Predictive Metagenomic Analysis of Autoimmune Disease Identifies Robust Autoimmunity and Disease Specific Microbial Signatures

by Angelina Volkova, Kelly V. Ruggles, Kelly V. Ruggles
Published 2021-03-01

Hypercluster: a flexible tool for parallelized unsupervised clustering optimization

by Lili Blumenberg, Kelly V. Ruggles
Published 2020-09-01

Gun possession among American youth: a discovery-based approach to understand gun violence.

by Kelly V Ruggles, Sonali Rajan
Published 2014-01-01

Data Science in the Research Domain Criteria Era: Relevance of Machine Learning to the Study of Stress Pathology, Recovery, and Resilience

by Isaac R. Galatzer-Levy, Kelly V. Ruggles, Zhe Chen
Published 2018-01-01

RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data

by Amanda W. Ernlund, Robert J. Schneider, Kelly V. Ruggles
Published 2018-11-01

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data

by Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser, Kelly V. Ruggles
Published 2018-06-01

Bacteriophages as potential new mammalian pathogens

by George V. Tetz, Kelly V. Ruggles, Hua Zhou, Adriana Heguy, Aristotelis Tsirigos, Victor Tetz
Published 2017-08-01

Betting on the fastest horse: Using computer simulation to design a combination HIV intervention for future projects in Maharashtra, India.

by Kelly V Ruggles, Anik R Patel, Stephen Schensul, Jean Schensul, Kimberly Nucifora, Qinlian Zhou, Kendall Bryant, R Scott Braithwaite
Published 2017-01-01

Evaluating Alternative Designs of a Multilevel HIV Intervention in Maharashtra, India: The Impact of Stakeholder Constraints

by Anik R. Patel, Kelly V. Ruggles, Kimberly Nucifora, Qinlian Zhou, Stephen Schensul, Jean Schensul, Kendall Bryant, R. Scott Braithwaite
Published 2018-10-01

Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village

by Kelly V. Ruggles, Jincheng Wang, Angelina Volkova, Monica Contreras, Oscar Noya-Alarcon, Orlana Lander, Hortensia Caballero, Maria G. Dominguez-Bello
Published 2018-08-01

Adverse Childhood Experiences Predict Early Initiation of Opioid Use Behaviors

by Honoria Guarino, Pedro Mateu-Gelabert, Kelly Quinn, Skultip Sirikantraporn, Kelly V. Ruggles, Cassandra Syckes, Elizabeth Goodbody, Lauren Jessell, Samuel R. Friedman
Published 2021-05-01

Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease

by Menghan Liu, Joseph C Devlin, Jiyuan Hu, Angelina Volkova, Thomas W Battaglia, Melody Ho, John R Asplin, Allyson Byrd, P'ng Loke, Huilin Li, Kelly V Ruggles, Aristotelis Tsirigos, Martin J Blaser, Lama Nazzal
Published 2021-03-01

Wnt signaling enhances macrophage responses to IL-4 and promotes resolution of atherosclerosis

by Ada Weinstock, Karishma Rahman, Or Yaacov, Hitoo Nishi, Prashanthi Menon, Cyrus A Nikain, Michela L Garabedian, Stephanie Pena, Naveed Akbar, Brian E Sansbury, Sean P Heffron, Jianhua Liu, Gregory Marecki, Dawn Fernandez, Emily J Brown, Kelly V Ruggles, Stephen A Ramsey, Chiara Giannarelli, Matthew Spite, Robin P Choudhury, P'ng Loke, Edward A Fisher
Published 2021-03-01

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

by Xue-Song Zhang, Jackie Li, Kimberly A Krautkramer, Michelle Badri, Thomas Battaglia, Timothy C Borbet, Hyunwook Koh, Sandy Ng, Rachel A Sibley, Yuanyuan Li, Wimal Pathmasiri, Shawn Jindal, Robin R Shields-Cutler, Ben Hillmann, Gabriel A Al-Ghalith, Victoria E Ruiz, Alexandra Livanos, Angélique B van ‘t Wout, Nabeetha Nagalingam, Arlin B Rogers, Susan Jenkins Sumner, Dan Knights, John M Denu, Huilin Li, Kelly V Ruggles, Richard Bonneau, R Anthony Williamson, Marcus Rauch, Martin J Blaser
Published 2018-07-01

Correction: Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

by Kuan-lin Huang, Shunqiang Li, Philipp Mertins, Song Cao, Harsha P. Gunawardena, Kelly V. Ruggles, D. R. Mani, Karl R. Clauser, Maki Tanioka, Jerry Usary, Shyam M. Kavuri, Ling Xie, Christopher Yoon, Jana W. Qiao, John Wrobel, Matthew A. Wyczalkowski, Petra Erdmann-Gilmore, Jacqueline E. Snider, Jeremy Hoog, Purba Singh, Beifang Niu, Zhanfang Guo, Sam Qiancheng Sun, Souzan Sanati, Emily Kawaler, Xuya Wang, Adam Scott, Kai Ye, Michael D. McLellan, Michael C. Wendl, Anna Malovannaya, Jason M. Held, Michael A. Gillette, David Fenyö, Christopher R. Kinsinger, Mehdi Mesri, Henry Rodriguez, Sherri R. Davies, Charles M. Perou, Cynthia Ma, R. Reid Townsend, Xian Chen, Steven A. Carr, Matthew J. Ellis, Li Ding
Published 2017-04-01

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

by Kuan-lin Huang, Shunqiang Li, Philipp Mertins, Song Cao, Harsha P. Gunawardena, Kelly V. Ruggles, D. R. Mani, Karl R. Clauser, Maki Tanioka, Jerry Usary, Shyam M. Kavuri, Ling Xie, Christopher Yoon, Jana W Qiao, John Wrobel, Matthew A. Wyczalkowski, Petra Erdmann-Gilmore, Jacqueline E. Snider, Jeremy Hoog, Purba Singh, Beifang Niu, Zhanfang Guo, Sam Qiancheng Sun, Souzan Sanati, Emily Kawaler, Xuya Wang, Adam Scott, Kai Ye, Michael D. McLellan, Michael C. Wendl, Anna Malovannaya, Jason M. Held, Michael A. Gillette, David Fenyö, Christopher R. Kinsinger, Mehdi Mesri, Henry Rodriguez, Sherri R. Davies, Charles M. Perou, Cynthia Ma, R. Reid Townsend, Xian Chen, Steven A. Carr, Matthew J. Ellis, Li Ding
Published 2017-03-01