Publications from the Department of Cell and Molecular Biology faculty at the University of Rhode Island.

Follow

Submissions from 2021

PDF

Entomological risk assessment for dengue virus transmission during 2016-2020 in Kamphaeng Phet, Thailand, Thanyalak Fansiri, Darunee Buddhari, Nattaphol Pathawong, Arissara Pongsiri, Chonticha Klungthong, Sopon Iamsirithaworn, Anthony R. Jones, Stefan Fernandez, Anon Srikiatkhachorn, Alan L. Rothman, Kathryn B. Anderson, Stephen J. Thomas, Timothy P. Endy, and Alongkot Ponlawat

PDF

Improved transformation efficiency of group A Streptococcus by inactivation of a type I restriction modification system, Meredith B. Flynn, Kathryn M. Ramsey, Hunter J. Tolliver, Simon L. Dove, and Michael R. Wessels

PDF

Effect of Low-Passage Number on Dengue Consensus Genomes and Intra-host Variant Frequencies, Christian K. Fung, Tao Li, Simon Pollett, Maria Theresa Alera, In-Kyu Yoon, Jun Hang, Louis Macareo, Anon Srikiatkhachorn, Damon Ellison, Alan L. Rothman, Stefan Fernandez, Richard G. Jarman, and Irina Maljkovic Berry

Link

QuickIsoSeq for Isoform Quantification in Large-Scale RNA Sequencing, Ramya Gamini, Reiko Nakashima, Wen He, Ying Huang, Ying Zhang, and Shanrong Zhao

Link

Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments, Fatma Gomaa, Daniel R. Utter, Christopher Powers, David J. Beaudoin, Virginia P. Edgcomb, Helena L. Filipsson, Colleen M. Hansel, Scott D. Wankel, Ying Zhang, and Joan M. Bernhard

PDF

Computational Study of Helical and Helix-Hinge-Helix Conformations of an Anti-Microbial Peptide in Solution by Molecular Dynamics and Vibrational Analysis, Faramarz Joodaki, Lenore M. Martin, and Michael L. Greenfield

PDF

Control of a Programmed Cell Death Pathway in Pseudomonas aeruginosa by an Antiterminator, Jennifer M. Peña, Samantha M. Prezioso, Kirsty A. McFarland, Tracy K. Kambara, Kathryn M. Ramsey, Padraig Deighan, and Simon L. Dove

PDF

Impaired Host Response and the Presence of Acinetobacter baumannii in the Serum Microbiome of Type-II Diabetic Patients, Dasith Perera, Sarah E. Kleinstein, Benjamin Hanson, Hatice Hasturk, Ryan Eveloff, Marcelo Freire, and Matthew M. Ramsey

Link

Microbiome Analysis Reveals Diversity and Function of Mollicutes Associated with the Eastern Oyster, Crassostrea virginica, Zachary T. Pimentel, Keith Dufault-Thompson, Kayla T. Russo, Abigail K. Scro, Roxanna M. Smolowitz, Marta Gomez-Chiarri, and Ying Zhang

Link

Transcriptional regulation of plant biomass degradation and carbohydrate utilization genes in the extreme thermophile caldicellulosiruptor bescii, Dmitry A. Rodionov, Irina A. Rodionova, Vladimir A. Rodionov, Aleksandr A. Arzamasov, Ke Zhang, Gabriel M. Rubinstein, Tania N.N. Tanwee, Ryan G. Bing, James R. Crosby, Intawat Nookaew, Mirko Basen, Steven D. Brown, Charlotte M. Wilson, Dawn M. Klingeman, Farris L. Poole, Ying Zhang, Robert M. Kelly, and Michael W.W. Adams

PDF

Disease-driven Reduction in Human Mobility Influences Human-Mosquito Contacts and Dengue Transmission Dynamics, Kathryn L. Schaber, T. Alex Perkins, Alun L. Lloyd, Lance A. Waller, Uriel Kitron, Valerie A. Paz-Soldan, John P. Elder, Alan L. Rothman, David J. Civitello, William H. Elson, Amy C. Morrison, Thomas W. Scott, and Gonzalo M. Vazquez-Prokopec

PDF

Extreme Levels of Ocean Acidification Restructure the Plankton Community and Biogeochemistry of a Temperate Coastal Ecosystem: A Mesocosm Study, Carsten Spisla, Jan Taucher, Lennart T. Bach, Mathias Haunost, Tim Boxhammer, Andrew L. King, Bethany D. Jenkins, Joselynn R. Wallace, Andrea Ludwig, Jana Meyer, Paul Stange, Fabrizio Minutolo, Kai T. Lohbeck, Alice Nauendorf, Verena Kalter, Silke Lischka, Michael Sswat, Isabel Dörner, Stefanie M. H. Ismar-Rebitz, Nicole Aberle, Jaw C. Yong, Jean-Marie Bouquet, Anna K. Lechtenbörger, Peter Kohnert, Michael Krudewig, and Ulf Riebesell

PDF

Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance, Maxim S. Svetlov, Egor A. Syroegin, Elena V. Aleksandrova, Gemma C. Atkinson, Steven Gregory, Alexander S. Mankin, and Yury S. Polikanov

PDF

Temporally Integrated Single Cell RNA Sequencing Analysis of PBMC from Experimental and Natural Primary Human DENV-1 Infections, Adam T. Waickman, Heather Friberg, Gregory D. Gromowski, Wiriya Rutvisuttinunt, Tao Li, Hayden Siegfried, Kaitlin Victor, Michael K. McCracken, Stefan Fernandez, Anon Srikiatkhachorn, Damon Ellison, Richard G. Jarman, Stephen J. Thomas, Alan L. Rothman, Timothy Endy, and Jeffrey R. Currier

Link

Genome-scale metabolic model of caldicellulosiruptor bescii reveals optimal metabolic engineering strategies for bio-based chemical production, Ke Zhang, Weishu Zhao, Dmitry A. Rodionov, Gabriel M. Rubinstein, Diep N. Nguyen, Tania N.N. Tanwee, James Crosby, Ryan G. Bing, Robert M. Kelly, Michael W.W. Adams, and Ying Zhang

Link

Histone demethylase complexes KDM3A and KDM3B cooperate with OCT4/SOX2 to define a pluripotency gene regulatory network, Zhenshuo Zhu, Xiaolong Wu, Qun Li, Juqing Zhang, Shuai Yu, Qiaoyan Shen, Zhe Zhou, Qin Pan, Wei Yue, Dezhe Qin, Ying Zhang, Wenxu Zhao, Rui Zhang, Sha Peng, Na Li, Shiqiang Zhang, Anmin Lei, Yi Liang Miao, Zhonghua Liu, Xingqi Chen, Huayan Wang, Mingzhi Liao, and Jinlian Hua

Submissions from 2020

PDF

An Innovative, Prospective, Hybrid Cohort-Cluster Study Design to Characterize Dengue Virus Transmission in Multigenerational Households in Kamphaeng Phet, Thailand, Kathryn B. Anderson, Darunee Buddhari, Anon Srikiatkhachorn, Gregory D. Gromowski, Sopon Iamsirithaworn, Alden L. Weg, Damon W. Ellison, Louis Macareo, Derek A T Cummings, In-Kyu Yoon, Ananda Nisalak, Alongkot Ponlawat, Stephen J. Thomas, Stefan Fernandez, Richard G. Jarman, Alan L. Rothman, and Timothy P. Endy

PDF

Stavudine exposure results in developmental abnormalities by causing DNA damage, inhibiting cell proliferation and inducing apoptosis in mouse embryos, Rui-Fang Ao, Yu-Xiang Liang, Xiao-Qing Liu, Kui Tan, Xiaoling Wang, Dan Liu, Ting Zhang, Gongqin Sun, and Jun Xie

PDF

Heterogeneity of Dengue Illness in Community-Based Prospective Study, Iquitos, Peru, William H. Elson, Robert C. Reiner, Crystyan Siles, Isabel Bazan, Stalin Vilcarromero, Amy R. Riley-Powell, Ania B. Kawiecki, Helvio Astete, Robert D. Hontz, Chris M. Barker, Gonzalo M. Vazquez-Prokopec, Amy C. Morrison, Thomas W. Scott, John P. Elder, Alan L. Rothman, and Valerie A. Paz-Soldan

PDF

Measuring Health Related Quality of Life for Dengue Patients in Iquitos, Peru, William H. Elson, Amy R. Riley-Powell, Amy C. Morrison, Esther E. Gotlieb, Erik J. Groessl, Jhonny J. Cordova, J. Esther Rios, W. Lorena Quiroz, Alfonso S. Vizcarra, Robert C. Reiner, Christopher M. Barker, Gonzalo M. Vazquez-Prokopec, Thomas W. Scott, Alan L. Rothman, John P. Elder, and Valerie A. Paz-Soldan

PDF

Immune-engineered H7N9 Influenza Hemagglutinin Improves Protection against Viral Influenza Virus Challenge, Hyesun Jang, Lauren M. Meyers, Christine Boyle, Anne S. De Groot, Leonard Moise, and Ted M. Ross

PDF

Tiamulin-Resistant Mutants of the Thermophilic Bacterium Thermus thermophilus, Erin E. Killeavy, Gerwald Jogl, and Steven T. Gregory

PDF

Degradation of MinD Oscillator Complexes by Escherichia coli ClpXP, Christopher J. LaBreck, Catherine E. Trebino, Colby N. Ferreira, Josiah Morrison, Eric C. DiBiasio, Joseph Conti, and Jodi L. Camberg

PDF

Cryo-electron Microscopy Structure of the 70S Ribosome from Enterococcus faecalis, Eileen L. Murphy, Kavindra V. Singh, Bryant Avila, Torsten Kleffmann, Steven Gregory, Barbara E. Murray, Kurt L. Krause, Reza Khayat, and Gerwald Jogl

PDF

Tn-Seq reveals hidden complexity in the utilization of host-derived glutathione in Francisella tularensis, Kathryn M. Ramsey, Hannah E. Ledvina, Tenayaann M. Tresko, Jamie M. Wandzilak, Catherine A. Tower, Thomas A. Tallo, Caroline E. Schramm, S. Brook Peterson, Shawn J. Skerrett, Joseph D. Mougous, and Simon L. Dove

PDF

Novel multiparameter correlates of Coxiella burnetii infection and vaccination identified by longitudinal deep immune profiling, P. M. Reeves, S. Raju Paul, L. Baeten, Y. Yi, J. Hess, D. Sobell, A. Scholzen, A. Garritsen, Anne S. De Groot, Leonard Moise, T. Brauns, R. Bowen, A. E. Sluder, and M. C. Poznansky

Link

Erratum: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest (BMC Biology (2020) 18 (90) DOI: 10.1186/s12915-020-00820-5), Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Delière, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck, Toni Gabaldón, Roderic Guigó, Frédérique Hilliou, Silvia Hinojosa-Alvarez, Yi Min Hsiao, Sylvie Hudaverdian, and Emmanuelle Jacquin-Joly

Link

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest, Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Delière, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck, Toni Gabaldón, Roderic Guigó, Frédérique Hilliou, Silvia Hinojosa-Alvarez, Yi Min Hsiao, Sylvie Hudaverdian, and Emmanuelle Jacquin-Joly

PDF

Correction to: The Genome Sequence of the Grape Phylloxera Provides Insights into the Evolution, Adaptation, and Invasion Routes of an Iconic Pest, Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Delière, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck, Toni Gabaldón, Roderic Guigó, Frédérique Hilliou, Silvia Hinojosa-Alvarez, Yi-min Hsiao, Sylvie Hudaverdian, Emmanuelle Jacquin-Joly, Edward B. James, Spencer Johnston, Benjamin Joubard, Gaëlle Le Goff, Gaël Le Trionnaire, Pablo Librado, Shanlin Liu, Eric Lombaert, Hsiao-ling Lu, Martine Maïbèche, Mohamed Makni, Marina Marcet-Houben, David Martínez-Torres, Camille Meslin, Nicolas Montagné, Nancy A. Moran, Daciana Papura, Nicolas Parisot, Yvan Rahbé, Mélanie Ribeiro Lopes, Aida Ripoll-Cladellas, Stéphanie Robin, Céline Roques, Pascale Roux, Julio Rozas, Alejandro Sánchez-Gracia, Jose F. Sánchez-Herrero, Didac Santesmasses, Iris Scatoni, Rémy-Félix Serre, Ming Tang, Wenhua Tian, Paul A. Umina, Manuella van Munster, Carole Vincent-Monégat, Joshua Wemmer, Alex C. C. Wilson, Ying Zhang, Chaoyang Zhao, Jing Zhao, Serena Zhao, Xin Zhou, François Delmotte, and Denis Tagu

PDF

Transcriptional and clonal characterization of B cell plasmablast diversity following primary and secondary natural DENV infection, Alan L. Rothman and Et Al

PDF

Analysis of cell-associated DENV RNA by oligo(dT) primed 5’ capture scRNAseq, Mark A. Sanborn, Tao Li, Kaitlin Victor, Hayden Siegfried, Christian Fung, Alan L. Rothman, Anon Srikiatkhachorn, Stefan Fernandez, Damon Ellison, Richard G. Jarman, Heather Friberg, Irina Maljkovic Berry, Jeffrey R. Currier, and Adam T. Waickman

PDF

T lymphocyte responses to flaviviruses — diverse cell populations affect tendency toward protection and disease, Luis Alberto Sanchez Vargas, Anuja Mathew, and Alan L. Rothman

PDF

A distinct role for recombination repair factors in an early cellular response to transcription–replication conflicts, Xin Shao, Amalie M. Joergensen, Niall G. Howlett, Michael Lisby, and Vibe H. Oestergaard

PDF

Application of a Biphasic Mathematical Model of Cancer Cell Drug Response for Formulating Potent and Synergistic Targeted Drug Combinations to Triple Negative Breast Cancer Cells, Jinyan Shen, Li Li, Niall G. Howlett, Paul S. Cohen, and Gongqin Sun

PDF

Biphasic Mathematical Model of Cell–Drug Interaction That Separates Target-Specific and Off-Target Inhibition and Suggests Potent Targeted Drug Combinations for Multi-Driver Colorectal Cancer Cells, Jinyan Shen, Li Li, Tao Yang, Paul S. Cohen, and Gongqin Sun

PDF

Alterations in the ribosomal protein bL12 of E. coli affecting the initiation, elongation and termination of protein synthesis, Adam D. Younkin, Steven T. Gregory, and Michael O'Connor

Submissions from 2019

PDF

Effects of Iron and Light Availability on Phytoplankton Photosynthetic Properties in the Ross Sea, Anne-Carlijn Alderkamp, Gert L. van Dijken, Kate E. Lowry, Kate M. Lewis, Hannah L. Joy-Warren, Willem van de Poll, Patrick Laan, Loes Gerringa, Tom O. Delmont, Bethany D. Jenkins, and Kevin R. Arrigo

Link

From the raw bar to the bench: Bivalves as models for human health, José A. Fernández Robledo, Raghavendra Yadavalli, Bassem Allam, Emmanuelle Pales Espinosa, Marco Gerdol, Samuele Greco, Rebecca J. Stevick, Marta Gómez-Chiarri, Ying Zhang, Cynthia A. Heil, Adrienne N. Tracy, David Bishop-Bailey, and Michael J. Metzger

PDF

Analysis of the TCR Repertoire in HIV-Exposed but Uninfected Infants, Benjamin Gabriel, Carey Medin, Jeremiah Alves, Ruth Nduati, Rose Kerubo Bosire, Dalton Wamalwa, Carey Farquhar, Grace John-Steward, and Barbara L. Lohman-Payne

PDF

Multi-antigen Vaccination With Simultaneous Engagement of the OX40 Receptor Delays Malignant Mesothelioma Growth and Increases Survival in Animal Models, Peter R. Hoffmann, Fukun W. Hoffmann, Thomas A. Premeaux, Tsuyoshi Fujita, Elisa Soprana, Maddalena Panigada, Glen M. Chew, Guilhem Richard, Pooja Hindocha, Mark Menor, Vedbar S. Khadka, Youping Deng, Leonard Moise, Lishomwa C. Ndhlovu, Antonio Siccardi, Andrew D. Weinberg, Anne S. De Groot, and Pietro Bertino

PDF

Planarity and out-of-plane vibrational modes of tryptophan and tyrosine in biomolecular modeling, Faramarz Joodaki, Lenore M. Martin, and Michael L. Greenfield

PDF

Immune escape and immune camouflage may reduce the efficacy of RTS,S vaccine in Malawi, Sundos Khan, Matthew Parrillo, Andres H. Gutierrez, Frances E. Terry, Leonard Moise, William D. Martin, and Anne S. De Groot

PDF

Evidence for activated Lck protein tyrosine kinase as the driver of proliferation in acute myeloid leukemia cell, CTV-1, Li Li, Yixin Cui, Jinyan Shen, Hannah Dobson, and Gongqin Sun

PDF

Ponatinib Inhibits Proliferation and Induces Apoptosis of Liver Cancer Cells, but Its Efficacy Is Compromised by Its Activation on PDK1/Akt/mTOR Signaling, Chang Liu, Xiuli Mu, Xuan Wang, Chan Zhang, Lina Zhang, Baofeng Yu, and Gongqin Sun

PDF

Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826), Chang Liu, Xuan Wang, Jiu-Bo Tian, Pei-Yuan Ma, Fan-Xiu Meng, Qi Zhang, Bao-Feng Yu, Rui Guo, Zhi-Zhen Liu, Hai-Long Wang, Jun Xie, Niu-Llang Cheng, Jian-Hua Wang, Bo Niu, and Gongqin Sun

PDF

Draft Genome Sequence of the Putative Marine Pathogen Thalassobius sp. I31.1, Hilary J. Ranson, Jason LaPorte, Edward Spinard, Andrei Y. Chistoserdov, Marta Gomez-Chiarri, David R. Nelson, and David C. Rowley

PDF

Longitudinal Analysis of Memory B and T Cell Responses to Dengue Virus in a 5-Year Prospective Cohort Study in Thailand, Luis A. Sánchez-Vargas, Sonia Kounlavouth, Madison L. Smith, Kathryn B. Anderson, Anon Srikiatkhachorn, Damon W. Ellison, Jeffrey R. Currier, Timothy P. Endy, Anuja Mathew, and Alan L. Rothman

PDF

Topological Scoring of Protein Interaction Networks, Mihaela E. Sardiu, Joshua M. Gilmore, Brad D. Groppe, Arnob Dutta, Laurence Florens, and Michael P. Washburn

PDF

Dengue illness impacts daily human mobility patterns in Iquitos, Peru, Kathryn L. Schaber, Valerie A. Paz-Soldan, Amy C. Morrison, William HD Elson, Alan L. Rothman, Christopher N. Mores, Helvio Astete-Vega, Thomas W. Scott, Lance A. Waller, Uriel Kitron, John P. Elder, Christopher M. Barker, T. Alex Perkins, and Gonzalo M. Vazquez-Prokopec

PDF

Promiscuous Coxiella burnetii CD4 Epitope Clusters Associated With Human Recall Responses Are Candidates for a Novel T-Cell Targeted Multi-Epitope Q Fever Vaccine, Anja Scholzen, Guilhem Richard, Leonard Moise, Laurie A. Baeten, Patrick M. Reeves, William D. Martin, Timothy A. Brauns, Christine M. Boyle, Susan Raju Paul, Richard Bucala, Richard A. Bowen, Anja Garritsen, Anne S. De Groot, Ann E. Sluder, and Mark C. Poznansky

PDF

Drug Sensitivity Screening and Targeted Pathway Analysis Reveal a Multi-Driver Proliferative Mechanism and Suggest a Strategy of Combination Targeted Therapy for Colorectal Cancer Cells, Jinyan Shen, Li Li, Tao Yang, Niuliang Cheng, and Gongqin Sun

PDF

Bacterial Community Dynamics in an Oyster Hatchery in Response to Probiotic Treatment, Rebecca J. Stevick, Saebom Sohn, Tejashree H. Modak, David R. Nelson, David C. Rowley, Karin Tammi, Roxanna Smolowitz, Kathryn Markey Lundgren, Anton F. Post, and Marta Gomez-Chiarri

PDF

Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100, Laura E. Williams, Nicole Cullen, Joseph A. DeGiorgis, Karla J. Martinez, Justina Mellone, Molly Oser, Jing Wang, and Ying Zhang

Submissions from 2018

PDF

Structural versatility that serves the function of the HRD motif in the catalytic loop of protein tyrosine kinase, Src, Yixin Cui and Gongqin Sun

Link

Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial, Emma E. Davenport, Tiffany Amariuta, Maria Gutierrez-Arcelus, Kamil Slowikowski, Harm Jan Westra, Yang Luo, Ciyue Shen, Deepak A. Rao, Ying Zhang, Stephen Pearson, David Von Schack, Jean S. Beebe, Nan Bing, Sally John, Michael S. Vincent, Baohong Zhang, and Soumya Raychaudhuri

PDF

Upregulation of HLA‐E by dengue and not Zika viruses, Elena Drews, Awadalkareem Adam, Phone Htoo, Elizabeth Townsley, and Anuja Mathew

Link

Using PSAMM for the curation and analysis of genome-scale metabolic models, Keith Dufault-Thompson, Jon Lund Steffensen, and Ying Zhang

PDF

An Essential Staphylococcus Aureus Cell Division Protein Directly Regulates FtsZ Dynamics, Prahathees J. Eswara, Robert S. Brzozowski, Marissa G. Viola, Gianni Graham, Catherine Spanoudis, Catherine Trebino, Jyoti Jha, Joseph I. Aubee, Karl M. Thompson, Jodi L. Camberg, and Kumaran S. Ramamurthi

PDF

Protective versus pathologic pre-exposure cytokine profiles in dengue virus infection, Heather Friberg, Coreen M. Beaumier, Sangshin Park, Pamela Pazoles, Timothy P. Endy, Anuja Mathew, Jeffrey R. Currier, Richard G. Jarman, Kathryn B. Anderson, Steve Hatch, Stephen J. Thomas, and Alan L. Rothman

PDF

Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2, Martin R. Higgs, Koichi Sato, John J. Reynolds, Shabana Begum, Rachel Bayley, Amalia Goula, Audrey Vernet, Karissa L. Paquin, David G. Skalnik, Wataru Kobayashi, Minoru Takata, Niall G. Howlett, Hitoshi Kurumizaka, Hiroshi Kimura, and Grant S. Stewart

PDF

Mass spectrometry-assisted identification of ADAMTS13-derived peptides presented on HLA-DR and HLA-DQ, Johana Hrodinová, Fabian C. Verbij, Paul H.P. Kaijen, Robin B. Hartholt, Floris van Alphen, Neubury Lardy, Anja ten Brinke, Karen Vanhoorelbeke, Pooja J. Hindocha, Anne S. De Groot, Alexander B. Meijer, Jan Voorberg, and Ivan Peyron

PDF

Draft Genome Sequence of Bowmanella denitrificans JL63, a Bacterium Isolated from Whiteleg Shrimp (Litopenaeus vannamei) That Can Inhibit the Growth of Vibrio Parahaemolyticus, Jason P. LaPorte, Edward J. Spinard, Marta Gomez-Chiarri, David C. Rowley, John J. Mekalanos, and David R. Nelson

PDF

High background in ELISpot assays is associated with elevated levels of immune activation in HIV‐1‐seronegative individuals in Nairobi, Amy Y. Liu, Stephen C. De Rosa, Brandon L. Guthrie, Robert Y. Choi, Rose Kerubo-Bosire, Barbara A. Richardson, James Kiarie, Carey Farquhar, and Barbara L. Lohman-Payne

PDF

HIV-exposed uninfected infants: elevated cord blood Interleukin 8 (IL-8) is significantly associated with maternal HIV infection and systemic IL-8 in a Kenyan cohort, Barbara L. Lohman-Payne, Benjamin Gabriel, Sangshin Park, Dalton Wamalwa, Elizabeth Maleche-Obimbo, Carey Farquhar, Rose Kerubo Bosire, and Grace John-Steward

PDF

Community clinic-based lifestyle change for prevention of metabolic syndrome: Rationale, design and methods of the ‘Vida Sana/healthy life’ program, Patricia Markham Risica, Megan McCarthy, Katherine Barry, Susan P. Oliverio, and Anne S. De Groot

PDF

T cell epitope engineering: an avian H7N9 influenza vaccine strategy for pandemic preparedness and response, Leonard Moise, Bethany M. Biron, Christine M. Boyle, Nese Kurt Yilmaz, Hyesun Jang, Celia Schiffer, Ted M. Ross, William D. Martin, and Anne S. De Groot

Link

A simple in vitro gut model for studying the interaction between Escherichia coli and the intestinal commensal microbiota in cecal mucus, Matthew E. Mokszycki, Mary Leatham-Jensen, Jon L. Steffensen, Ying Zhang, Karen A. Krogfelt, Matthew E. Caldwell, Tyrrell Conway, and Paul S. Cohen

PDF

Use of structural equation models to predict dengue illness phenotype, Sangshin Park, Anon Srikiatkhachorn, Siripen Kalayanarooj, Louis Macareo, Sharone Green, Jennifer F. Friedman, and Alan L. Rothman

PDF

Evolution of the Natural Transformation Protein, ComEC, in Bacteria, Zachary T. Pimentel and Ying Zhang

PDF

Draft Genome Sequence of the Putative Marine Pathogen Aquimarina sp. Strain I32.4, Hilary J. Ranson, Edward Spinard, Andrei Y. Chistoserdov, Marta Gomez-Chiarri, David R. Nelson, and David C. Rowley

PDF

Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.), David W. Waite, Inka Vanwonterghem, Christian Rinke, Donovan H. Parks, Ying Zhang, Ken Takai, Stefan M. Sievert, Jörg Simon, Barbara J. Campbell, Thomas E. Hanson, Tanja Woyke, Martin G. Klotz, and Philip Hugenholtz

Link

Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: PolyA+ selection versus rRNA depletion, Shanrong Zhao, Ying Zhang, Ramya Gamini, Baohong Zhang, and David Von Schack

Submissions from 2017

PDF

Dengue virus induces mitochondrial elongation through impairment of Drp1-triggered mitochondrial fission, Vincent Barbier, Diane Lang, Dierra Valois, Alan L. Rothman, and Carey L. Medin

PDF

An immunoinformatics-derived DNA vaccine encoding human class II T cell epitopes of Ebola virus, Sudan virus, and Venezuelan equine encephalitis virus is immunogenic in HLA transgenic mice, Callie E. Bounds, Frances E. Terry, Leonard Moise, Drew Hannaman, William D. Martin, Anne S. De Groot, John J. Suschak, Lesley C. Dupuy, and Connie S. Schmaljohn

PDF

Knowledge, attitudes, practices and willingness to vaccinate in preparation for the introduction of HPV vaccines in Bamako, Mali, Anne S. De Groot, Karamoko Tounkara, Mali Rochas, Sarah Beseme, Shahla Yekta, Fanta Siby Diallo, J. Kathleen Tracy, Ibrahima Teguete, and Ousmane A. Koita

PDF

A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation, Keith Dufault-Thompson, Huahua Jian, Ruxue Cheng, Jiefu Li, Fengping Wang, and Ying Zhang

PDF

Composition and Function of Mutant Swi/Snf Complexes, Arnob Dutta, Mihaela Sardiu, Madelaine Gogol, Joshua Gilmore, Daoyong Zhang, Laurence Florens, Susan M. Abmayr, Michael P. Washburn, and Jerry L. Workman

PDF

T‐cell epitope content comparison (EpiCC) of swine H1 influenza A virus hemagglutinin, Andres H. Gutiérrez, Vicki J. Rapp-Gabrielson, Frances E. Terry, Crystal L. Loving, Leonard Moise, William D. Martin, and Anne S. De Groot

PDF

Proteomic responses to elevated ocean temperature in ovaries of the ascidian Ciona intestinalis, Chelsea E. Lopez, Hannah C. Sheehan, David A. Vierra, Paul A. Azzinaro, Thomas H. Meedel, Niall G. Howlett, and Steven Q. Irvine

PDF

Selectable marker independent transformation of recalcitrant maize inbred B73 and sorghum P898012 mediated by morphogenic regulators BABY BOOM and WUSCHEL2, Muruganatham Mookkan, Kimberly Nelson-Vasilchik, Joel Hague, Zhanyuan J. Zhang, and Albert P. Kausch

PDF

Isocitrate Dehydrogenase Mutation in Vibrio anguillarum Results in Virulence Attenuation and Immunoprotection in Rainbow Trout (Oncorhynchus mykiss), Xiangyu Mou, Edward J. Spinard, Shelby L. Hillman, and David R. Nelson

PDF

Defining Genetic Fitness Determinants and Creating Genomic Resources for an Oral Pathogen, Ajay M. Narayanan, Matthew M. Ramsey, Apollo Stacy, and Marvin Whiteley

PDF

Modulation of the Fanconi anemia pathway via chemically induced changes in chromatin structure, David A. Vierra, Jada L. Garzon, Meghan A. Rego, Morganne M. Adroved, Maurizio Mauro, and Niall G. Howlett

PDF

Proteolysis-Dependent Remodeling of the Tubulin Homolog FtsZ at the Division Septum in Escherichia coli, Marissa G. Viola, Christopher J. LaBreck, Joseph Conti, and Jodi L. Camberg

PDF

A humanized mouse model identifies key amino acids for low immunogenicity of H7N9 vaccines, Yamato Wada, Arnone Nithichanon, Eri Nobusawa, Leonard Moise, William D. Martin, Norio Yamamoto, Kazutaka Terahara, Haruhisa Hagiwara, Takato Odagiri, Masato Tashiro, Ganjana Lertmemongkolchai, Haruko Takeyama, Anne S. De Groot, Manabu Ato, and Yoshimasa Takahashi

PDF

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.), David W. Waite, Inka Vanwonterghem, Christian Rinke, Donovan H. Parks, Ying Zhang, Ken Takai, Stefan M. Sievert, Jörg Simon, Barbara J. Campbell, Thomas E. Hanson, Tanja Woyke, Martin G. Klotz, and Philip Hugenholtz

Submissions from 2016

PDF

Advancing Crop Transformation in the Era of Genome Editing, Fredy Altpeter, Nathan M. Springer, Laura E. Bartley, Ann E. Blechl, Thomas P. Brutnell, Vitaly Citovsky, Liza J. Conrad, Stanton B. Gelvin, David P. Jackson, Albert P. Kausch, Peggy G. Lemaux, June I. Medford, Martha L. Orozco-Cárdenas, David M. Tricoli, Joyce Van Eck, Daniel F. Voytas, Virginia Walbot, Kan Wang, Zhanyuan J. Zhang, and C. Neal Stewart Jr.

PDF

Draft Genome Sequence of the New Pathogen for Bivalve Larvae Vibrio bivalvicida, Javier Dubert, Edward J. Spinard, David R. Nelson, Marta Gomez-Chiarri, Jesus L. Romalde, and Juan L. Barja

PDF

Contributions of Tropodithietic Acid and Biofilm Formation to the Probiotic Activity of Phaeobacter Inhibens, Marta Gomez-Chiarri, David C. Rowley, and David R. Nelson

PDF

In Vivo Validation of Predicted and Conserved T Cell Epitopes in a Swine Influenza Model, Andres H. Gutiérrez, Crystal Loving, Leonard Moise, Frances E. Terry, Susan L. Brockmeier, Holly R. Hughes, William D. Martin, and Anne S. De Groot

PDF

Control of sexuality by the sk1-encoded UDP-glycosyltransferase of maize, Andrew P. Hayward, Maria A. Moreno, Thomas P. Howard III, Joel Hague, Kimberly Nelson, Christopher Heffelfinger, Sandra Romero, Albert P. Kausch, Gaétan Glauser, Ivan F. Acosta, John P. Mottinger, and Stephen L. Dellaporta

PDF

Thyrotropin Receptor Epitope and Human Leukocyte Antigen in Graves’ Disease, Hidefumi Inaba, Leslie J. De Groot, and Takashi Akamizu

PDF

In situ embryo rescue for generation of wide intra- and interspecific hybrids of Panicum virgatum L., Albert P. Kausch, Michael Tilelli, Joel Hague, Christopher Heffelfinger, David Cunha, Maria Moreno, Stephen L. Dellaporta, and Kimberly Nelson

PDF

Draft Genome Sequence of Aliiroseovarius crassostreae CV919-312, the Causative Agent of Roseovarius Oyster Disease (Formerly Juvenile Oyster Disease), Linda Kessner, Edward Spinard, Marta Gomez-Chiarri, David C. Rowley, and David R. Nelson

PDF

Uropathogenic Escherichia coli Metabolite-Dependent Quiescence and Persistence May Explain Antibiotic Tolerance during Urinary Tract Infection, Mary P. Leatham-Jensen, Matthew E. Mokszycki, David C. Rowley, Robert Deering, Jodi L. Camberg, Evgeni V. Sokurenko, Veronika L. Tchesnokova, Jakob Frimodt-Møller, Karen A. Krogfelt, Karen Leth Nielsen, Niels Frimodt-Møller, Gongqin Sun, and Paul S. Cohen

PDF

Draft Genome Sequence of the Emerging Bivalve Pathogen Vibrio tubiashii subsp. europaeus, Edward J. Spinard, Javier Dubert, David R. Nelson, Marta Gomez-Chiarri, and Juan L. Barja

PDF

The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia, Edward C. Stanley, Paul A. Azzinaro, David A. Vierra, Niall G. Howlett, and Steven Q. Irvine

PDF

PSAMM: A Portable System for the Analysis of Metabolic Models, Jon Lund Steffensen, Keith Dufault-Thompson, and Ying Zhang

PDF

The PTEN Phosphatase Functions Cooperatively with the Fanconi Anemia Proteins in DNA Crosslink Repair, Elizabeth A. Vuono, Ananda Mukherjee, David A. Vierra, Morganne M. Adroved, Charlotte Hodson, Andrew J. Deans, and Niall G. Howlett

Submissions from 2015

PDF

Structure-Based Redesign of Lysostaphin Yields Potent Antistaphylococcal Enzymes that Evade Immune Cell Surveillance, Kristina Blazanovic, Hongliang Zhao, Yoonjoo Choi, Wen Li, Regina S. Salvat, Daniel C. Osipovitch, Jennifer Fields, Leonard Moise, Brett L. Berwin, Steven N. Fiering, Chris Bailey-Kellogg, and Karl E. Griswold