Analyzing large biological datasets with association networks

por Karpinets, Tatiana V., Park, Byung H., Uberbacher, Edward C.
Publicado 2012

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

por Karpinets, Tatiana V, Greenwood, Duncan J, Sams, Carl E, Ammons, John T
Publicado 2006

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

por Nag, Ambarish, Karpinets, Tatiana V., Chang, Christopher H., Bar-Peled, Maor
Publicado 2012

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

por Leuze, Michael R., Karpinets, Tatiana V., Syed, Mustafa H., Beliaev, Alexander S., Uberbacher, Edward C.
Publicado 2012

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

por Karpinets, Tatiana V., Gopalakrishnan, Vancheswaran, Wargo, Jennifer, Futreal, Andrew P., Schadt, Christopher W., Zhang, Jianhua
Publicado 2018

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

por Syed, Mustafa H, Karpinets, Tatiana V, Leuze, Michael R, Kora, Guruprasad H, Romine, Margaret R, Uberbacher, Edward C
Publicado 2009

Phenotype Fingerprinting Suggests the Involvement of Single-Genotype Consortia in Degradation of Aromatic Compounds by Rhodopseudomonas palustris

por Karpinets, Tatiana V., Pelletier, Dale A., Pan, Chongle, Uberbacher, Edward C., Melnichenko, Galina V., Hettich, Robert L., Samatova, Nagiza F.
Publicado 2009

BESC knowledgebase public portal

por 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.
Publicado 2012

Feasibility of a novel non-invasive swab technique for serial whole-exome sequencing of cervical tumors during chemoradiation therapy

por 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.
Publicado 2022

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

por 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.
Publicado 2010

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

por 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.
Publicado 2009

Oncogenic Kras drives invasion and maintains metastases in colorectal cancer

por Boutin, Adam T., Liao, Wen-Ting, Wang, Melody, Hwang, Soyoon Sarah, Karpinets, Tatiana V., Cheung, Hannah, Chu, Gerald C., Jiang, Shan, Hu, Jian, Chang, Kyle, Vilar, Eduardo, Song, Xingzhi, Zhang, Jianhua, Kopetz, Scott, Futreal, Andrew, Wang, Y. Alan, Kwong, Lawrence N., DePinho, Ronald A.
Publicado 2017

Immune environment and antigen specificity of the T cell receptor repertoire of malignant ascites in ovarian cancer

por 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.
Publicado 2023

Fusobacterium is enriched in oral cancer and promotes induction of programmed death-ligand 1 (PD-L1)

por Michikawa, Chieko, Gopalakrishnan, Vancheswaran, Harrandah, Amani M., Karpinets, Tatiana V, Garg, Rekha Rani, Chu, Randy A., Park, Yuk Pheel, Chukkapallia, Sasanka S., Yadlapalli, Nikhita, Erikson-Carter, Kelly C., Gleber-Netto, Frederico Omar, Sayour, Elias, Progulske-Fox, Ann, Chan, ‏Edward K.L., Wu, Xiaogang, Zhang, Jianhua, Jobin, Christian, Wargo, Jennifer A., Pickering, Curtis R., Myers, Jeffrey N., Silver, Natalie
Publicado 2022

A prospective study of the adaptive changes in the gut microbiome during standard-of-care chemoradiotherapy for gynecologic cancers

por 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, Klopp, Ann H., Colbert, Lauren E.
Publicado 2021

Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure

por 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, Ajami, Nadim, Jenq, Robert R., Futreal, Andrew, Zhang, Jianhua, Klopp, Ann H., Colbert, Lauren E.
Publicado 2022

HPV-related anal cancer is associated with changes in the anorectal microbiome during cancer development

por 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., Klopp, Ann H., Futreal, P. Andrew, Taniguchi, Cullen M., Schmeler, Kathleen M., Colbert, Lauren E.
Publicado 2023

Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation

por 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., Ajami, Nadim J., Wargo, Jennifer, Colbert, Lauren E., Klopp, Ann H.
Publicado 2021

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

por 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., Chen, Ken, Forget, Marie-Andrée, Haymaker, Cara L., Chen, Jie Qing, Meric-Bernstam, Funda, Eterovic, Agda K., Shaw, Kenna R., Mills, Gordon B., Gershenwald, Jeffrey E., Radvanyi, Laszlo G., Hwu, Patrick, Futreal, P. Andrew, Gibbons, Don L., Lazar, Alexander J., Bernatchez, Chantale, Davies, Michael A., Woodman, Scott E.
Publicado 2016