
- Eifel, Patricia J.;
- Schmeler, Kathleen M.;
- Wargo, Jennifer
Publication type:
Article
Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA.
Published in:
Gene Regulation & Systems Biology, 2012, n. 6, p. 93, doi. 10.4137/GRSB.S9357
By:
- Leuze, Michael R.;
- Karpinets, Tatiana V.;
- Syed, Mustafa H.;
- Beliaev, Alexander S.;
- Uberbacher, Edward C.
Publication type:
Article
Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation.
Published in:
Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-01741-x
By:
- Sims, Travis T.;
- El Alam, Molly B.;
- Karpinets, Tatiana V.;
- Dorta-Estremera, Stephanie;
- Hegde, Venkatesh L.;
- Nookala, Sita;
- Yoshida-Court, Kyoko;
- Wu, Xiaogang;
- Biegert, Greyson W. G.;
- Delgado Medrano, Andrea Y.;
- Solley, Travis;
- Ahmed-Kaddar, Mustapha;
- Chapman, Bhavana V.;
- Sastry, K. Jagannadha;
- Mezzari, Melissa P.;
- Petrosino, Joseph F.;
- Lin, Lilie L.;
- Ramondetta, Lois;
- Jhingran, Anuja;
- Schmeler, Kathleen M.
Publication type:
Article
HPV-related anal cancer is associated with changes in the anorectal microbiome during cancer development.
Published in:
Frontiers in Immunology, 2023, v. 14, p. 01, doi. 10.3389/fimmu.2023.1051431
By:
- Elnaggar, Jacob H.;
- Huynh, Victoria O.;
- Lin, Daniel;
- Hillman, R. Tyler;
- Abana, Chike O.;
- El Alam, Molly B.;
- Tomasic, Katarina C.;
- Karpinets, Tatiana V.;
- Kouzy, Ramez;
- Phan, Jae L.;
- Wargo, Jennifer;
- Holliday, Emma B.;
- Das, Prajnan;
- Mezzari, Melissa P.;
- Ajami, Nadim J.;
- Lynn, Erica J.;
- Minsky, Bruce D.;
- Morris, Van K.;
- Milbourne, Andrea;
- Messick, Craig A.
Publication type:
Article
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.
Published in:
Carcinogenesis, 2006, v. 27, n. 6, p. 1180, doi. 10.1093/carcin/bgi364
By:
- Igor P. Pogribny;
- Sharon A. Ross;
- Tatiana V. Karpinets
Publication type:
Article
Tumorigenesis: the adaptation of mammalian cells to sustained stress environment by epigenetic alterations and succeeding matched mutations.
Published in:
Carcinogenesis, 2005, v. 26, n. 8, p. 1323, doi. 10.1093/carcin/bgi079
By:
- Tatiana V. Karpinets;
- Brent D. Foy
Publication type:
Article
RNA:protein ratio of the unicellular organism as a characteristic of phosphorous and nitrogen stoichiometry and of the cellular requirement of ribosomes for protein synthesis.
Published in:
BMC Biology, 2006, v. 4, p. 30, doi. 10.1186/1741-7007-4-30
By:
- Karpinets, Tatiana V.;
- Greenwood, Duncan J.;
- Sams, Carl E.;
- Ammons, John T.
Publication type:
Article
Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks.
Published in:
Frontiers in Microbiology, 2018, p. 1, doi. 10.3389/fmicb.2018.00297
By:
- Karpinets, Tatiana V.;
- Gopalakrishnan, Vancheswaran;
- Wargo, Jennifer;
- Futreal, Andrew P.;
- Schadt, Christopher W.;
- Zhang, Jianhua
Publication type:
Article
Tailored gene array databases: applications in mechanistic toxicology.
Published in:
Bioinformatics, 2004, v. 20, n. 4, p. 507, doi. 10.1093/bioinformatics/btg436
By:
- Tatiana V. Karpinets;
- Brent D. Foy;
- John M. Frazier
Publication type:
Article
Immune environment and antigen specificity of the T cell receptor repertoire of malignant ascites in ovarian cancer.
Published in:
PLoS ONE, 2023, v. 17, n. 1, p. 1, doi. 10.1371/journal.pone.0279590
By:
- Yoshida-Court, Kyoko;
- Karpinets, Tatiana V.;
- Mitra, Aparna;
- Solley, Travis N.;
- Dorta-Estremera, Stephanie;
- Sims, Travis T.;
- Delgado Medrano, Andrea Y.;
- El Alam, Molly B.;
- Ahmed-Kaddar, Mustapha;
- Lynn, Erica J.;
- Sastry, K. Jagannadha;
- Zhang, Jianhua;
- Futreal, Andrew;
- Nick, Alpa;
- Lu, Karen;
- Colbert, Lauren E.;
- Klopp, Ann H.
Publication type:
Article
Feasibility of a novel non-invasive swab technique for serial whole-exome sequencing of cervical tumors during chemoradiation therapy.
Published in:
PLoS ONE, 2022, v. 17, n. 10, p. 1, doi. 10.1371/journal.pone.0274457
By:
- Bronk, Julianna K.;
- Kapadia, Chiraag;
- Wu, Xiaogang;
- Chapman, Bhavana V.;
- Wang, Rui;
- Karpinets, Tatiana V.;
- Song, Xingzhi;
- Futreal, Andrew M.;
- Zhang, Jianhua;
- Klopp, Ann H.;
- Colbert, Lauren E.
Publication type:
Article
Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure.
Published in:
2022
By:
- Karpinets, Tatiana V.;
- Wu, Xiaogang;
- Solley, Travis;
- El Alam, Molly B.;
- Sims, Travis T.;
- Yoshida-Court, Kyoko;
- Lynn, Erica;
- Ahmed-Kaddar, Mustapha;
- Biegert, Greyson;
- Yue, Jingyan;
- Song, Xingzhi;
- Sun, Huandong;
- Petrosino, Joseph F.;
- Mezzari, Melissa P.;
- Okhuysen, Pablo;
- Eifel, Patricia J.;
- Jhingran, Anuja;
- Lin, Lilie L.;
- Schmeler, Kathleen M.;
- Ramondetta, Lois
Publication type:
journal article
CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.
Published in:
Glycobiology, 2010, v. 20, n. 12, p. 1574, doi. 10.1093/glycob/cwq106
By:
- Park, Byung H.;
- Karpinets, Tatiana V.;
- Syed, Mustafa H.;
- Leuze, Michael R.;
- Uberbacher, Edward C.
Publication type:
Article
Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set.
Published in:
BMC Medicine, 2016, v. 14, p. 1, doi. 10.1186/s12916-016-0705-4
By:
- Roszik, Jason;
- Haydu, Lauren E.;
- Hess, Kenneth R.;
- Oba, Junna;
- Joon, Aron Y.;
- Siroy, Alan E.;
- Karpinets, Tatiana V.;
- Stingo, Francesco C.;
- Baladandayuthapani, Veera;
- Tetzlaff, Michael T.;
- Wargo, Jennifer A.;
- Ken Chen;
- Forget, Marie-Andrée;
- Haymaker, Cara L.;
- Jie Qing Chen;
- Meric-Bernstam, Funda;
- Eterovic, Agda K.;
- Shaw, Kenna R.;
- Mills, Gordon B.;
- Gershenwald, Jeffrey E.
Publication type:
Article
BESC knowledgebase public portal†.
Published in:
Bioinformatics, 2012, v. 28, n. 5, p. 750, doi. 10.1093/bioinformatics/bts016
By:
- Syed, Mustafa H.;
- Karpinets, Tatiana V.;
- Parang, Morey;
- Leuze, Michael R.;
- Park, Byung H.;
- Hyatt, Doug;
- Brown, Steven D.;
- Moulton, Steve;
- Galloway, Michael D.;
- Uberbacher, Edward C.
Publication type:
Article
A Unifying Concept for the Dependence of Whole-crop N : P Ratio on Biomass: Theory and Experiment.
Published in:
Annals of Botany, 2008, v. 102, n. 6, p. 967, doi. 10.1093/aob/mcn188
By:
- Duncan J. Greenwood;
- Tatiana V. Karpinets;
- Kefeng Zhang;
- Angela Bosh-Serra;
- Arianna Boldrini;
- Lyudmila Karawulova
Publication type:
Article

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