bioconductor: ArrayExpress | Projects

10.1371/journal.pntd.0001458

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi
Cited by: 5
Author(s): Priti Parikh, Todd Minning, Vinh Nguyen, Sarasi Lalithsena, Amir Asiaee, Satya S. Sahoo, Prashant Doshi, Rick L. Tarleton, Amit P. Sheth
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pntd.0004624

Comprehensive Transcriptome Meta-analysis to Characterize Host Immune Responses in Helminth Infections
Cited by: 25
Author(s): Guohui Zhou, Mary M. Stevenson, Timothy G. Geary, Jianguo Xia
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pntd.0005302

Pyrethroid Resistance in Malaysian Populations of Dengue Vector Aedes aegypti Is Mediated by CYP9 Family of Cytochrome P450 Genes
Cited by: 44
Author(s): Intan H. Ishak, Basile Kamgang, Sulaiman S. Ibrahim, Jacob M. Riveron, Helen Irving, Charles S. Wondji
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0127127

RulNet: A Web-Oriented Platform for Regulatory Network Inference, Application to Wheat –Omics Data
Cited by: 7
Author(s): Jonathan Vincent, Pierre Martre, Benjamin Gouriou, Catherine Ravel, Zhanwu Dai, Jean-Marc Petit, Marie Pailloux
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0233818

Intracellular Cryptococcus neoformans disrupts the transcriptome profile of M1- and M2-polarized host macrophages
Cited by: 16
Author(s): Aarthi Subramani, Prianca Griggs, Niah Frantzen, James Mendez, Jamila S Tucker, Jada Murriel, Linda M. Sircy, Grace E. Millican, Erin E. McClelland, Rebecca L. Seipelt-Thiemann, David E. Nelson
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0255679

Development of the petaloid bracts of a paleoherb species, Saururus chinensis
Cited by: 1
Author(s): Yanyan Zhao, Xuemei Zhang, Li D
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0224854

Acute Influenza A virus outbreak in an enzootic infected sow herd: Impact on viral dynamics, genetic and antigenic variability and effect of maternally derived antibodies and vaccination
Cited by: 20
Author(s): Pia Ryt-Hansen, Anders Gorm Pedersen, Inge Larsen, Jesper Schak Krog, Charlotte Sonne Kristensen, Lars Erik Larsen
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0235852

Astrocytes influence medulloblastoma phenotypes and CD133 surface expression
Cited by: 8
Author(s): Emily Gronseth, Ankan Gupta, Chris Koceja, Suresh Kumar, Raman G. Kutty, Kevin R. Rarick, Ling Wang, Ramani Ramchandran
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0246263

Nutrient availability is a dominant predictor of soil bacterial and fungal community composition after nitrogen addition in subtropical acidic forests
Cited by: 17
Author(s): Juyan Cui, Xiaochun Yuan, Qiufang Zhang, Junyi Zhou, Kaimiao Lin, Jianguo Xu, Yaozhong Zeng, Yue Wu, Leping Cheng, Quanxin Zeng, Kongcan Mei, Yuehmin Chen
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0232023

Epithelial changes of congenital intestinal obstruction in a rat model
Cited by: 0
Author(s): Quentin Ballouhey, Laurent Fourcade, Laurence Richard, Camille Bellet, Chaharazed El Hamel, Jean Michel Vallat, Franck Sturtz, Sylvie Bourthoumieu
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0242770

Comparison of the human microbiome in adults and children with chronic rhinosinusitis
Cited by: 4
Author(s): Il Ho Park, Joong Seob Lee, Joo Hoo Park, Suk Ho Kang, Seong Ahn Hong, Il Seok Park, Joo Heung Yoon
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0049831

Molecular Pathways Involved in Prostate Carcinogenesis: Insights from Public Microarray Datasets
Cited by: 18
Author(s): Sarah C. Baetke, Michiel E. Adriaens, Renaud Seigneuric, Chris T. Evelo, Lars Eijssen
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0231503

Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates
Cited by: 7
Author(s): Katarina Benulič, Mateja Pirš, Natacha Couto, Monika A. Chlebowicz, John W. A. Rossen, Tomaž Mark Zorec, Katja Seme, Mario Poljak, Tatjana Lejko Zupanc, Eva Ružić‐Sabljić, Tjaša Cerar
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0009779

Hepatic Gene Expression Profile in Mice Perorally Infected with Echinococcus multilocularis Eggs
Cited by: 30
Author(s): Bruno Gottstein, Matthias Wittwer, Marc Schild, Michael Merli, Stephen L. Leib, Norbert Müller, Joachim Müller, Rolf Jaggi
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0256884

Seed dressing with mefenpyr-diethyl as a safener for mesosulfuron-methyl application in wheat: The evaluation and mechanisms
Cited by: 8
Author(s): Li‐Bing Yuan, Guiping Ma, Yaling Geng, Xiaomin Liu, Hua Wang, Jian Li, Shanshan Song, Wenliang Pan, Hun Zhi-ying
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0091272

Increasing Consistency of Disease Biomarker Prediction Across Datasets
Cited by: 5
Author(s): Maria Chikina, Stuart C. Sealfon
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0015068

Analysis of Kinase Gene Expression Patterns across 5681 Human Tissue Samples Reveals Functional Genomic Taxonomy of the Kinome
Cited by: 45
Author(s): Sami Kilpinen, K. Ojala, Olli Kallioniemi
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0244227

Whole genome sequencing of Clostridioides difficile PCR ribotype 046 suggests transmission between pigs and humans
Cited by: 11
Author(s): Anders Werner, Paula Mölling, Anna Fagerström, Fredrik Dyrkell, Dimitrios Arnellos, Karin Johansson, Martin Sundqvist, Torbjörn Norén
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0062870

Gene Expression Analysis of Peripheral Blood Cells Reveals Toll-Like Receptor Pathway Deregulation in Colorectal Cancer
Cited by: 10
Author(s): Ye Xu, Qinghua Xu, Yang Li, Fang Liu, Xun Ye, Fei Wu, Shujuan Ni, Cong Tan, Guoxiang Cai, Meng Xia, Sanjun Cai, Xiang Du
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0246844

alms1 mutant zebrafish do not show hair cell phenotypes seen in other cilia mutants
Cited by: 0
Author(s): Lauren Parkinson, Tamara M. Stawicki
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0244755

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya
Cited by: 8
Author(s): Samuel Mwangangi Muturi, Lucy Muthui, Paul Njogu, Justus M. Onguso, Francis N. Wachira, Stephen O. Opiyo, Roger Pellé
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0236424

Salt stress induces endoplasmic reticulum stress-responsive genes in a grapevine rootstock
Cited by: 22
Author(s): Birsen Aydemir, Canan Yüksel Özmen, Umut Kibar, Filiz Mutaf, Pelin Burcu Büyük, Melike Bakır, Ali Ergül
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0181365

Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice
Cited by: 6
Author(s): Olusegun Oshota, Max Conway, María Fookes, Fernanda Schreiber, Roy R. Chaudhuri, Lu Yu, Fiona J. E. Morgan, Simon Clare, Jyoti S. Choudhary, Nicholas R. Thomson, Píetro Lió, Duncan J. Maskell, Pietro Mastroeni, A. Grant
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0044800

Mining Gene Expression Signature for the Detection of Pre-Malignant Melanocytes and Early Melanomas with Risk for Metastasis
Cited by: 21
Author(s): Cláudia Souza, Patrícia Xander, Ana Carolina Monteiro, Amanda Gonçalves dos Santos Silva, Débora Castanheira Pereira da Silva, Sabine Mai, Viviane Bernardo, José Daniel Lopes, Miriam Galvonas Jasiulionis
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0200004

Activation of Nrf2 in the liver is associated with stress resistance mediated by suppression of the growth hormone-regulated STAT5b transcription factor
Cited by: 36
Author(s): John P. Rooney, Keiyu Oshida, Naresh Vasani, Beena Vallanat, Natalia Ryan, Brian N. Chorley, Xuting Wang, Douglas A. Bell, Kai Wu, Lauren M. Aleksunes, Curtis D. Klaassen, Thomas W. Kensler, J. Christopher Corton
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0235551

An iron-dependent metabolic vulnerability underlies VPS34-dependence in RKO cancer cells
Cited by: 7
Author(s): M.J. Kobylarz, Jonathan M. Goodwin, Kang Zhao, John W. Annand, Sarah Hevi, Ellen O’Mahony, Gregory McAllister, John S. Reece‐Hoyes, Qiong Wang, John Alford, Carsten Russ, Alicia Lindeman, Martin Beibel, Guglielmo Roma, Walter Carbone, Judith Knehr, Joseph Loureiro, Christophe Antczak, Dmitri Wiederschain, Leon O. Murphy, Suchithra Menon, Beat Nyfeler
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0036351

Transcriptome Sequencing Revealed Significant Alteration of Cortical Promoter Usage and Splicing in Schizophrenia
Cited by: 96
Author(s): Jing Qin Wu, Xi Wang, Natalie J. Beveridge, Paul A. Tooney, Rodney J. Scott, Vaughan J. Carr, Murray J. Cairns
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0230157

Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils
Cited by: 57
Author(s): Anastasia A. Ivanova, А. Д. Железова, Т. И. Чернов, Svetlana N. Dedysh
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0042297

Distinct Cardiac Transcriptional Profiles Defining Pregnancy and Exercise
Cited by: 34
Author(s): Eunhee Chung, Joseph Heimiller, Leslie A. Leinwand
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0237541

Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity
Cited by: 3
Author(s): Aurore Duquenoy, Maryne Ania, Noémie Boucher, Frédéric Reynier, Lilia Boucinha, C. Andréoni, Vincent Thomas
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0249537

Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence
Cited by: 3
Author(s): Marie Gurke, Amalia Vidal-Gorosquieta, Johanna L. A. Pajimans, Karolina Wȩcek, Axel Barlow, Gloria González-Fortes, Stefanie Hartmann, Aurora Grandal-d’Anglade, Michael Hofreiter
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0245171

Manganese exposure in juvenile C57BL/6 mice increases glial inflammatory responses in the substantia nigra following infection with H1N1 influenza virus
Cited by: 6
Author(s): Collin M. Bantle, C. Tenley French, Jason E. Cummings, Shankar Sadasivan, Kevin Tran, Richard A. Slayden, Richard J. Smeyne, Ronald B. Tjalkens
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0031475

LAL Regulators SCO0877 and SCO7173 as Pleiotropic Modulators of Phosphate Starvation Response and Actinorhodin Biosynthesis in Streptomyces coelicolor
Cited by: 32
Author(s): Susana Guerra, Antonio Rodríguez‐García, Javier Santos‐Aberturas, Cláudia M. Vicente, Tamara D. Payero, Juan F. Martı́n, Jesús F. Aparicio
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0042490

Gene Profile of Chemokines on Hepatic Stellate Cells of Schistosome-Infected Mice and Antifibrotic Roles of CXCL9/10 on Liver Non-Parenchymal Cells
Cited by: 26
Author(s): Yuejin Liang, Jie Luo, Qiao Lu, Ying Zhou, Hai Wei Wu, Dan Zheng, Yong ya Ren, Ke Sun, Yong Wang, Zhao Song Zhang
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0242939

DamID identifies targets of CEH-60/PBX that are associated with neuron development and muscle structure in Caenorhabditis elegans
Cited by: 5
Author(s): Pieter Van de Walle, Celia Muñoz-Jiménez, Peter Askjaer, Liliane Schoofs, Liesbet Temmerman
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0022196

Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes
Cited by: 119
Author(s): Kevin L. Childs, Rebecca M. Davidson, C. Robin Buell
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0232297

Association between the rs1544410 polymorphism in the vitamin D receptor (VDR) gene and insulin secretion after gestational diabetes mellitus
Cited by: 6
Author(s): Nael Shaat, Anastasia Katsarou, Bushra Shahida, Rashmi B. Prasad, Karl Kristensen, Tereza Planck
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0236460

Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy
Cited by: 12
Author(s): Thanawat Rattanathammethee, Pimchanok Tuitemwong, Parameth Thiennimitr, Phinitphong Sarichai, Sarisa Na Pombejra, Pokpong Piriyakhuntorn, Sasinee Hantrakool, Chatree Chai‐Adisaksopha, Ekarat Rattarittamrong, Adisak Tantiworawit, Lalita Norasetthada
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0110840

Measuring the Effect of Inter-Study Variability on Estimating Prediction Error
Cited by: 19
Author(s): Shuyi Ma, Jaeyun Sung, Andrew T. Magis, Yuliang Wang, Donald Geman, Nathan D. Price
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0072591

Comparative Gene Expression Profiling Identifies Common Molecular Signatures of NF-κB Activation in Canine and Human Diffuse Large B Cell Lymphoma (DLBCL)
Cited by: 74
Author(s): Manikhandan Mudaliar, Ross Haggart, Gino Miele, Grant C. Sellar, Karen A. L. Tan, John Goodlad, Elspeth Milne, David M. Vail, Ilene D. Kurzman, Daniel Crowther, David Argyle
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0083762

The Effect of Gestational Age on Angiogenic Gene Expression in the Rat Placenta
Cited by: 13
Author(s): Kanchan Vaswani, Melissa Hum, Hsiu‐Wen Chan, Jennifer Ryan, Ryan J Wood-Bradley, Marloes Dekker Nitert, Murray D. Mitchell, James A. Armitage, Gregory E. Rice
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0009114

Functional Overlap between eIF4G Isoforms in Saccharomyces cerevisiae
Cited by: 51
Author(s): Bryan K. Clarkson, Wendy V. Gilbert, Jennifer A. Doudna
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0238923

Maternal supplementation with Bifidobacterium breve M-16V prevents their offspring from allergic airway inflammation accelerated by the prenatal exposure to an air pollutant aerosol
Cited by: 16
Author(s): Chiyoko Terada-Ikeda, Masahiro Kitabatake, Akari Hiraku, Koichi Kato, Satsuki Yasui, Natsuko Imakita, Noriko Ouji-Sageshima, Noriyuki Iwabuchi, Kaoru Hamada, Toshihiro Ito
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0242297

Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates
Cited by: 0
Author(s): Swarnali Louha, Richard J. Meinersmann, Travis C. Glenn
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0243065

Differential plasma exosomal long non-coding RNAs expression profiles and their emerging role in E-cigarette users, cigarette, waterpipe, and dual smokers
Cited by: 16
Author(s): Gagandeep Kaur, K. R. P. Singh, Krishna Prahlad Maremanda, Dongmei Li, Hitendra S. Chand, Irfan Rahman
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0232972

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet
Cited by: 17
Author(s): Lei Chen, Liangyu Zhang, Wendong Wang, Wei Qiu, Lei Liu, Anhong Ning, Jing Cao, Min Huang, Ming-Chao Zhong
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0244056

Viruses in unexplained encephalitis cases in American black bears (Ursus americanus)
Cited by: 10
Author(s): Charles E. Alex, Elizabeth Fahsbender, Eda Altan, Robert J. Bildfell, Peregrine L. Wolff, Ling Jin, Wendy Black, K. A. Jackson, Leslie W. Woods, Brandon Munk, Tiffany Tse, Eric Delwart, Patricia A. Pesavento
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0237245

Increasing temperature can modify the effect of straw mulching on soil C fractions, soil respiration, and microbial community composition
Cited by: 10
Author(s): Xin Fu, Jun Wang, Meng-Yi Xie, Fazhu Zhao, Russell Doughty
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0121042

Host Glycan Sugar-Specific Pathways in Streptococcus pneumonia: Galactose as a Key Sugar in Colonisation and Infection
Cited by: 67
Author(s): Laura Paixão, J.Santos Oliveira, André Veríssimo, Susana Vinga, Eva C. Lourenço, M. Rita Ventura, Morten Kjos, Jan‐Willem Veening, Vitor E. Fernandes, Peter W. Andrew, Hasan Yeşilkaya, Ana Rute Neves
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0237463

Bio-activating ultrafine grain titanium: RNA sequencing reveals enhanced mechano-activation of osteoconduction on nanostructured substrates
Cited by: 4
Author(s): Rebecca A. Reiss, Terry C. Lowe, Johnny A. Sena, Oleg Makhnin, Melanie C. Connick, Patrick Erik Illescas, Casey F. Davis
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0148957

Low Concordance between Gene Expression Signatures in ER Positive HER2 Negative Breast Carcinoma Could Impair Their Clinical Application
Cited by: 9
Author(s): Enora Laas, Peter Mallon, François P. Duhoux, Amina Hamidouche, Roman Rouzier, Fabien Reyal
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0240025

PLA2R antibody, PLA2R rs4664308 polymorphism and PLA2R mRNA levels in Tunisian patients with primary membranous nephritis
Cited by: 2
Author(s): Tarak Dhaouadi, Jihen Abdellatif, R. Trabelsi, H. Gaied, Sameh Chamkhi, Imen Sfar, R. Goucha, Fethi Ben Hamida, T. Ben Abdallah, Yousr Gorgi
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0058992

Spatio-Temporal Expression Patterns of Arabidopsis thaliana and Medicago truncatula Defensin-Like Genes
Cited by: 55
Author(s): Mesfin Tesfaye, Kevin A.T. Silverstein, Sumitha Nallu, Lin Wang, Christopher Botanga, S. Karen Gomez, Liliana M. Costa, Maria J. Harrison, Deborah A. Samac, Jane Glazebrook, Fumiaki Katagiri, José Gutierrez-Marcos, Kathryn A. VandenBosch
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0249757

Genome-wide identification and expression analysis of late embryogenesis abundant protein-encoding genes in rye (Secale cereale L.)
Cited by: 7
Author(s): Mengyue Ding, Lijian Wang, Weimin Zhan, Guanghua Sun, Xiaolin Jia, Shizhan Chen, Wusi Ding, Jianping Yang
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0253866

Have maternal or paternal ages any impact on the prenatal incidence of genomic copy number variants associated with fetal structural anomalies?
Cited by: 4
Author(s): Marta Larroya, Marta Tortajada, Eduard Mensión, Montse Pauta, Laia Rodríguez‐Revenga, Antoni Borrell
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0004818

PTCH1+/− Dermal Fibroblasts Isolated from Healthy Skin of Gorlin Syndrome Patients Exhibit Features of Carcinoma Associated Fibroblasts
Cited by: 27
Author(s): Alexandre Valin, Stéphanie Barnay‐Verdier, Robert Thomas, Hugues Ripoche, Florence Brellier, Odile Chevallier-Lagente, Marie-Françoise Avril, Thierry Magnaldo
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0229415

Identification of two novel adenoviruses in smooth-billed ani and tropical screech owl
Cited by: 10
Author(s): Ana Paula Jejesky de Oliveira, Maria Cristina Valdetaro Rangel, Márton Z. Vidovszky, João Luiz Rossi, Fernando Vicentini, Balázs Harrach, Győző L. Kaján
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0166991

dCITE: Measuring Necessary Cladistic Information Can Help You Reduce Polytomy Artefacts in Trees
Cited by: 2
Author(s): Michael J. Wise
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0019651

Platelets Alter Gene Expression Profile in Human Brain Endothelial Cells in an In Vitro Model of Cerebral Malaria
Cited by: 35
Author(s): Mathieu Barbier, Dorothée Faille, Béatrice Loriod, Julien Textoris, Claire Camus, Denis Puthier, Laurence Flori, Samuel C. Wassmer, Geneviève Victoréro, Marie‐Christine Alessi, Thierry Fusaı̈, Catherine Nguyen, Georges E. Grau, Pascal Rihet
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0052836

An Integrative Approach to Inferring Gene Regulatory Module Networks
Cited by: 5
Author(s): Michael Baitaluk, Sergey Kozhenkov, Julia Ponomarenko
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0244455

Genome-wide association analysis of Russian wheat aphid (Diuraphis noxia) resistance in Dn4 derived wheat lines evaluated in South Africa
Cited by: 5
Author(s): Lavinia Kisten, V. Tolmay, Isack Mathew, Scott L. Sydenham, Eduard Venter
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0241914

Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves
Cited by: 4
Author(s): Ruixue Wang, Peng Yin, Ruixia Yang, Xiao Liu, Lijie Luo, Junfeng Xu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0130028

Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex
Cited by: 43
Author(s): Evelina Sjöstedt, Linn Fagerberg, Björn M. Hallström, Anna Häggmark, Nicholas Mitsios, Peter Nilsson, Fredrik Pontén, Tomas Hökfelt, Mathias Uhlén, Jan Mulder
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0037209

Transcriptomic Characterization of Temperature Stress Responses in Larval Zebrafish
Cited by: 149
Author(s): Yong Long, Linchun Li, Qing Li, Xiaozhen He
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0159934

Nutritional Evaluation of an EPA-DHA Oil from Transgenic Camelina sativa in Feeds for Post-Smolt Atlantic Salmon (Salmo salar L.)
Cited by: 63
Author(s): Mónica B. Betancor, Matthew Sprague, Olga Sayanova, Sarah Usher, Christoforos Metochis, Patrick Campbell, Johnathan A. Napier, Douglas R. Tocher
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0243681

Genomic surveillance of antimicrobial resistance shows cattle and poultry are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico
Cited by: 11
Author(s): Enrique Jesús Delgado-Suárez, Tania Palós-Guitérrez, Francisco Alejandro Ruíz-López, Cindy Fabiola Hernández Pérez, Nayarit Emérita Ballesteros-Nova, Orbelín Soberanis-Ramos, Rubén Danilo Méndez-Medina, Marc W. Allard, María Salud Rubio Lozano
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0238190

Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria
Cited by: 26
Author(s): Abdurrahman Hassan Jibril, Iruka N. Okeke, Anders Dalsgaard, Eglė Kudirkienė, Olabisi C. Akinlabi, Muhammad Bashir Bello
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0019650

A Variable Region within the Genome of Streptococcus pneumoniae Contributes to Strain-Strain Variation in Virulence
Cited by: 48
Author(s): Richard M. Harvey, Uwe H. Stroeher, Abiodun D. Ogunniyi, Heidi Smith‐Vaughan, Amanda J. Leach, James C. Paton
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0241942

Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences
Cited by: 6
Author(s): Abdoulie Kanteh, Jarra Manneh, Sona Jabang, Mariama A Kujabi, Bakary Sanyang, Mary Aigbiremo Oboh, Abdoulie Bojang, Haruna S. Jallow, Davis Nwakanma, Ousman Secka, Anna Roca, Alfred Amambua-Ngwa, Martín Antonio, Ignatius Baldeh, Karen Forrest, Ahmadou Lamin Samateh, Umberto D’Alessandro, Abdul Karim Sesay
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0165543

Identification of Genes Discriminating Multiple Sclerosis Patients from Controls by Adapting a Pathway Analysis Method
Cited by: 4
Author(s): Lei Zhang, Linlin Wang, Pu Tian, Suyan Tian
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0228463

Induction of systemic immunity through nasal-associated lymphoid tissue (NALT) of mice intranasally immunized with Brucella abortus malate dehydrogenase-loaded chitosan nanoparticles
Cited by: 12
Author(s): Soojin Shim, Sang Hee Soh, Young Jae Im, Cheol‐Hee Ahn, Hong-Tae Park, Woo Bin Park, Suji Kim, Han Sang Yoo
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0237242

Transcriptome analysis of the eggs of the silkworm pale red egg (rep-1) mutant at 36 hours after oviposition
Cited by: 1
Author(s): Meina Wu, Pingyang Wang, Mengjie Gao, Dongxu Shen, Qiaoling Zhao
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0256181

Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability
Cited by: 1
Author(s): Hemant Bengani, Detelina Grozeva, Lambert Moyon, Shipra Bhatia, Susana R. Louros, Jilly Hope, Adam D. Jackson, James Prendergast, Liusaidh J Owen, Magali Naville, Jacqueline K. Rainger, Graeme R. Grimes, Mihail Halachev, Laura C. Murphy, Olivera Spasić-Bošković, Veronica van Heyningen, P. Kind, Catherine M. Abbott, Emily K. Osterweil, F. Lucy Raymond, Hugues Roest Crollius, David R. FitzPatrick
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0255410

Prevalence and risk factors for antimicrobial resistance among newborns with gram-negative sepsis
Cited by: 16
Author(s): Semaria Solomon, Oluwasefunmi Akeju, Oludare A. Odumade, Rozina Ambachew, Zenebe Gebreyohannes, Kimiko Van Wickle, Mahlet Abayneh, Gesit Metaferia, Maria J. Carvalho, Kathryn Thomson, Kirsty Sands, Timothy R. Walsh, Rebecca Milton, Frederick G. B. Goddard, Delayehu Bekele, Grace J Chan
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0256979

Longitudinal detection of somatic mutations in saliva and plasma for the surveillance of oral squamous cell carcinomas
Cited by: 13
Author(s): Ying Cui, Hae-Suk Kim, Eunae Sandra Cho, Dawool Han, Jung A Park, Ju Yeong Park, Woong Nam, Hyung Jun Kim, In‐Ho Cha, Yong Hoon
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0241098

Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis
Cited by: 7
Author(s): Prateek Dey, Sanjeev Kumar Sharma, Indrani Sarkar, Swapna Devi Ray, Padmanabhan Pramod, Venkata Hanumat Sastry Kochiganti, Goldin Quadros, Saurabh Singh Rathore, Vikram Singh, Ram Pratap Singh
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0166520

Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii
Cited by: 38
Author(s): Shahid Manzoor, Erik Bongcam‐Rudloff, Anna Schnürer, Bettina Müller
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0034158

Coexpression of Nuclear Receptors and Histone Methylation Modifying Genes in the Testis: Implications for Endocrine Disruptor Modes of Action
Cited by: 18
Author(s): Alison Anderson, Kim W. Carter, Denise Anderson, Michael J. Wise
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0059459

Global Gene Expression Profiling Reveals SPINK1 as a Potential Hepatocellular Carcinoma Marker
Cited by: 60
Author(s): Aileen Marshall, Margus Lukk, Claudia Kutter, Susan Davies, Graeme Alexander, Duncan T. Odom
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0229797

Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome
Cited by: 2
Author(s): Michelle Coleman, Canaan Whitfield-Cargile, Noah D. Cohen, Jennifer S. Goldsby, Laurie A. Davidson, Ana M. Chamoun‐Emanuelli, Ivan Ivanov, Susan C. Eades, Nancy H. Ing, Robert S. Chapkin
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0074712

A Degenerative Retinal Process in HIV-Associated Non-Infectious Retinopathy
Cited by: 25
Author(s): Igor Kozák, Roman Šášik, William R. Freeman, Leslee Sprague, María Laura Gomez, Lingyun Cheng, Sharif El-Emam, Francesca Mojana, Dirk-Uwe Bartsch, Jenny Bosten, Radha Ayyagari, Gary Hardiman
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0116309

Gene Expression Dosage Regulation in an Allopolyploid Fish
Cited by: 14
Author(s): Isa Matos, Miguel P. Machado, Manfred Schartl, M. M. Coelho
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0246603

Establishment of the TALE-code reveals aberrantly activated homeobox gene PBX1 in Hodgkin lymphoma
Cited by: 13
Author(s): Stefan Nagel, Claudia Pommerenke, Corinna Meyer, Roderick A.F. MacLeod, Hans Drexler
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0012339

Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution
Cited by: 63
Author(s): Pawandeep Dhami, Peter Saffrey, Alexander W. Bruce, Shane C. Dillon, Kelly Chiang, Nicolas Bonhoure, Christof Koch, Jackie Bye, Keith James, Nicola Foad, Peter Ellis, Nicholas A. Watkins, Willem H. Ouwehand, Cordelia Langford, Robert Andrews, Ian Dunham, David Vetrie
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0248405

Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection
Cited by: 5
Author(s): Hadeer M. Aboshady, Nathalie Mandonnet, Anna M. Johansson, Elisabeth Jonas, Jean-Christophe Bambou
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0039469

Deregulation of Rab and Rab Effector Genes in Bladder Cancer
Cited by: 94
Author(s): Joël Rainui Ho, Élodie Chapeaublanc, Lisa A. Kirkwood, Rémy Nicolle, Simone Benhamou, Thierry Lebrét, Yves Allory, Jennifer Southgate, François Radvanyi, Bruno Goud
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0051693

StRAP: An Integrated Resource for Profiling High-Throughput Cancer Genomic Data from Stress Response Studies
Cited by: 0
Author(s): Seth Johnson, Biju Issac, Shuping Zhao, Mohit Bisht, Orieta Celiku, Philip J. Tofilon, Kevin Camphausen, Uma Shankavaram
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0066513

Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks – Evidence of a Tail Biting Resistant Phenotype
Cited by: 27
Author(s): Emma Brunberg, Per Jensen, Anders Isaksson, Linda J. Keeling
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0224927

Integrating long noncoding RNAs and mRNAs expression profiles of response to Plasmodiophora brassicae infection in Pakchoi (Brassica campestris ssp. chinensis Makino)
Cited by: 5
Author(s): Huifen Zhu, Xiaofeng Li, Dandan Xi, Wentao Zhai, Zhaohui Zhang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0004128

Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments
Cited by: 26
Author(s): Luca Beltrame, Lisa Rizzetto, Raffaele Paola, Philippe Rocca-Serra, Luca Gambineri, Cristina Battaglia, Duccio Cavalieri
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0229536

Identification of trypanosomatids and blood feeding preferences of phlebotomine sand fly species common in Sicily, Southern Italy
Cited by: 30
Author(s): Jessica Maria Abbate, Carla Maia, André Pereira, Francesca Arfuso, Gabriella Gaglio, Maria Rizzo, Giulia Caracappa, Gabriele Marino, Matthias Pollmeier, S. Giannetto, Emanuele Brianti
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0242874

Interaction of preimplantation factor with the global bovine endometrial transcriptome
Cited by: 3
Author(s): Ruth Wonfor, Christopher J. Creevey, Manuela Natoli, Matthew J. Hegarty, Deborah Nash, Michael T. Rose
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0235401

Antimalarial drug resistance molecular makers of Plasmodium falciparum isolates from Sudan during 2015–2017
Cited by: 13
Author(s): Maazza Hussien, Muzamil Mahdi Abdel Hamid, Elamin Abdelkarim Elamin, Abdalla O. Hassan, Arwa Elaagip, Abusofyan Hamattallah A. Salama, Mohammed H. Abdelraheem, Abdelrahim Mohamed
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0249432

PAH-pollution effects on sensitive and resistant embryos: Integrating structure and function with gene expression
Cited by: 4
Author(s): Goran Bozinovic, Damian Shea, Zuying Feng, David E. Hinton, Tim L. Sit, Marjorie F. Oleksiak
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0225873

Dual oxidase Duox and Toll-like receptor 3 TLR3 in the Toll pathway suppress zoonotic pathogens through regulating the intestinal bacterial community homeostasis in Hermetia illucens L.
Cited by: 17
Author(s): Yaqing Huang, Yongqiang Yu, Shuai Zhan, Jeffery K. Tomberlin, Dian Huang, Minmin Cai, Longyu Zheng, Yu Zhou, Jibin Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0106479

De-Novo Learning of Genome-Scale Regulatory Networks in S. cerevisiae
Cited by: 19
Author(s): Sisi Ma, Patrick Kemmeren, David Gresham, Alexander Statnikov
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0248233

R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting
Cited by: 3
Author(s): Takeshi Kawakami, Meghan K. Jensen, Andrea Slavney, Petra E. Deane, Ausra Milano, Vandana Raghavan, Brett Ford, Erin T. Chu, Aaron J. Sams, Adam R. Boyko
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0246144

Xylanase modulates the microbiota of ileal mucosa and digesta of pigs fed corn-based arabinoxylans likely through both a stimbiotic and prebiotic mechanism
Cited by: 14
Author(s): Amy L Petry, John F. Patience, Lucas R Koester, Nichole F. Huntley, M.R. Bedford, Stephan Schmitz‐Esser
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0211716

Sepsis induces long-lasting impairments in CD4+ T-cell responses despite rapid numerical recovery of T-lymphocyte populations
Cited by: 22
Author(s): Christoph Ammer‐Herrmenau, Upasana Kulkarni, Nico Andreas, Martin Ungelenk, Sarina Ravens, Christian G. Hübner, Angela Kather, Ingo Kurth, Michael Bauer, Thomas Kamradt
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0245160

Rapid detection of ERG11 polymorphism associated azole resistance in Candida tropicalis
Cited by: 6
Author(s): Saikat Paul, Rajneesh Dadwal, Shreya Singh, Dipika Shaw, Arunaloke Chakrabarti, Shivaprakash M Rudramurthy, Anup Ghosh
Software Mentions: 2
Published: over 5 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962