Ecosyste.ms: Papers

10.7150/thno.43528

Rhein modulates host purine metabolism in intestine through gut microbiota and ameliorates experimental colitis
Cited by: 152
Author(s): Jiawei Wu, Zhonghong Wei, Peng Cheng, Cheng Qian, Fangming Xu, Yang Yu, Aiyun Wang, Wenxing Chen, Ziying Sun, Lu Yin
Software Mentions: 2
Published: almost 5 years ago

10.3390/toxins11010049

Gut Microbiota Profiling of Aflatoxin B1-Induced Rats Treated with Lactobacillus casei Shirota
Cited by: 22
Author(s): Winnie-Pui-Pui Liew, Mohd Sabran, Leslie Thian Lung Than
Software Mentions: 2
Published: almost 6 years ago

10.1128/mBio.00190-20

Modulation of the Gut Microbiota during High-Dose Glycerol Monolaurate-Mediated Amelioration of Obesity in Mice Fed a High-Fat Diet
Cited by: 53
Author(s): Minjie Zhao, Zengliang Jiang, Hong Cai, Li Yang, Qiufen Mo, Lingli Deng, Hao Zhong, Tao Liu, Hui Zhang, Jing Kang, Fengqin Feng
Software Mentions: 2
Published: over 4 years ago

10.1128/mSphere.00229-18

Potential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating Pandas
Cited by: 49
Author(s): Lifeng Zhu, Yang Zhang, Ru Yao, Liangliang Xu, Hua Chen, Xun Gu, Tonggui Wu, Xiangdong Yang
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.00127-16

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
Cited by: 419
Author(s): A. Comeau, Gavin M. Douglas, Morgan G. I. Langille
Software Mentions: 2
Published: over 7 years ago

10.1128/mSystems.00169-19

Time Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated Sludge
Cited by: 22
Author(s): Maidelyn Díaz Pérez, Leandro D. Guerrero, Esteban Orellana, Eva Lucía Margarita Figuerola, Leonardo Erijman
Software Mentions: 2
Published: about 5 years ago

10.1128/mSystems.00457-20

Formula Diet Alters the Ileal Metagenome and Transcriptome at Weaning and during the Postweaning Period in a Porcine Model
Cited by: 10
Author(s): Ahmed A. Elolimy, Charity L. Washam, Stephanie D. Byrum, Celine Chen, Harry Dawson, Anne K. Bowlin, Christopher E. Randolph, Manish Kumar Saraf, Laxmi Yeruva
Software Mentions: 2
Published: about 4 years ago

10.1128/mSystems.00824-20

Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
Cited by: 15
Author(s): Aldo Moreno‐Ulloa, Victoria Sicairos Diaz, Javier A. Tejeda-Mora, Marla I. Macias Contreras, Fernando Díaz Castillo, Abraham Guerrero, Ricardo González Sánchez, Omar Mendoza‐Porras, Rafael Vázquez Duhalt, Alexei F. Licea-Navarro
Software Mentions: 2
Published: almost 4 years ago

10.1038/ismej.2013.254

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
Cited by: 295
Author(s): Olivia U. Mason, Nicole M. Scott, Antonio G. González, Adam Robbins‐Pianka, Jacob Bælum, Jeffrey A. Kimbrel, Nicholas J. Bouskill, Emmanuel Prestat, Sharon Borglin, Dominique C. Joyner, Julian L. Fortney, Diogo Jurelevicius, William T. Stringfellow, Lisa Alvarez‐Cohen, Terry C. Hazen, Rob Knight, Jack A. Gilbert, Janet Jansson
Software Mentions: 2
Published: almost 11 years ago

10.3390/jof7070578

Fungal Endophytic Community and Diversity Associated with Desert Shrubs Driven by Plant Identity and Organ Differentiation in Extremely Arid Desert Ecosystem
Cited by: 19
Author(s): Yiling Zuo, Li Xia, Jingya Yang, Jiaqiang Liu, Lili Zhao, Xueli He
Software Mentions: 2
Published: over 3 years ago

10.3390/ijerph110807678

Assessing Program Efficiency: A Time and Motion Study of the Mental Health Emergency Care — Rural Access Program in NSW Australia
Cited by: 19
Author(s): Emily Saurman, David Lyle, Sue Kirby, Russell Roberts
Software Mentions: 2
Published: over 10 years ago

10.3390/ijerph16142474

Implications of Soil Pollution with Diesel Oil and BP Petroleum with ACTIVE Technology for Soil Health
Cited by: 33
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
Software Mentions: 2
Published: over 5 years ago

10.1080/2162402X.2015.1107698

Perspectives on sipuleucel-T: Its role in the prostate cancer treatment paradigm
Cited by: 27
Author(s): James L. Gulley, Peter F.A. Mulders, Peter Albers, Jacques Banchereau, M. Bolla, Klaus Pantel, Thomas Powles
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.08973

Bidirectional interactions between indomethacin and the murine intestinal microbiota
Cited by: 74
Author(s): Xue Liang, Kyle Bittinger, Xuanwen Li, Darrell R. Abernethy, Frederic D. Bushman, Garret A. FitzGerald
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.36842

Essential metabolism for a minimal cell
Cited by: 94
Author(s): Marian Breuer, Tyler M. Earnest, Chuck Merryman, Kim S. Wise, Lijie Sun, Michaela Lynott, Clyde A. Hutchison, Hamilton O. Smith, John D. Lapek, David J. Gonzalez, Valérie de Crécy‐Lagard, Drago Haas, Andrew D. Hanson, Piyush Labhsetwar, John I. Glass, Zaida Luthey‐Schulten
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms20205047

Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies
Cited by: 5
Author(s): Jing Tu, Liang Chen, Shen Gao, Jun‐Yi Zhang, Changwei Bi, Yuhan Tao, Na Lü, Lu Zhang
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms21041357

Tinkering Cis Motifs Jigsaw Puzzle Led to Root-Specific Drought-Inducible Novel Synthetic Promoters
Cited by: 12
Author(s): Aysha Jameel, Muhammad Noman, Weican Liu, Naveed Ahmad, Fawei Wang, Xiaowei Li, Haiyan Li
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms22179626

Increase in Akkermansiaceae in Gut Microbiota of Prostate Cancer-Bearing Mice
Cited by: 12
Author(s): Pin-Yu Huang, Yu Yang, Chun I. Wang, Pei Wen Hsiao, Hung‐Ting Chiang, Ting-Wen Chen
Software Mentions: 2
Published: about 3 years ago

10.1080/20002297.2019.1581513

Diversity and functional analysis of salivary microflora of Indian Antarctic expeditionaries
Cited by: 10
Author(s): Brij Bhushan, Anand Prakash Yadav, Shashi Bala Singh, Lilly Ganju
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.jsb.2014.03.019

A structural analysis of the AAA+ domains in Saccharomyces cerevisiae cytoplasmic dynein
Cited by: 20
Author(s): Emma S Gleave, Helgo Schmidt, Andrew P. Carter
Software Mentions: 2
Published: over 10 years ago

10.1186/s13023-019-1193-3

The use or generation of biomedical data and existing medicines to discover and establish new treatments for patients with rare diseases – recommendations of the IRDiRC Data Mining and Repurposing Task Force
Cited by: 18
Author(s): Noel Southall, Madhusudan Natarajan, Lilian Pek Lian Lau, Anneliene Hechtelt Jonker, Benoît Déprez, Tim Guilliams, Lawrence Hunter, Carin M. A. Rademaker, Virginie Hivert, Diego Ardigò, Repurposing Task Force
Software Mentions: 2
Published: about 5 years ago

10.1128/JVI.00528-18

Evolution-Guided Structural and Functional Analyses of the HERC Family Reveal an Ancient Marine Origin and Determinants of Antiviral Activity
Cited by: 23
Author(s): Ermela Paparisto, Matthew Woods, Macon D. Coleman, Seyed Arad Moghadasi, Divjyot S. Kochar, Sean K. Tom, Hinissan P. Kohio, Richard Gibson, Taryn J. Rohringer, Nina R Hunt, Eric J. Di Gravio, Jonathan Y. Zhang, Mingxing Tian, Yong Gao, Eric J. Arts, Stephen D. Barr
Software Mentions: 2
Published: over 6 years ago

10.1128/JVI.01601-16

Structure of Aichi Virus 1 and Its Empty Particle: Clues to Kobuvirus Genome Release Mechanism
Cited by: 12
Author(s): C. Sabin, T. Füzik, Karel Škubník, Lenka Pálková, Anders Lindberg, Pavel Plevka
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12937-019-0475-x

The study evaluating the effect of probiotic supplementation on the mental status, inflammation, and intestinal barrier in major depressive disorder patients using gluten-free or gluten-containing diet (SANGUT study): a 12-week, randomized, double-blind, and placebo-controlled clinical study protocol
Cited by: 40
Author(s): Hanna Karakuła-Juchnowicz, Joanna Róg, Dariusz Juchnowicz, Igor Łoniewski, Karolina Skonieczna-Żydecka, Paweł Krukow, Małgorzata Futyma-Jędrzejewska, Mariusz Kaczmarczyk
Software Mentions: 2
Published: about 5 years ago

10.3390/nu12030732

α-Linolenic Acid-Rich Diet Influences Microbiota Composition and Villus Morphology of the Mouse Small Intestine
Cited by: 21
Author(s): Hristo Todorov, Bettina Kollar, Franziska Bayer, Inês Brandão, Amrit Mann, Julia Mohr, Giulia Pontarollo, Henning Formes, Roland H. Stauber, Jens M. Kittner, Kristina Endres, Bernhard Watzer, Wolfgang Andreas Nockher, Felix Sommer, Susanne Gerber, Carsten Reinhardt
Software Mentions: 2
Published: over 4 years ago

10.3390/nu12082193

Dynamics of Structural and Functional Changes in Gut Microbiota during Treatment with a Microalgal β-Glucan, Paramylon and the Impact on Gut Inflammation
Cited by: 12
Author(s): Harrison B. Taylor, Radhika Gudi, Robert R. Brown, Chenthamarakshan Vasu
Software Mentions: 2
Published: over 4 years ago

10.1093/ofid/ofab162

Early Empirical Tuberculosis Treatment in HIV-Positive Patients Admitted to Hospital in South Africa: An Observational Cohort Study
Cited by: 3
Author(s): Carolin Bresges, Douglas P. Wilson, Katherine Fielding, Elizabeth L. Corbett, Fabrizia Del-Greco, Daniel Grint, J Peters, Ankur Gupta-Wright
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0136389

Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene
Cited by: 132
Author(s): Guillem Estruch, María Carmen Collado, David S. Peñaranda, Ana Tomás Vidal, Miguel Jover Cerdá, Gaspar Pérez-Martı́nez, Silvia Martínez‐Llorens
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0131819

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma
Cited by: 80
Author(s): Marcos Pérez‐Losada, Eduardo Castro-Nallar, Matthew L. Bendall, Robert J. Freishtat, Keith A. Crandall
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2014.00130

Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities
Cited by: 140
Author(s): Regina Lamendella, Steven Strutt, Sharon Borglin, Romy Chakraborty, Neslihan Taş, Olivia U. Mason, Jenni Hultman, Emmanuel Prestat, Terry C. Hazen, Janet Jansson
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-6-129

Diversity in domain architectures of Ser/Thr kinases and their homologues in prokaryotes
Cited by: 66
Author(s): A. Krupa, N. Srinivasan
Software Mentions: 1
Published: about 19 years ago

10.3389/fmicb.2018.01988

Intestinal Microbiome-Metabolome Responses to Essential Oils in Piglets
Cited by: 55
Author(s): Yuan Li, Xin Fu, Xin Ma, Shijie Geng, Xin Jiang, Qingyao Huang, Caihong Hu, Xinyan Han
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0130201

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers
Cited by: 117
Author(s): Kelly L. Cobaugh, Sean M. Schaeffer, Jennifer M. DeBruyn
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2021.688839

Variations of Soybean Meal and Corn Mixed Substrates in Physicochemical Characteristics and Microbiota During Two-Stage Solid-State Fermentation
Cited by: 19
Author(s): Weixu Su, Zipeng Jiang, Lihong Hao, Wentao Li, Tao Gong, Yu Zhang, Shuai Du, Cheng Wang, Zhaoqing Lu, Mingliang Jin, Yizhen Wang
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-12-S4-S8

Molecular dynamics study of the archaeal aquaporin AqpM
Cited by: 14
Author(s): Raúl Araya-Secchi, JA Garate, David S. Holmes, Tomás Pérez-Acle
Software Mentions: 1
Published: almost 14 years ago

10.1515/biol-2019-0009

Effect of Lactobacillus plantarum supplementation on production performance and fecal microbial composition in laying hens
Cited by: 9
Author(s): Hongxing Qiao, Hongtao Shi, Liheng Zhang, Yuzhen Song, Xiaojing Zhang, Chuanzhou Bian
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2020.00896

Detection of Viable and Total Bacterial Community in the Pit Mud of Chinese Strong-Flavor Liquor Using Propidium Monoazide Combined With Quantitative PCR and 16S rRNA Gene Sequencing
Cited by: 11
Author(s): Guangxun Tan, Rui Zhou, Wenqian Zhang, Yuanliang Hu, Zhiyong Ruan, Jing Li, Changyi Zhang, Dengjin Shen, Nan Peng, Yunxiang Liang, Siming Zhao
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0104752

Microbial Community Structure of Relict Niter-Beds Previously Used for Saltpeter Production
Cited by: 4
Author(s): Takashi Narihiro, Hideyuki Tamaki, Aya Akiba, Kazuto Takasaki, K. Nakano, Yoichi Kamagata, Satoshi Hanada, Taizo Maji
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2021.671683

Early-Life Intervention Using Exogenous Fecal Microbiota Alleviates Gut Injury and Reduce Inflammation Caused by Weaning Stress in Piglets
Cited by: 18
Author(s): Xin Ma, Yuchen Zhang, Tingting Xu, Mengqi Qian, Zhiren Yang, Xiuan Zhan, Xinyan Han
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2407-10-128

STAMP alters the growth of transformed and ovarian cancer cells
Cited by: 7
Author(s): Yuanzheng He, John A. Blackford, Elise C. Kohn, S. Stoney Simons
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0164036

The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health
Cited by: 96
Author(s): Özgün Candan Onarman Umu, Christine Bäuerl, Marije Oostindjer, Phillip B. Pope, Pablo E. Hernández, Gaspar Pérez-Martı́nez, Dzung B. Diep
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0117441

The Dynamic Distribution of Porcine Microbiota across Different Ages and Gastrointestinal Tract Segments
Cited by: 262
Author(s): Wenjing Zhao, Yapeng Wang, Shuyun Liu, Jiaojiao Huang, Zhengxiao Zhai, Chuan He, Jinmei Ding, Jun Wang, Huijuan Wang, Fan Wang, Jianguo Zhao, He Meng
Software Mentions: 1
Published: almost 10 years ago

10.3389/fmicb.2020.01548

Gastric Mucosa-Associated Microbial Signatures of Early Gastric Cancer
Cited by: 28
Author(s): Lili Wang, Yongning Xin, Jianhua Zhou, Ziqiang Tian, Chenguang Liu, Xinjuan Yu, Xiangchuan Meng, Weina Jiang, Shou‐Feng Zhao, Qi Dong
Software Mentions: 1
Published: over 4 years ago

10.1186/s13063-020-04853-7

Comparison of peri-implant submucosal microbiota in arches with zirconia or titanium implant-supported fixed complete dental prostheses: a study protocol for a randomized controlled trial
Cited by: 3
Author(s): Pingyi Jia, Jingwen Yang, Zhaoguo Yue, Jianzhang Liu, Qi Liu, Zhongning Liu, Lin Tang, Jianxia Hou
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0163099

Xenobiotic Metabolism and Gut Microbiomes
Cited by: 48
Author(s): Anubhav Das, Meenakshi Srinivasan, Tarini Shankar Ghosh, Sharmila S. Mande
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-017-1703-z

PFASUM: a substitution matrix from Pfam structural alignments
Cited by: 14
Author(s): Frank Keul, Martin Heß, Michael Goesele, Kay Hamacher
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0229825

Preventing slips, overruns, and cancellations: Application of system accident investigations and theory to the understanding and prevention of engineering project failures
Cited by: 1
Author(s): Diane Aloisio, Karen Marais
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2018.02890

Echinococcus granulosus Infection Results in an Increase in Eisenbergiella and Parabacteroides Genera in the Gut of Mice
Cited by: 16
Author(s): Jianling Bao, Huajun Zheng, Yuezhu Wang, Xiao Zheng, Li He, Wenjing Qi, Tian Wang, Baoqiang Guo, Gang Guo, Zhaoxia Zhang, Wenbao Zhang, Jun Li, Donald P. McManus
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0216211

Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning
Cited by: 22
Author(s): Ubaldo De La Torre, John D. Henderson, Kathleen L Furtado, Madeleine Pedroja, O'Malley Elenamarie, Anthony Mora, Monica Y. Pechanec, Elizabeth A. Maga, Michael J. Mienaltowski
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0184719

Infections by human gastrointestinal helminths are associated with changes in faecal microbiota diversity and composition
Cited by: 83
Author(s): Timothy Jenkins, Yasara Rathnayaka, Piyumali K. Perera, Laura Peachey, Matthew J. Nolan, Lutz Krause, R. S. Rajakaruna, Cinzia Cantacessi
Software Mentions: 1
Published: about 7 years ago

10.1128/mBio.02948-19

A Multiorgan Trafficking Circuit Provides Purifying Selection of Listeria monocytogenes Virulence Genes
Cited by: 20
Author(s): Alan K. Louie, Ting Zhang, Simone Becattini, Matthew K. Waldor, Daniel A. Portnoy
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2019.01682

Metagenomic Functional Shifts to Plant Induced Environmental Changes
Cited by: 25
Author(s): Svetlana N. Yurgel, Jacob T. Nearing, Gavin M. Douglas, Morgan G. I. Langille
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2019.01439

Compositional and Functional Analysis of the Microbiome in Tissue and Saliva of Oral Squamous Cell Carcinoma
Cited by: 45
Author(s): Zhen Zhang, Junjie Yang, Qiang Feng, Bin Chen, Meihui Li, Cheng Liang, Mingyu Li, Zhihui Li, Qin Xu, Lei Zhang, Wantao Chen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0255446

Characteristics of gut microbiota in people with obesity
Cited by: 74
Author(s): Mengmeng Duan, Yuezhu Wang, Qiang Zhang, Rong Zou, Min Guo, Huajun Zheng
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2018.02695

Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation
Cited by: 26
Author(s): Dongjuan Dai, William J. Rhoads, Marc Edwards, Amy Pruden
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2020.00929

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae
Cited by: 8
Author(s): Tianbo Liu, Yunhua Xiao, Jie Yin, Tuyong Yi, Zhi Zhou, Tom Hsiang, Qianjun Tang, Ching Ching Wu
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2019.01292

Diet Control More Intensively Disturbs Gut Microbiota Than Genetic Background in Wild Type and ob/ob Mice
Cited by: 12
Author(s): Jing-Hua Wang, Na Rae Shin, Soo-Kyoung Lim, Ungjin Im, Eun-Ji Song, Young-Do Nam, Hojun Kim
Software Mentions: 1
Published: over 5 years ago

10.1098/rsif.2021.0179

A farewell to <i>R</i> : time-series models for tracking and forecasting epidemics
Cited by: 7
Author(s): Andrew Harvey, Paul Kattuman
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0074767

Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp. Strain SC2
Cited by: 52
Author(s): Bomba Dam, Somasri Dam, Jochen Blom, Werner Liesack
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0251512

Effects of Gasterophilus pecorum infestation on the intestinal microbiota of the rewilded Przewalski’s horses in China
Cited by: 7
Author(s): Dini Hu, Yuzhu Chao, Boru Zhang, Chen Wang, Yue Qi, Make Ente, Dong Zhang, Kai Li, Kai Meng Mok
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0059907

An Appraisal of Human Mitochondrial DNA Instability: New Insights into the Role of Non-Canonical DNA Structures and Sequence Motifs
Cited by: 24
Author(s): Pedro H. Oliveira, Cláudia Lobato da Silva, Joaquim M. S. Cabral
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pntd.0000676

Computational Identification of Uncharacterized Cruzain Binding Sites
Cited by: 38
Author(s): Jacob D. Durrant, Henrik Keränen, Benjamin A. Wilson, J. Andrew McCammon
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1002359

Activation of Bmp2-Smad1 Signal and Its Regulation by Coordinated Alteration of H3K27 Trimethylation in Ras-Induced Senescence
Cited by: 58
Author(s): Atsushi Kaneda, Takanori Fujita, Motonobu Anai, Shozo Yamamoto, Genta Nagae, Masato Morikawa, Shingo Tsuji, Masanobu Oshima, Kohei Miyazono, Hiroyuki Aburatani
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2105-13-S17-S2

Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases
Cited by: 14
Author(s): Rithvik S. Vinekar, Chandra Verma, Indira Ghosh
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1004155

Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals
Cited by: 45
Author(s): Federica Gilardi, Eugenia Migliavacca, Aurélien Naldi, Michaël Baruchet, Donatella Canella, Gwendal Le Martelot, Nicolas Guex, Béatrice Desvergne
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1004560

A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila
Cited by: 98
Author(s): Lídia Mateo, Anna Ullastres, Josefa González
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1002097

Interferon Regulatory Factor 8 Regulates Pathways for Antigen Presentation in Myeloid Cells and during Tuberculosis
Cited by: 64
Author(s): Jean-François Marquis, Oxana Kapoustina, David Langlais, Rebecca Ruddy, Catherine R. Dufour, Bae-Hoon Kim, John D. MacMicking, Vincent Giguère, Philippe Gros
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1000335

Accurate Prediction of Peptide Binding Sites on Protein Surfaces
Cited by: 138
Author(s): Evangelia Petsalaki, Alexander Stark, Eduardo García‐Urdiales, Robert B. Russell
Software Mentions: 1
Published: over 15 years ago

10.3389/fmicb.2019.02547

Microbiome and Metabolome Analyses of Milk From Dairy Cows With Subclinical Streptococcus agalactiae Mastitis—Potential Biomarkers
Cited by: 35
Author(s): Jinjin Tong, Hua Zhang, Yonghong Zhang, Benhai Xiong, Linshu Jiang
Software Mentions: 1
Published: about 5 years ago

10.3390/nu12082298

Lactobacillus reuteri Ameliorates Intestinal Inflammation and Modulates Gut Microbiota and Metabolic Disorders in Dextran Sulfate Sodium-Induced Colitis in Mice
Cited by: 43
Author(s): Gang Wang, Shuo Huang, Shuang Cai, Haitao Yu, Yuming Wang, Xiangfang Zeng, Shiyan Qiao
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pcbi.1004368

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
Cited by: 25
Author(s): Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, Benoı̂t Roux
Software Mentions: 1
Published: about 9 years ago

10.1111/pbi.12761

Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome
Cited by: 20
Author(s): Jean‐Michel Hily, Sandrine Demanèche, Nils Poulicard, Mélanie Tannières, Samia Djennane, Monique Beuve, Emmanuelle Vigne, Gérard Demangeat, Véronique Komar, Claude Gertz, Aurélie Marmonier, Caroline Hemmer, Sophie Vigneron, Armelle Marais, Thierry Candresse, Pascal Simonet, Olivier Lemaire
Software Mentions: 1
Published: over 7 years ago

10.3390/ph6081055

Characterization of Antimicrobial Peptides toward the Development of Novel Antibiotics
Cited by: 190
Author(s): Wataru Aoki, Mitsuyoshi Ueda
Software Mentions: 1
Published: over 11 years ago

10.3389/fmicb.2018.02777

A Pilot Study: Changes of Gut Microbiota in Post-surgery Colorectal Cancer Patients
Cited by: 37
Author(s): Jing Cong, Hua Zhu, Dong Liu, Tianjun Li, Chuantao Zhang, Junmin Zhu, Hongying Lv, Kewei Liu, Chenxing Hao, Zibin Tian, Jianli Zhang, Xiaochun Zhang
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2018.01187

Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome
Cited by: 37
Author(s): Svetlana N. Yurgel, Gavin M. Douglas, Ashley Dusault, David Percival, Morgan G. I. Langille
Software Mentions: 1
Published: over 6 years ago

10.3390/ph14040329

Metformin Modifies the Gut Microbiota of Mice Infected with Helicobacter pylori
Cited by: 3
Author(s): Marine Jauvain, Sarah Courtois, Philippe Lehours, Emilie Bessède
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-9-436

Prediction of TF target sites based on atomistic models of protein-DNA complexes
Cited by: 40
Author(s): Vladimir Espinosa Angarica, Abel González Pérez, Ana Tereza Ribeiro de Vasconcelos, Julio Collado‐Vides, Bruno Contreras‐Moreira
Software Mentions: 1
Published: about 16 years ago

10.3389/fmicb.2019.01168

The Composition, Diversity and Predictive Metabolic Profiles of Bacteria Associated With the Gut Digesta of Five Sea Urchins in Luhuitou Fringing Reef (Northern South China Sea)
Cited by: 13
Author(s): Xiaopeng Yu, Kefu Yu, Jiayuan Liang, Yinghui Wang, Baoqing Hu, Xueyong Huang, Biao Chen, Zhenjun Qin
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-8-444

Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions
Cited by: 49
Author(s): Haiyan Jiang, Christian Blouin
Software Mentions: 1
Published: about 17 years ago

10.7717/peerj-cs.362

Data-flow-based adaption of the System-Theoretic Process Analysis for Security (STPA-Sec)
Cited by: 5
Author(s): Jinghua Yu, Stefan Wagner, Feng Luo
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.3666

Aura-biomes are present in the water layer above coral reef benthic macro-organisms
Cited by: 21
Author(s): Kevin Walsh, John M. Haggerty, Michael P. Doane, John J. Hansen, Megan M. Morris, Ana Paula B. Moreira, Luciana de Oliveira, Luciana Leomil, Gizele D. Garcia, Fabiano L. Thompson, Elizabeth A. Dinsdale
Software Mentions: 1
Published: over 7 years ago

10.1128/mSphere.00735-19

<i>Campylobacter</i> Abundance in Breastfed Infants and Identification of a New Species in the Global Enterics Multicenter Study
Cited by: 28
Author(s): Xiaoming Bian, Jolene M. Garber, Kerry K. Cooper, Steven Huynh, Jennifer Jones, Michael K. Mills, Daniel Rafala, Dilruba Nasrin, Karen L. Kotloff, Craig T. Parker, Sharon M. Tennant, William G. Miller, Christine M. Szymanski
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.4080

Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation
Cited by: 16
Author(s): Ehsan Pashay Ahi, Kristina M. Sefc
Software Mentions: 1
Published: about 7 years ago

10.3390/nu13072131

Oleuropein Ameliorates Advanced Stage of Type 2 Diabetes in db/db Mice by Regulating Gut Microbiota
Cited by: 25
Author(s): Shujuan Zheng, Yanan Wang, Jing-Jing Fang, Ruixuan Geng, Mengjie Li, Yuhan Zhao, Seong‐Gook Kang, Kunlun Huang, Teng Tong
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.9032

Comparative study of gut microbiota in Tibetan wild asses (<i>Equus kiang</i>) and domestic donkeys (<i>Equus asinus</i>) on the Qinghai-Tibet plateau
Cited by: 16
Author(s): Hongjin Liu, Xinquan Zhao, Xueping Han, Shixiao Xu, Liang Zhao, Linyong Hu, Tianwei Xu, Na Zhao, Xiaoling Zhang, Dongdong Chen, Fahu He, Xin Chen
Software Mentions: 1
Published: over 4 years ago

10.1128/mSystems.00169-16

Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets
Cited by: 105
Author(s): Vijay Shankar, Mostafa Gouda, Jessica Moncivaiz, Alex H. Gordon, Nicholas V. Reo, Laila Hussein, Oleg Paliy
Software Mentions: 1
Published: over 7 years ago

10.1128/mSystems.00006-17

Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome
Cited by: 58
Author(s): Emily Lamoureux, Scott A. Grandy, Morgan G. I. Langille
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.7117

Effect of heat-killed<i>Streptococcus thermophilus</i>on type 2 diabetes rats
Cited by: 12
Author(s): Xiangyang Gao, Fei Wang, Peng Zhao, Rong Zhang, Qiang Zeng
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.8137

Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea
Cited by: 15
Author(s): Wuttichai Mhuantong, Handung Nuryadi, Agus Trianto, Agus Sabdono, Sithichoke Tangphatsornruang, Lily Eurwilaichitr, Pattanop Kanokratana, Verawat Champreda
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.10946

Comparison of gut microbiota between adults with autism spectrum disorder and obese adults
Cited by: 19
Author(s): Qiang Zhang, Rong Zou, Min Guo, Mengmeng Duan, Li Quan, Huajun Zheng
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2020.01827

Evaluation of Enzymatic Cleaning on Food Processing Installations and Food Products Bacterial Microflora
Cited by: 18
Author(s): Laurent Delhalle, Bernard Taminiau, Sebastien Fastrez, Abdoulaye Fall, Marina Ballesteros, Sophie Burteau, Georges Daube
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.968

Back from the dead; the curious tale of the predatory cyanobacterium<i>Vampirovibrio chlorellavorus</i>
Cited by: 88
Author(s): Rochelle M. Soo, Ben J. Woodcroft, Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2019.02415

Immunodeficiency Promotes Adaptive Alterations of Host Gut Microbiome: An Observational Metagenomic Study in Mice
Cited by: 52
Author(s): Shuyu Zheng, Tingting Zhao, Shuijuan Yuan, Lingyu Yang, Jinmei Ding, Li Cui, Mingqing Xu
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-018-2404-y

Structure-function analysis of Sedolisins: evolution of tripeptidyl peptidase and endopeptidase subfamilies in fungi
Cited by: 2
Author(s): Facundo Orts, Arjen ten Have
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2020.00363

Gut Microbiomes of Endangered Przewalski’s Horse Populations in Short- and Long-Term Captivity: Implication for Species Reintroduction Based on the Soft-Release Strategy
Cited by: 13
Author(s): Liping Tang, Yimeng Li, Amrita Srivathsan, Yunyun Gao, Kai Li, Defu Hu, Dong Zhang
Software Mentions: 1
Published: over 4 years ago

10.3390/pathogens9010035

The Xylella fastidiosa-Resistant Olive Cultivar “Leccino” Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS)
Cited by: 35
Author(s): Marzia Vergine, Joana Beatrice Meyer, Massimiliano Cardinale, Erika Sabella, Martin Hartmann, Paolo Cherubini, Luigi De Bellis, Andrea Luvisi
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2018.01295

Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays
Cited by: 66
Author(s): Sarah A. Maarastawi, Katharina Frindte, Marius Linnartz, Claudia Knief
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-7-382

MultiSeq: unifying sequence and structure data for evolutionary analysis
Cited by: 354
Author(s): Elijah Roberts, John M. Eargle, D. Wright, Zaida Luthey‐Schulten
Software Mentions: 1
Published: over 18 years ago

10.3389/fmicb.2014.00799

Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis
Cited by: 8
Author(s): Renmao Tian, On On Lee, Yong Wang, Chunye Lin, Salim Bougouffa, Jill Man Ying Chiu, Rudolf S.S. Wu, Pei‐Yuan Qian
Software Mentions: 1
Published: almost 10 years ago

10.3389/fmicb.2016.00731

Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well
Cited by: 47
Author(s): Steven J. Robbins, Paul N. Evans, Donovan H. Parks, Suzanne D. Golding, Gene W. Tyson
Software Mentions: 1
Published: over 8 years ago