bioconductor: ArrayExpress | Projects

10.1186/1752-0509-8-26

Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions
Cited by: 5
Author(s): Shubhada R. Hegde, Khushbu Pal, Shekhar C. Mande
Software Mentions: 2
Published: almost 11 years ago

10.1186/1752-0509-2-36

A logic-based diagram of signalling pathways central to macrophage activation
Cited by: 65
Author(s): Sobia Raza, Kevin A. Robertson, Paul Lacaze, David L. Page, Anton J. Enright, Peter Ghazal, Tom C. Freeman
Software Mentions: 2
Published: over 16 years ago

10.1186/s12918-017-0466-5

Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma
Cited by: 8
Author(s): Xinan Yang, Fangming Tang, Jisu Shin, John M. Cunningham
Software Mentions: 2
Published: about 7 years ago

10.1186/s13040-014-0035-z

Identifying genetic interactions associated with late-onset Alzheimer’s disease
Cited by: 17
Author(s): Charalampos S. Floudas, Nara Um, M. Ilyas Kamboh, M. Michael Barmada, Shyam Visweswaran
Software Mentions: 2
Published: almost 10 years ago

10.1093/bioinformatics/btv002

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
Cited by: 11
Author(s): Andrew S. Warren, Cristina Aurrecoechea, Brian P. Brunk, Prerak Desai, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Deborah Hix, Daniel Lawson, Dustin Machi, Chunhong Mao, Michael McClelland, Eric K. Nordberg, Maulik Shukla, Leslie B. Vosshall, Alice R. Wattam, Rebecca Will, Hyun Seung Yoo, Bruno W. S. Sobral
Software Mentions: 2
Published: almost 10 years ago

10.1155/2014/170289

Clinic-Genomic Association Mining for Colorectal Cancer Using Publicly Available Datasets
Cited by: 5
Author(s): Fang Liu, Feng Yi, Zhenye Li, Chao Pan, Yuncong Su, Rui Yang, Lei Song, Huilong Duan, Ning Deng
Software Mentions: 2
Published: almost 11 years ago

10.1155/2021/8849415

Identification of Multiple Hub Genes and Pathways in Hepatocellular Carcinoma: A Bioinformatics Analysis
Cited by: 8
Author(s): Junwei Liu, Fang Han, Jianyi Ding, Xiaodong Liang, Jie Liu, Dongsheng Huang, Chengwu Zhang
Software Mentions: 2
Published: over 3 years ago

10.3390/biom9070282

Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray
Cited by: 12
Author(s): Ali Mohamed Alshabi, Basavaraj Vastrad, Ibrahim Ahmed Shaikh, Chanabasayya Vastrad
Software Mentions: 2
Published: over 5 years ago

10.1002/biot.201100305

Molecular signatures from omics data: From chaos to consensus
Cited by: 103
Author(s): Jaeyun Sung, Yuliang Wang, Sriram Chandrasekaran, Daniela Witten, Nathan D. Price
Software Mentions: 2
Published: over 12 years ago

10.1590/1414-431X2020e10388

Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification
Cited by: 0
Author(s): Lucas Delmonico, John C. Obenauer, Thomas P. Stockfisch, Marcia V. Fournier
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13058-015-0539-6

Mouse mammary stem cells express prognostic markers for triple-negative breast cancer
Cited by: 32
Author(s): Kelly Soady, Howard Kendrick, Qiong Gao, Andrew Tutt, Marketa Zvelebil, Liliana Ordonez, Jelmar Quist, David Wei-Min Tan, Clare M. Isacke, Anita Grigoriadis, Matthew J. Smalley
Software Mentions: 2
Published: over 9 years ago

10.1186/bcr3403

Embryonic mammary signature subsets are activated in Brca1 -/- and basal-like breast cancers
Cited by: 47
Author(s): Marketa Zvelebil, Erik Oliemuller, Qiong Gao, Olivia Wansbury, Alan Mackay, Howard Kendrick, Matthew J. Smalley, Jorge S. Reis‐Filho, Beatrice A. Howard
Software Mentions: 2
Published: over 11 years ago

10.1186/bcr2334

Genomic profiling of breast tumours in relation to BRCAabnormalities and phenotypes
Cited by: 131
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Óskar Þór Jóhannsson, Katrín Ólafsdóttir, Margrét Steinarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 2
Published: over 15 years ago

10.1186/bcr2192

A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer
Cited by: 117
Author(s): Fabien Reyal, Martin H. van Vliet, Nicola J. Armstrong, Hugo M. Horlings, Karin E. de Visser, M Kok, Andrew E. Teschendorff, Stella Mook, Laura van ’t Veer, Carlos Caldas, Rémy Salmon, Marc J. van de Vijver, Lodewyk F.A. Wessels
Software Mentions: 2
Published: about 16 years ago

10.1186/bcr2109

PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes
Cited by: 25
Author(s): Anna Git, Inmaculada Spiteri, Cherie Blenkiron, Mark J. Dunning, Jessica C. Pole, Suet-Feung Chin, Yanzhong Wang, James Smith, Frederick J. Livesey, Carlos Caldas
Software Mentions: 2
Published: over 16 years ago

10.1186/bcr2256

Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression
Cited by: 46
Author(s): Cecilia Williams, Luísa A. Helguero, Karin Edvardsson, Lars Arne Haldosén, Jan‐Åke Gustafsson
Software Mentions: 2
Published: over 15 years ago

10.1093/bib/bbw044

Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned
Cited by: 9
Author(s): Gerald Li, Peter Bankhead, Philip D. Dunne, Paul G. O’Reilly, Jacqueline James, Manuel Salto-Tellez, Peter Hamilton, Darragh G. McArt
Software Mentions: 2
Published: over 8 years ago

10.26508/lsa.201900356

Oxidised metabolites of the omega-6 fatty acid linoleic acid activate dFOXO
Cited by: 15
Author(s): So Yeon Kwon, Karen A. Massey, Mark A. Watson, Tayab Hussain, Giacomo Volpe, Christopher D. Buckley, Anna Nicolaou, Paul Badenhorst
Software Mentions: 2
Published: almost 5 years ago

10.3390/metabo8040084

An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction
Cited by: 12
Author(s): Amornpan Klanchui, Sudarat Dulsawat, Kullapat Chaloemngam, Supapon Cheevadhanarak, Peerada Prommeenate, Asawin Meechai
Software Mentions: 2
Published: about 6 years ago

10.1007/s11306-015-0810-y

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access
Cited by: 122
Author(s): Reza M. Salek, Steffen Neumann, Daniel Schober, Jan Hummel, Kenny Billiau, Joachim Kopka, Elon Correa, Theo H. Reijmers, Antonio Rosato, Leonardo Tenori, Paola Turano, Silvia Marín, Catherine Deborde, Daniel Jacob, Dominique Rolin, Benjamin Dartigues, Pablo Conesa, Kenneth Haug, Philippe Rocca-Serra, Steve O’Hagan, Jie Hao, Michael Van Vliet, Marko Sysi-Aho, Christian Ludwig, Jildau Bouwman, Marta Cascante, Timothy M. D. Ebbels, Julian L. Griffin, Annick Moing, Macha Nikolski, Matej Orešič, Susanna-Assunta Sansone, Mark R. Viant, Royston Goodacre, Ulrich L. Günther, Thomas Hankemeier, Claudio Luchinat, Dirk Walther, Christoph Steinbeck
Software Mentions: 2
Published: over 9 years ago

10.1186/s13229-017-0136-x

Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder—implications of a copy number variation involving DPP10
Cited by: 12
Author(s): A. Mak, Annie Ting Gee Chiu, Gordon Leung, Christopher Chun Yu Mak, Yoyo Wing Yiu Chu, Gary Tsz Kin Mok, Wing Fai Tang, Kelvin Y.K. Chan, Mary Hoi Yin Tang, Elizabeth Tak-Kwong Lau Yim, Kin Wai So, Victoria Qinchen Tao, Cheuk Wing Fung, Virginia Wong, Mohammed Uddin, So Lun Lee, Christian R. Marshall, Stephen W. Scherer, Anita Sik Yau Kan, Brian Hon Yin Chung
Software Mentions: 2
Published: over 7 years ago

10.1093/molbev/msu226

Transcript Length Mediates Developmental Timing of Gene Expression Across Drosophila
Cited by: 51
Author(s): Carlo G. Artieri, Hunter B. Fraser
Software Mentions: 2
Published: over 10 years ago

10.1186/1476-4598-10-29

miR-449 inhibits cell proliferation and is down-regulated in gastric cancer
Cited by: 199
Author(s): Tony Bou Kheir, Ewa Futoma-Kazmierczak, Anders Jacobsen, Anders Krogh, Linda Bardram, Christoffer Hother, Kirsten Grønbæk, Birgitte Federspiel, Anders H. Lund, Lennart Friis‐Hansen
Software Mentions: 2
Published: over 13 years ago

10.1186/1476-4598-7-6

Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile
Cited by: 69
Author(s): Ingrid Cifola, Roberta Spinelli, Luca Beltrame, Clelia Peano, Ester Fasoli, Stefano Ferrero, Silvano Bòsari, Stefano Signorini, Francesco Rocco, R Perego, Vanessa Proserpio, Francesca Raimondo, Paolo Mocarelli, Cristina Battaglia
Software Mentions: 2
Published: almost 17 years ago

10.1186/1476-4598-9-115

Determination of genes and microRNAs involved in the resistance to fludarabine in vivo in chronic lymphocytic leukemia
Cited by: 73
Author(s): Etienne Moussay, Valérie Palissot, Laurent Vallar, Hélène Poirel, Thomas Wenner, Victoria El Khoury, Nasséra Aouali, Kris Van Moer, Bernadette Leners, François Bernardin, Arnaud Muller, Pascale Cornillet‐Lefèbvre, Alain Delmer, Caroline Duhem, F. Ries, Eric Van Dyck, Guy Berchem
Software Mentions: 2
Published: almost 15 years ago

10.1186/1476-4598-12-130

miR-125b targets erythropoietin and its receptor and their expression correlates with metastatic potential and ERBB2/HER2 expression
Cited by: 74
Author(s): Manuela Ferracin, Cristian Bassi, Massimo Pedriali, Sara Pagotto, Lucilla D’Abundo, Barbara Zagatti, Fabio Corrà, Gentian Musa, Elisa Callegari, Laura Lupini, Stefano Volpato, Patrizia Querzoli, Massimo Negrini
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12943-020-01217-2

LINC00173.v1 promotes angiogenesis and progression of lung squamous cell carcinoma by sponging miR-511-5p to regulate VEGFA expression
Cited by: 85
Author(s): Jia‐Rong Chen, Aibin Liu, Zhihui Wang, Bin Wang, Xingxing Chai, Wenjie Lu, Ting Cao, Ronggang Li, Mingyan Wu, Zhuming Lu, Wei Pang, Lin Xiao, Xiangmeng Chen, Yan Zheng, Qiong Chen, Jincheng Zeng, Jun Li, Xin Zhang, Dong Ren, Yanming Huang
Software Mentions: 2
Published: over 4 years ago

10.3390/molecules23071763

Genome Identification of B-BOX Gene Family Members in Seven Rosacea Species and Their Expression Analysis in Response to Flower Induction in Malus domestica
Cited by: 31
Author(s): Abdullah Shalmani, Shiliang Fan, Peng Jia, Guofang Li, Izhar Muhammad, Youmei Li, Rahat Sharif, Feng Dong, Xia Zuo, Ké Li, Kun-Ming Chen, Mingyu Han
Software Mentions: 2
Published: over 6 years ago

10.1016/j.molmet.2019.03.012

Dietary calories and lipids synergistically shape adipose tissue cellularity during postnatal growth
Cited by: 14
Author(s): Irina Meln, Gretchen Wolff, Thomas Gajek, Johanna Koddebusch, Sarah Lerch, Liza Harbrecht, Wujun Hong, Irem Bayindir‐Buchhalter, Damir Krunic, Hellmut G. Augustin, Alexandros Vegiopoulos
Software Mentions: 2
Published: over 5 years ago

10.1111/j.1365-2958.2009.06883.x

Role of the heat shock transcription factor, Hsf1, in a major fungal pathogen that is obligately associated with warm-blooded animals
Cited by: 89
Author(s): Susan M. Nicholls, Michelle Leach, Claire L. Priest, Alistair J. P. Brown
Software Mentions: 2
Published: about 15 years ago

10.1002/1878-0261.12068

Gain-of-function p53 activates multiple signaling pathways to induce oncogenicity in lung cancer cells
Cited by: 13
Author(s): Catherine Vaughan, S. K. Singh, Steven R. Grossman, Brad E. Windle, Sumitra Deb, Sumitra Deb
Software Mentions: 2
Published: over 7 years ago

10.1002/1878-0261.12107

Prognostic and functional role of subtype-specific tumor-stroma interaction in breast cancer
Cited by: 5
Author(s): Giuseppe Merlino, Patrizia Miodini, Maurizio Callari, Francesca D'Aiuto, Vera Cappelletti, Maria Grazia Daidone
Software Mentions: 2
Published: over 7 years ago

10.15252/msb.20145172

Cell cycle population effects in perturbation studies
Cited by: 103
Author(s): Eoghan O’Duibhir, Philip Lijnzaad, Joris J. Benschop, Tineke L. Lenstra, Dik van Leenen, Marian J. A. Groot Koerkamp, Thanasis Margaritis, Mariël Brok, Patrick Kemmeren, Frank C. P. Holstege
Software Mentions: 2
Published: over 10 years ago

10.3390/v4101844

miRNA Profiles of Monocyte-Lineage Cells Are Consistent with Complicated Roles in HIV-1 Restriction
Cited by: 31
Author(s): Jeanne M. Sisk, Janice E. Clements, Kenneth W. Witwer
Software Mentions: 2
Published: about 12 years ago

10.12688/wellcomeopenres.13119.2

Using mitoribosomal profiling to investigate human mitochondrial translation
Cited by: 2
Author(s): Fei Gao, Maria Wesołowska, Reuven Agami, Koos Rooijers, Fabricio Loayza‐Puch, Conor Lawless, RN Lightowlers, Z. Chrzanowska-Lightowlers
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13071-016-1945-z

Immune and biochemical responses in skin differ between bovine hosts genetically susceptible and resistant to the cattle tick Rhipicephalus microplus
Cited by: 32
Author(s): Alessandra Mara Franzin, Sandra Regina Maruyama, Gustavo García, Rosane Oliveira, José M. C. Ribeiro, Richard P. Bishop, Antônio Augusto Mendes Maia, Daniela D. Moré, Beatriz Rossetti Ferreira, Isabel Kinney Ferreira de Miranda Santos
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.618

Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells
Cited by: 2
Author(s): Virginie Mournetas, Quentin Nunes, Patricia Murray, Christopher M. Sanderson, David G. Fernig
Software Mentions: 2
Published: about 10 years ago

10.1016/j.placenta.2010.10.010

Genome-wide expression profile of first trimester villous and extravillous human trophoblast cells
Cited by: 114
Author(s): Richard Apps, Andrew Sharkey, Lucy Gardner, Victoria Male, Matthew Trotter, Nigel Miller, Robyn A. North, Sandra A. Founds, Ashley Moffett
Software Mentions: 2
Published: almost 14 years ago

10.1093/pcp/pct178

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants
Cited by: 92
Author(s): Takeshi Obayashi, Yasunobu Okamura, Satoshi Ito, Shu Tadaka, Yosuke Aoki, Matsuyuki Shirota, Kengo Kinoshita
Software Mentions: 2
Published: almost 11 years ago

10.1093/pcp/pcu183

Triticeae Resources in Ensembl Plants
Cited by: 57
Author(s): Dan Bolser, Arnaud Kerhornou, Brandon Walts, Paul J. Kersey
Software Mentions: 2
Published: about 10 years ago

10.1007/s00497-015-0261-7

A decade of pollen transcriptomics
Cited by: 113
Author(s): Nicholas Rutley, David Twell
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pbio.0060225

A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth
Cited by: 200
Author(s): Todd P. Michael, Ghislaı̀n Breton, Samuel P. Hazen, Henry D. Priest, Todd C. Mockler, Steve A. Kay, Joanne Chory
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pcbi.1005873

A FAIR guide for data providers to maximise sharing of human genomic data
Cited by: 24
Author(s): Manuel Corpas, Nadezda V. Kovalevskaya, Amanda McMurray, Fiona Nielsen
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1000779

A Quick Guide to Large-Scale Genomic Data Mining
Cited by: 38
Author(s): Curtis Huttenhower, Oliver Hofmann
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pgen.1007440

Antimicrobial peptides modulate long-term memory
Cited by: 45
Author(s): Raquel Barajas-Azpeleta, Jianping Weng, Jason Gill, Ryan Welte, Chris Seidel, Sean A. McKinney, Stephane Dissel, Kausik Si
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1005251

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding
Cited by: 34
Author(s): Xin Xie, Michael J. T. Stubbington, Jesper K. Nissen, Kristian G. Andersen, Daniel Hebenstreit, Sarah A. Teichmann, Alexander G. Betz
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1009297

Dis3L2 regulates cell proliferation and tissue growth through a conserved mechanism
Cited by: 12
Author(s): Benjamin P. Towler, Amy L. Pashler, Hope J. Haime, Katarzyna M. Przybyl, Sandra C. Viegas, Rute G. Matos, Simon Morley, Cecília M. Arraiano, Sarah F. Newbury
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1004288

Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip
Cited by: 188
Author(s): Yujia Alina Chan, Maria J. Aristizabal, Phoebe Y. T. Lu, Zongli Luo, Akil Hamza, Michæl S. Kobor, Peter C. Stirling, Philip Hieter
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1000663

Imprinting of the Polycomb Group Gene MEDEA Serves as a Ploidy Sensor in Arabidopsis
Cited by: 137
Author(s): Aleksandra Erilova, Lynette Brownfield, Vivien Exner, Marisa Rosa, David Twell, Ortrun Mittelsten Scheid, Lars Hennig, Claudia Köhler
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pgen.1002505

Coexpression Network Analysis in Abdominal and Gluteal Adipose Tissue Reveals Regulatory Genetic Loci for Metabolic Syndrome and Related Phenotypes
Cited by: 56
Author(s): Josine L. Min, George Nicholson, Ingileif Halgrimsdottir, Kristian Almstrup, Andreas Petri, Amy Barrett, Mary E. Travers, Nigel W. Rayner, Reedik Mägi, Fredrik Pettersson, John Broxholme, Matt J. Neville, Quin F. Wills, Jane Cheeseman, Maxine Allen, Chris Holmes, Tim D. Spector, Jan Fleckner, Mark I. McCarthy, Fredrik Karpe, Cecilia M. Lindgren, Krina T. Zondervan
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pgen.1004684

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability
Cited by: 65
Author(s): Ayesha Hasan, Cristina Cotobal, Caia D. S. Duncan, Juan Mata
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1008837

Control of mRNA translation by dynamic ribosome modification
Cited by: 12
Author(s): Lucia Grenga, Richard Little, Govind Chandra, Stuart Daniel Woodcock, Gerhard Saalbach, Richard J. Morris, Jacob G. Malone
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1004112

Transcriptomics and Functional Genomics of ROS-Induced Cell Death Regulation by RADICAL-INDUCED CELL DEATH1
Cited by: 83
Author(s): Mikael Brosché, Tiina Blomster, Jarkko Salojärvi, Fuqiang Cui, Nina Sipari, Johanna Leppälä, Airi Lamminmäki, Gloria Tomai, Shaman Narayanasamy, Ramesha A. Reddy, Markku Keinänen, Kirk Overmyer, Jaakko Kangasjärvi
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1000161

Delayed and Accelerated Aging Share Common Longevity Assurance Mechanisms
Cited by: 186
Author(s): Björn Schumacher, Ingrid van der Pluijm, Michael Moorhouse, Theodoros Kosteas, Andria Rasile Robinson, Yousin Suh, Timo M. Breit, Harry van Steeg, Laura J. Niedernhofer, Wilfred F. J. van IJcken, Andrzej Bartke, Stephen R. Spindler, Jan H.J. Hoeijmakers, Gijsbertus T. J. van der Horst, George A. Garinis
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pgen.1006682

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus
Cited by: 37
Author(s): Anchel de Jaime-Soguero, Francesco Aulicino, Gökhan Ertaylan, Anna Griego, Aniello Cerrato, Aravind Tallam, Antonio del Sol, María Pía Cosma, Frederic Lluı́s
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1000605

CHD3 Proteins and Polycomb Group Proteins Antagonistically Determine Cell Identity in Arabidopsis
Cited by: 151
Author(s): Ernst Aichinger, Corina Belle R. Villar, Sara Farrona, José Carlos Castañeda Reyes, Lars Hennig, Claudia Köhler
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pgen.1004903

The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response
Cited by: 37
Author(s): Christopher J. Kershaw, Joseph L. Costello, Lydia M. Castelli, David Talavera, William Rowe, Paul F. G. Sims, Mark P. Ashe, Simon J. Hubbard, Graham D. Pavitt, Chris M. Grant
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pgen.1000859

Structure, Function, and Evolution of the Thiomonas spp. Genome
Cited by: 119
Author(s): Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean‐Yves Coppée, Michaël Chandler, Violaine Bonnefoy, Céline Brochier-Armanet, Mohamed Barakat, Valérie Barbe, Fabienne Battaglia-Brunet, Odile Bruneel, Christopher G. Bryan, Jessica Cleiss-Arnold, Stéphane Cruveiller, Mathieu Erhardt, Audrey Heinrich-Salmeron, Florence Hommais, Catherine Joulian, Evelyne Krin, Aurélie Lieutaud, Didier Lièvremont, Caroline Michel, Daniel Müller, Philippe Ortet, Caroline Proux, Patricia Siguier, David Roche, Zoé Rouy, Grégory Salvignol, Djamila Slyemi, Emmanuel Talla, Stéphanie Weiss, Jean Weissenbach, Claudine Médigue, Philippe Bertin
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pmed.1002352

Signatures of inflammation and impending multiple organ dysfunction in the hyperacute phase of trauma: A prospective cohort study
Cited by: 73
Author(s): Claudia Cabrera, Joanna Manson, Joanna Shepherd, Hew D.T. Torrance, David S. Watson, M. Paula Longhi, Mimoza Hoti, Minal Patel, Michael J. O’Dwyer, Sussan Nourshargh, Daniel J. Pennington, Michael R. Barnes, Karim Brohi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pntd.0000543

Anti-schistosomal Intervention Targets Identified by Lifecycle Transcriptomic Analyses
Cited by: 117
Author(s): Jennifer M. Fitzpatrick, Emily Peak, Samïrah Perally, Iain W. Chalmers, John Barrett, Timothy P. Yoshino, Alasdair Ivens, Karl F. Hoffmann
Software Mentions: 2
Published: about 15 years ago

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: almost 13 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: over 8 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: almost 8 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: over 9 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 4 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: about 3 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: about 5 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: over 4 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: almost 4 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: over 4 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: almost 4 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: about 12 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: over 4 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: over 14 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: about 3 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: over 10 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: almost 14 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: almost 4 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: over 11 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: over 3 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: almost 4 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 4 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 7 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: about 12 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 6 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 4 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: over 12 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: over 4 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 12 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 4 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: over 3 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: almost 4 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: almost 13 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 12 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: almost 4 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 13 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: over 4 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: about 4 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: about 10 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: about 11 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962