bioconductor: ArrayExpress | Projects

10.1186/1471-2164-10-306

Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model
Cited by: 30
Author(s): Jin Hwan, Rui Yamaguchi, Satoru Miyano
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-8-401

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome
Cited by: 12
Author(s): Santiago P. Aubourg, Marie‐Laure Martin‐Magniette, Véronique Brunaud, Ludivine Taconnat, Frédérique Bitton, Sandrine Balzergue, Pauline E. Jullien, Mathieu Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, Jean-Pierre Renou
Software Mentions: 1
Published: almost 20 years ago

10.1038/s41598-020-69254-x

Identification of potential biomarkers for predicting the early onset of diabetic cardiomyopathy in a mouse model
Cited by: 8
Author(s): Rabia Johnson, Xolisa Nxele, Martin Cour, Nonhlakanipho F. Sangweni, Tracey Jooste, Nkanyiso Hadebe, Ebrahim Samodien, Mongi Benjeddou, Mikateko Mazino, Johan Louw, Sandrine Lecour
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-10-42

Positive correlation between gene coexpression and positional clustering in the zebrafish genome
Cited by: 28
Author(s): Yen Kaow Ng, Wei Wu, Louxin Zhang
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-12-620

An expression map for Anopheles gambiae
Cited by: 27
Author(s): Robert M. MacCallum, Seth Redmond, George K. Christophides
Software Mentions: 1
Published: almost 15 years ago

10.1186/s13059-016-0996-y

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data
Cited by: 17
Author(s): Thomas Rensch, Diego Villar, Julie E. Horvath, Duncan T. Odom, Paul Flicek
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-9-340

Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis
Cited by: 87
Author(s): Marcel Scheideler, Christian Elabd, Laure‐Emmanuelle Zaragosi, Chiara Chiellini, Hubert Hackl, Fátima Sánchez‐Cabo, Sunaina Yadav, Kalina Duszka, Gerald Friedl, Christine Papak, Andreas Prokesch, Reinhard Windhager, Gérard Ailhaud, Christian Dani, Ez-Zoubir Amri, Zlatko Trajanoski
Software Mentions: 1
Published: about 18 years ago

10.1186/s13059-016-1064-3

Correlation of an epigenetic mitotic clock with cancer risk
Cited by: 183
Author(s): Zhen Yang, Andrew Wong, Diana Kuh, Dirk S. Paul, Vardhman K. Rakyan, Richard Leslie, Shiqing Zheng, Martin Widschwendter, Stephan Beck, Andrew E. Teschendorff
Software Mentions: 1
Published: about 10 years ago

10.1098/rsob.120091

Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations
Cited by: 27
Author(s): Matthew D. Rolfe, Andrea Ocone, Melanie R. Stapleton, Simon T.E. Hall, Eleanor W. Trotter, Robert K. Poole, Guido Sanguinetti, Jeffrey Green
Software Mentions: 1
Published: over 14 years ago

10.1186/1743-7075-7-56

Identification of the Eph receptor pathway as a novel target for eicosapentaenoic acid (EPA) modification of gene expression in human colon adenocarcinoma cells (HT-29)
Cited by: 5
Author(s): Joanne F. Doleman, John J. Eady, Ruan Elliott, Robert J. Foxall, John Seers, Ian T. Johnson, Elizabeth K. Lund
Software Mentions: 1
Published: almost 17 years ago

10.1186/gb-2004-6-1-r1

Cited by: 33
Author(s): Jeffrey G. Mandell, Jürg Bähler, Thomas A. Volpe, Robert A. Martienssen, Thomas R. Cech
Software Mentions: 1
Published: almost 23 years ago

10.1186/ar2294

Expression and regulation of CCL18 in synovial fluid neutrophils of patients with rheumatoid arthritis
Cited by: 49
Author(s): Judith Auer, Bläss Markus, Hendrik Schulze‐Koops, Stefan Rußwurm, Thomas Nagel, Joachim R. Kalden, Martin Röllinghoff, H U Beuscher
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-6-178

GPX-Macrophage Expression Atlas: A database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults
Cited by: 16
Author(s): Graeme R. Grimes, Stuart Moodie, John S. Beattie, Marie Craigon, Paul Dickinson, Thorsten Forster, Andrew D. Livingston, Muriel Mewissen, Kevin A. Robertson, Alan J. Ross, Garwin K. Sing, Peter Ghazal
Software Mentions: 1
Published: almost 21 years ago

10.1186/1471-2164-9-221

Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA
Cited by: 5
Author(s): Matthijs Raaben, Penn Whitley, Diane Bouwmeester, Robert A. Setterquist, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 18 years ago

10.1186/s13059-018-1472-7

Evolutionarily conserved partial gene duplication in the Triticeae tribe of grasses confers pathogen resistance
Cited by: 9
Author(s): Jeyaraman Rajaraman, Dimitar Douchkov, Stefanie Lück, Goetz Hensel, Daniela Nowara, Maria Pogoda, Twan Rutten, Tobias Meitzel, Jonathan Brassac, Caroline Höfle, Ralph Hückelhoven, Jörn Klinkenberg, Marco Trujillo, Eva Bauer, Thomas Schmutzer, Axel Himmelbach, Martin Mascher, Barbara Lazzari, Nils Stein, Jochen Kumlehn, Patrick Schweizer
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2164-13-33

Transcriptional ontogeny of the developing liver
Cited by: 41
Author(s): Janice S. Lee, William O. Ward, Geremy W. Knapp, Hongzu Ren, Beena Vallanat, Barbara D. Abbott, Karen J. Ho, Seth J. Karp, J. Christopher Corton
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-11-418

Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar)
Cited by: 124
Author(s): Samuel Martín, Alex Douglas, D.F. Houlihan, Christopher J. Secombes
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12864-019-5464-0

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes
Cited by: 3
Author(s): Marzena Mura, Roman Jaksik, Anna Lalik, Krzysztof Biernacki, Marek Kimmel, Joanna Rzeszowska-Wolny, Krzysztof Fujarewicz
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-7-319

Systematic interpretation of microarray data using experiment annotations
Cited by: 17
Author(s): Kurt Fellenberg, Christian Busold, Olaf Witt, Andrea S. Bauer, Boris Beckmann, Nicole Hauser, Marcus Frohme, Stefan Winter, Jürgen Dippon, Jörg D. Hoheisel
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-9-3

Switch-like genes populate cell communication pathways and are enriched for extracellular proteins
Cited by: 36
Author(s): Adam Ertel, Aydın Tözeren
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2164-8-202

Species differences in brain gene expression profiles associated with adult behavioral maturation in honey bees
Cited by: 48
Author(s): Moushumi Sen Sarma, Charles W. Whitfield, Gene E. Robinson
Software Mentions: 1
Published: almost 20 years ago

10.1371/journal.pone.0052321

Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes
Cited by: 37
Author(s): Candy Kumps, Annelies Fieuw, Pieter Mestdagh, Björn Menten, Steve Lefever, Filip Pattyn, Sara De Brouwer, Tom Sante, Johannes H. Schulte, Alexander Schramm, Nadine Van Roy, Tom Van Maerken, Rosa Noguera, Valérie Combaret, Christine Devalck, Frank Westermann, Geneviève Laureys, Angelika Eggert, Jo Vandesompele, Katleen De Preter, Franki Speleman
Software Mentions: 1
Published: almost 14 years ago

10.1186/ar2002

Cited by: 54
Author(s): Betti Giusti, Gabriella Fibbi, Francesca Margheri, Simona Serratì, Luciana Rossi, Filippo Poggi, Ilaria Lapini, Alberto Magi, Angela Del Rosso, Marina Cinelli, Serena Guiducci, Bashar Kahaleh, Laura Bazzichi, Stefano Bombardieri, Marco Matucci‐Cerinic, Gian Franco Gensini, Mario Del Rosso, Rosanna Abbate
Software Mentions: 1
Published: almost 21 years ago

10.1371/journal.pntd.0002438

Temephos Resistance in Aedes aegypti in Colombia Compromises Dengue Vector Control
Cited by: 106
Author(s): Nelson Grisales, Rodolphe Poupardin, Santiago Gómez, Idalyd Fonseca-González, Hilary Ranson, Audrey Lenhart
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0043249

Induction of Endoplasmic Reticulum Stress Response by the Indole-3-Carbinol Cyclic Tetrameric Derivative CTet in Human Breast Cancer Cell Lines
Cited by: 43
Author(s): Luca Galluzzi, Mauro De Santi, Rita Crinelli, Cinzia De Marco, Nadia Zaffaroni, Andrea Duranti, Giorgio Brandi, Mauro Magnani
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pntd.0002607

Bioassay-Guided Fractionation of Extracts from Codiaeum variegatum against Entamoeba histolytica Discovers Compounds That Modify Expression of Ceramide Biosynthesis Related Genes
Cited by: 14
Author(s): Emmanuel Mfotie Njoya, Christian Weber, Nora Adriana Hernández‐Cuevas, Chung-Chau Hon, Yves L. Janin, Melanie F. G. Kamini, Paul Fewou Moundipa, Nancy Guillén
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0141710

Expression of CCL20 and Its Corresponding Receptor CCR6 Is Enhanced in Active Inflammatory Bowel Disease, and TLR3 Mediates CCL20 Expression in Colonic Epithelial Cells
Cited by: 51
Author(s): Helene Kolstad Skovdahl, Atle van Beelen Granlund, Ann Elisabet Østvik, Ingrid Bakke, Sverre Helge Torp, Jan Kristian Damås, Arne K. Sandvik
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-14-169

Transcriptome analysis of pigeon milk production – role of cornification and triglyceride synthesis genes
Cited by: 38
Author(s): Meagan J Gillespie, Tamsyn M. Crowley, Volker Häring, Susanne Wilson, Jennifer Harper, Jean Payne, Diane Green, Paul Monaghan, John A. Donald, Kevin R. Nicholas, Robert J. Moore
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pntd.0005069

Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection
Cited by: 67
Author(s): Kayvan Etebari, Sultan Asad, Guangmei Zhang, Sassan Asgari
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0009867

Oral Activated Charcoal Prevents Experimental Cerebral Malaria in Mice and in a Randomized Controlled Clinical Trial in Man Did Not Interfere with the Pharmacokinetics of Parenteral Artesunate
Cited by: 10
Author(s): J. Brian de Souza, Uduak Okomo, Alexander Nast, Naveed Aziz, Benjamin M. J. Owens, Harsimran Kaur, Momodou Jasseh, Sant Muangnoicharoen, Percy F. Sumariwalla, David C. Warhurst, Stephen A. Ward, David J. Conway, Luis Ulloa, Kevin J. Tracey, Brian M. J. Foxwell, Paul M. Kaye, Michael Walther
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pntd.0001692

Gene Amplification, ABC Transporters and Cytochrome P450s: Unraveling the Molecular Basis of Pyrethroid Resistance in the Dengue Vector, Aedes aegypti
Cited by: 156
Author(s): Vassiliki Bariami, Christopher M. Jones, Rodolphe Poupardin, John Vontas, Hilary Ranson
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pntd.0005972

Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes
Cited by: 28
Author(s): Juan Mucci, Santiago J. Carmona, Romina Volcovich, Jaime Altcheh, Estefanisa Bracamonte, Jorge Diego Marco, Morten Nielsen, Carlos A. Buscaglia, Fernán Agüero
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0183410

snoRNA and piRNA expression levels modified by tobacco use in women with lung adenocarcinoma
Cited by: 25
Author(s): Natasha Andressa Nogueira Jorge, Gabriel Wajnberg, Carlos Gil Ferreira, Benilton Carvalho, Fábio Passetti
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0013658

Whole Blood Transcriptomics in Cardiac Surgery Identifies a Gene Regulatory Network Connecting Ischemia Reperfusion with Systemic Inflammation
Cited by: 34
Author(s): Orfeas Liangos, Sophie Domhan, Christian Schwager, Martin Zeier, Peter E. Huber, Francesco Addabbo, Michael S. Goligorsky, Lynn Hlatky, Bertrand L. Jaber, Amir Abdollahi
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-8-181

Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni
Cited by: 34
Author(s): Michael Waisberg, Francisco Pereira Lobo, Gustavo C. Cerqueira, Liana Konovaloff Jannotti Passos, Omar S. Carvalho, Glória Regina Franco, Najib M. El-Sayed
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-8-387

BMDExpress: a software tool for the benchmark dose analyses of genomic data
Cited by: 160
Author(s): Longlong Yang, Bruce C. Allen, Russell S. Thomas
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pone.0013079

QKI-7 Regulates Expression of Interferon-Related Genes in Human Astrocyte Glioma Cells
Cited by: 8
Author(s): Lin Jiang, Peter Saetre, Katarzyna J. Radomska, Elena Jazin, Eva Carlström
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pmed.1000046

A Compendium of Potential Biomarkers of Pancreatic Cancer
Cited by: 256
Author(s): H. C. Harsha, Kumaran Kandasamy, Prathibha Ranganathan, Sandhya Rani, Subhashri Ramabadran, Sashikanth Gollapudi, Lavanya Balakrishnan, Sutopa B. Dwivedi, Deepthi Telikicherla, Lakshmi Dhevi N. Selvan, Renu Goel, Suresh Mathivanan, Arivusudar Marimuthu, Manoj Kumar Kashyap, Robert F. Vizza, Robert J. Mayer, James A. DeCaprio, Sudhir Srivastava, Samir Hanash, Ralph H. Hruban, Akhilesh Pandey
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0049077

Gadd45α: A Novel Diabetes-Associated Gene Potentially Linking Diabetic Cardiomyopathy and Baroreflex Dysfunction
Cited by: 13
Author(s): Ning Wang, Chao Yang, Fang Xie, Lichao Sun, Xiaolin Su, Ying Wang, Ran Wei, Rong Zhang, Xia Li, Baofeng Yang, Jing Ai
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0118511

MicroRNA-572 Improves Early Post-Operative Cognitive Dysfunction by Down-Regulating Neural Cell Adhesion Molecule 1
Cited by: 31
Author(s): Xiuchong Yu, Shupeng Liu, Jinbao Li, Xiaoping Fan, Yuanjie Chen, Xiaoying Bi, Shanrong Liu, Xiaoming Deng
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0055506

Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?
Cited by: 34
Author(s): David Cohen, Marie‐Béatrice Bogeat‐Triboulot, Silvère Vialet-Chabrand, Rémy Merret, Pierre‐Emmanuel Courty, Sébastien Moretti, François Bizet, Agnès Guilliot, Irène Hummel
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0199991

PASI: A novel pathway method to identify delicate group effects
Cited by: 4
Author(s): Maria K. Jaakkola, Aidan McGlinchey, Рику Клен, Laura L. Elo
Software Mentions: 1
Published: over 8 years ago

10.1186/ar2090

Cited by: 71
Author(s): Johan Lindberg, Erik af Klint, Anca I. Catrina, Peter Nilsson, Lars Klareskog, Ann‐Kristin Ulfgren, Joakim Lundeberg
Software Mentions: 1
Published: almost 21 years ago

10.1186/s13073-016-0329-5

Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network
Cited by: 15
Author(s): Alison F. Richard, James E. Peters, James C. Lee, Golnaz Vahedi, Alejandro A. Schäffer, Richard M. Siegel, Paul Lyons, Kenneth G. C. Smith
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pmed.1002786

Host-response-based gene signatures for tuberculosis diagnosis: A systematic comparison of 16 signatures
Cited by: 115
Author(s): Hayley Warsinske, Rohit Vashisht, Purvesh Khatri
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-016-2562-0

Effects of drought and salt-stresses on gene expression in Caragana korshinskii seedlings revealed by RNA-seq
Cited by: 44
Author(s): Shaofeng Li, Chengming Fan, Yán Li, Jianhui Zhang, Jie Sun, Yuhong Chen, Tian Chen, Xiaohua Su, Mengzhu Lu, Chengzhi Liang, Zhongliang Hu
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-018-4954-9

Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression
Cited by: 13
Author(s): Jochen T. Bick, Veronika L. Flöter, Mark D. Robinson, Stefan Bauersachs, Susanne E. Ulbrich
Software Mentions: 1
Published: about 8 years ago

10.1016/j.gpb.2019.10.003

Schizophrenia-associated MicroRNA–Gene Interactions in the Dorsolateral Prefrontal Cortex
Cited by: 21
Author(s): Danielle M. Santarelli, Adam P. Carroll, Heath M. Cairns, Paul A. Tooney, Murray J. Cairns
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pgen.1003163

Increased Maternal Genome Dosage Bypasses the Requirement of the FIS Polycomb Repressive Complex 2 in Arabidopsis Seed Development
Cited by: 55
Author(s): David Kradolfer, Lars Hennig, Claudia Köhler
Software Mentions: 1
Published: almost 14 years ago

10.1186/s13742-015-0064-7

Investigation into the annotation of protocol sequencing steps in the sequence read archive
Cited by: 20
Author(s): Jamie J. Alnasir, H. P. Shanahan
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0123342

Differential Transcriptional Profiling of Damaged and Intact Adjacent Dorsal Root Ganglia Neurons in Neuropathic Pain
Cited by: 39
Author(s): Ann-Kristin Reinhold, Laura Batti, Daniel Bilbao, Andreas Buneß, Heike L. Rittner, Paul A. Heppenstall
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0045200

Transcriptomic Assay of CD8+ T Cells in Treatment-Naïve HIV, HCV-Mono-Infected and HIV/HCV-Co-Infected Chinese
Cited by: 7
Author(s): Jin Zhao, Yi Liu, Jing Lu, Zheng Yang, Ying Chen, Chenli Zheng, Dan Huang, Yufeng Li, Lin Chen, Jinquan Cheng, Hsiang‐Fu Kung, Ming‐Liang He
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pgen.1000286

Field-Caught Permethrin-Resistant Anopheles gambiae Overexpress CYP6P3, a P450 That Metabolises Pyrethroids
Cited by: 293
Author(s): Pie Müller, Emma Warr, Bradley J. Stevenson, Pasquale Pignatelli, John C. Morgan, Andrew Steven, Alexander Egyir Yawson, Sara N. Mitchell, Hilary Ranson, Janet Hemingway, Mark J. I. Paine, Martin J. Donnelly
Software Mentions: 1
Published: almost 18 years ago

10.1186/2047-217X-2-14

Biodiversity research in the “big data” era: GigaScience and Pensoft work together to publish the most data-rich species description
Cited by: 6
Author(s): Scott Edmunds, Chris Hunter, Vincent Smith, Pavel Stoev, Lyubomir Penev
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1007256

Broken replication forks trigger heritable DNA breaks in the terminus of a circular chromosome
Cited by: 35
Author(s): Anurag Kumar Sinha, Christophe Possoz, Adeline Durand, Jean-Michel Desfontaines, François‐Xavier Barre, David R. F. Leach, Bertrand Michel
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0073072

Transmembrane Prostatic Acid Phosphatase (TMPAP) Interacts with Snapin and Deficient Mice Develop Prostate Adenocarcinoma
Cited by: 27
Author(s): Ileana B. Quintero, Annakaisa Herrala, César L. Araujo, Anitta E. Pulkka, Sampsa Hautaniemi, Kristian Ovaska, Evgeny Pryazhnikov, Evgeny Kulesskiy, Maija Ruuth, Ylermi Soini, Raija Sormunen, Leonard Khirug, Pirkko Vihko
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0007158

miR-155 Inhibition Sensitizes CD4+ Th Cells for TREG Mediated Suppression
Cited by: 81
Author(s): Heiko Stahl, Tanja Fauti, Nina D. Ullrich, Tobias Bopp, Jan Kubach, Werner Rust, Paul Labhart, Vassili Alexiadis, Christian Becker, Mathias Hafner, Andreas Weith, Martin Lenter, Helmut Jonuleit, Edgar Schmitt, Detlev Mennerich
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pgen.1005153

A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression
Cited by: 43
Author(s): Marta Garrido, Benjamin Frage, Patrick R. Wright, Anke Becker
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0152786

Adipocytes as a Link Between Gut Microbiota-Derived Flagellin and Hepatocyte Fat Accumulation
Cited by: 13
Author(s): Eveliina Munukka, Petri Wiklund, Tiina Partanen, Sakari Välimäki, Eija K. Laakkonen, Maarit Lehti, Pamela Fischer-Posovzsky, Martin Wabitsch, Sulin Cheng, Pentti Huovinen, Satu Pekkala
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1002398

Widespread Cotranslational Formation of Protein Complexes
Cited by: 104
Author(s): Caia D. S. Duncan, Juan Mata
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pgen.1006000

Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development—Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus
Cited by: 50
Author(s): Katarina Truvé, Peter J. Dickinson, Anqi Xiong, Daniel York, Kartika Jayashankar, Gerli Pielberg, Michele Koltookian, Eva Murén, Hans Henrik Fuxelius, Holger Weishaupt, Fredrik J. Swartling, Gerhard Andersson, Åke Hedhammar, Erik Bongcam‐Rudloff, Karin Forsberg-Nilsson, Danika L. Bannasch, Kerstin Lindblad‐Toh
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-7-113

Cross-species hybridizations on a multi-species cDNA microarray to identify evolutionarily conserved genes expressed in oocytes
Cited by: 41
Author(s): Maud Vallée, Claude Robert, S. Méthot, Marie‐France Palin, Marc‐André Sirard
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pgen.1003734

Comparative Oncogenomic Analysis of Copy Number Alterations in Human and Zebrafish Tumors Enables Cancer Driver Discovery
Cited by: 31
Author(s): Guangjun Zhang, Sebastian Hoersch, Adam Amsterdam, Charles A. Whittaker, Eline Beert, Julian M. Catchen, Sarah Farrington, John H. Postlethwait, Eric Legius, Nancy Hopkins, Jacqueline A. Lees
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0048896

Survival of Staphylococcus aureus ST398 in the Human Nose after Artificial Inoculation
Cited by: 23
Author(s): Bibi C. G. C. Slingerland, Mehri Tavakol, Alex J. McCarthy, Jodi A. Lindsay, Susan V. Snijders, Jaap A. Wagenaar, Alex van Belkum, Margreet C. Vos, Henri A. Verbrugh, Willem J. B. van Wamel
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1000470

SWI/SNF Associates with Nascent Pre-mRNPs and Regulates Alternative Pre-mRNA Processing
Cited by: 75
Author(s): Anu Tyagi, Jessica Ryme, David Brodin, A K Ostlund Farrants, Neus Visa
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pgen.1000479

Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference
Cited by: 117
Author(s): Eric A. Stone, Julien F. Ayroles
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0070294

Prediction Errors in Learning Drug Response from Gene Expression Data – Influence of Labeling, Sample Size, and Machine Learning Algorithm
Cited by: 15
Author(s): Immanuel Bayer, Philip Groth, Sebastian Schneckener
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0131336

MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing
Cited by: 29
Author(s): Li Zhang, Pengfei Wei, Xudong Shen, Yuanwei Zhang, Bo Xu, Jun Zhou, Song Fan, Zongyao Hao, Hao Shi, Xiansheng Zhang, Rui Kong, Lingfan Xu, Duohong Zou, Chaozhao Liang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0002798

Diurnal and Circadian Rhythms in the Tomato Transcriptome and Their Modulation by Cryptochrome Photoreceptors
Cited by: 63
Author(s): Paolo Facella, Loredana Lopez, Fabrizio Carbone, David W. Galbraith, Giovanni Giuliano, Gaetano Perrotta
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0008018

Sulfur Metabolism Actively Promotes Initiation of Cell Division in Yeast
Cited by: 17
Author(s): Heidi M. Blank, Shefali Rajendra Gajjar, Andrey Belyanin, Michael Polymenis
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-14-301

Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis
Cited by: 53
Author(s): Victoria A Jenkins, Geraint Barton, Brian D. Robertson, Katrina Williams
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0161993

PKC-ALDH2 Pathway Plays a Novel Role in Adipocyte Differentiation
Cited by: 20
Author(s): Yu-Hsiang Yu, Pei Ru Liao, Chien Jung Guo, Che Hong Chen, Daria Mochly‐Rosen, Lee‐Ming Chuang
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0079627

Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts
Cited by: 1
Author(s): Thong Tien Nguyen, Cathal Seoighe
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-8-450

Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance
Cited by: 75
Author(s): Fanny Ramel, Cécile Sulmon, Francisco Cabello‐Hurtado, Ludivine Taconnat, Marie‐Laure Martin‐Magniette, Jean-Pierre Renou, Abdelhak El Amrani, Ivan Couée, Gwenola Gouesbet
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pone.0001546

Systematic Validation and Atomic Force Microscopy of Non-Covalent Short Oligonucleotide Barcode Microarrays
Cited by: 13
Author(s): Michael A. Cook, Chi Kin Chan, Paul Jorgensen, Troy Ketela, Daniel K. C. So, Mike Tyers, Chi Yip Ho
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-14-710

Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression
Cited by: 26
Author(s): Paul Golby, Javier Nuñez, Adam A. Witney, Jason Hinds, Michael A. Quail, Stephen D. Bentley, Simon R. Harris, Noel H. Smith, R. Glyn Hewinson, Stephen V. Gordon
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1000846

Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome
Cited by: 220
Author(s): Juan M. Vaquerizas, Ritsuko Suyama, Jop Kind, Kota Miura, Nicholas M. Luscombe, Asifa Akhtar
Software Mentions: 1
Published: over 16 years ago

10.1186/s12864-020-6712-z

Lung transcriptomic clock predicts premature aging in cigarette smoke-exposed mice
Cited by: 12
Author(s): Mohamed-Amin Choukrallah, Julia Hoeng, Manuel C. Peitsch, Florian Martin
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0048363

Functional Similarities between Pigeon ‘Milk’ and Mammalian Milk: Induction of Immune Gene Expression and Modification of the Microbiota
Cited by: 28
Author(s): Meagan J Gillespie, Dragana Stanley, Honglei Chen, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1008549

Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs
Cited by: 15
Author(s): Satesh Ramdhani, Elisa Navarro, Evan Udine, Anastasia G. Efthymiou, Brian M Schilder, Madison Parks, Alison M. Goate, Towfique Raj
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0080747

PaGenBase: A Pattern Gene Database for the Global and Dynamic Understanding of Gene Function
Cited by: 100
Author(s): Jianbo Pan, Shichang Hu, Dan Shi, Mei-Chun Cai, Yin-Bo Li, Quan Zou, Zhi-Liang Ji
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1003160

Insulin and IGF1 Receptors Are Essential for XX and XY Gonadal Differentiation and Adrenal Development in Mice
Cited by: 110
Author(s): Jean-Luc Pitetti, Pierre Calvel, Yannick Romero, Béatrice Conne, Vy Truong, Marilena D. Papaioannou, Olivier Schaad, Mylène Docquier, Pedro Luis Herrera, Dagmar Wilhelm, Serge Nef
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12864-017-4200-x

Genes for asparagine metabolism in Lotus japonicus: differential expression and interconnection with photorespiration
Cited by: 8
Author(s): Margarita García‐Calderón, Carmen M. Pérez-Delgado, Alfredo Credali, José M. Vega, Marco Betti, Antonio J. Márquez
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0026023

Hormone Receptor and ERBB2 Status in Gene Expression Profiles of Human Breast Tumor Samples
Cited by: 6
Author(s): Anna Dvorkin‐Gheva, John A. Hassell
Software Mentions: 1
Published: about 15 years ago

10.3390/ijms21103480

The GOLIATH Project: Towards an Internationally Harmonised Approach for Testing Metabolism Disrupting Compounds
Cited by: 33
Author(s): Juliette Legler, Daniel Zalko, Fabien Jourdan, Miriam N. Jacobs, Bernard Fromenty, Patrick Balaguer, William Bourguet, Vesna Munić Kos, Ángel Nadal, Claire Beausoleil, Susana Cristóbal, Sylvie Remy, Sibylle Ermler, Luigi Margiotta-Casaluci, Julian L. Griffin, Bruce Blumberg, Christophe Chesné, Sebastian Hoffmann, Patrik L. Andersson, Jorke H. Kamstra
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0250747

Glycans unique to the relapse-prone subset within triple-negative breast cancer as revealed by lectin array-based analysis of surgical specimens
Cited by: 3
Author(s): Madoka Sakata-Matsuzawa, Kaori Denda-Nagai, Haruhiko Fujihira, Miki Noji, Katrin Ishii-Schrade, Atsushi Matsuda, Atsushi Kuno, Misato Okazaki, Keiichi Nakai, Yoshiya Horimoto, Mitsue Saito, Tatsuro Irimura
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1000599

A Mouse Model for the Metabolic Effects of the Human Fat Mass and Obesity Associated FTO Gene
Cited by: 290
Author(s): Chris Church, Sheena Lee, Eleanor A. L. Bagg, James S. McTaggart, Robert M. J. Deacon, Thomas A. Gerken, Angela Lee, Lee Moir, Jasmin Mecinović, Mohamed M. Quwailid, Christopher J. Schofield, Frances M. Ashcroft, Roger D. Cox
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pgen.1002362

Caenorhabditis elegans Cyclin D/CDK4 and Cyclin E/CDK2 Induce Distinct Cell Cycle Re-Entry Programs in Differentiated Muscle Cells
Cited by: 32
Author(s): Jerome Korzelius, Suzan Ruijtenberg, Martine B.W. Prinsen, Vincent Portegijs, Teije C. Middelkoop, Marian J. A. Groot Koerkamp, Frank C. P. Holstege, Mike Boxem, Sander van den Heuvel
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0113053

Toward Computational Cumulative Biology by Combining Models of Biological Datasets
Cited by: 8
Author(s): Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, Samuel Kaski
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-12-12

Mesenteric lymph node transcriptome profiles in BALB/c mice sensitized to three common food allergens
Cited by: 12
Author(s): Mainul Husain, Herman J. Boermans, Niel A. Karrow
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0080047

A Small RNA Encoded in the Rv2660c Locus of Mycobacterium tuberculosis Is Induced during Starvation and Infection
Cited by: 32
Author(s): Joanna Houghton, Teresa Cortes, Olga T. Schubert, Graham Rose, Angela Rodgers, Megan De Ste Croix, Rudolf Aebersold, Douglas B. Young, Kristine B. Arnvig
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0139446

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions
Cited by: 32
Author(s): Francesco Iorio, Roshan L. Shrestha, Nicolas Levin, Viviane Boilot, Mathew J. Garnett, Julio Sáez-Rodríguez, Viji M. Draviam
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0001403

Probing Host Pathogen Cross-Talk by Transcriptional Profiling of Both Mycobacterium tuberculosis and Infected Human Dendritic Cells and Macrophages
Cited by: 185
Author(s): Ludovic Tailleux, Simon J. Waddell, Mattia Pelizzola, Alessandra Mortellaro, Michael Withers, Antoine Tanne, Paola Ricciardi Castagnoli, Brigitte Gicquel, Neil G. Stoker, Philip D. Butcher, Maria Foti, Olivier Neyrolles
Software Mentions: 1
Published: almost 19 years ago

10.1186/s12864-016-2803-2

Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana
Cited by: 9
Author(s): Robert Hoffmann, Michael G. Palmgren
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0082684

Genetic Interaction between Mutations in c-Myb and the KIX Domains of CBP and p300 Affects Multiple Blood Cell Lineages and Influences Both Gene Activation and Repression
Cited by: 27
Author(s): Lawryn H. Kasper, Tsutomu Fükuyama, Stephanie Lerach, Yunchao Chang, Wu Xu, Song Wu, Kelli L. Boyd, Paul K. Brindle
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0106278

SDF-1 Chemokine Signalling Modulates the Apoptotic Responses to Iron Deprivation of Clathrin-Depleted DT40 Cells
Cited by: 2
Author(s): Alena Pance, Frank Ralf Morrissey-Wettey, Helen Craig, Alison Downing, Richard Talbot, Antony P. Jackson
Software Mentions: 1
Published: about 12 years ago

10.3390/ijms21113749

17-Aminogeldanamycin Inhibits Constitutive Nuclear Factor-Kappa B (NF-κB) Activity in Patient-Derived Melanoma Cell Lines
Cited by: 7
Author(s): Mariusz L. Hartman, Magdalena Rogut, Aleksandra Mielczarek-Lewandowska, Michal Wozniak, Małgorzata Czyż
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0030781

Circadian Rhythms of Fetal Liver Transcription Persist in the Absence of Canonical Circadian Clock Gene Expression Rhythms In Vivo
Cited by: 8
Author(s): Chengwei Li, Shuang Yu, Xiaoling Zhong, Jianguo Wu, Xiaodong Li
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1003594

DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts
Cited by: 38
Author(s): Daria V. Zhernakova, Eleonora de Klerk, Harm-Jan Westra, Anastasios Mastrokolias, Shoaib Amini, Yavuz Ariyürek, Ritsert C. Jansen, Brenda W. J. H. Penninx, Jouke Jan Hottenga, Gonneke Willemsen, Eco J. C. de Geus, Dorret I. Boomsma, Jan H. Veldink, Leonard H van den Berg, Cisca Wijmenga, Johan T. den Dunnen, Gert‐Jan B. van Ommen, Peter A C ‘t Hoen, Lude Franke
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0004955

A Cross-Study Transcriptional Analysis of Parkinson's Disease
Cited by: 79
Author(s): Greg T. Sutherland, Nicholas Matigian, Alistair M. Chalk, Matthew Anderson, Peter A. Silburn, Alan Mackay‐Sim, Christine A. Wells, George D. Mellick
Software Mentions: 1
Published: over 17 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

Bonuses:

Penalties:

Papers Mentioning ArrayExpress 1,962