bioconductor: ArrayExpress | Projects

10.1186/gb-2007-8-10-r229

Simplified ontologies allowing comparison of developmental mammalian gene expression
Cited by: 13
Author(s): Adéle Kruger, Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, Winston Hide
Software Mentions: 1
Published: about 19 years ago

10.18632/oncotarget.9578

Functional/activity network (FAN) analysis of gene-phenotype connectivity liaised by grape polyphenol resveratrol
Cited by: 15
Author(s): Tze Chen Hsieh, Sing-Yung Wu, Dylan John Bennett, Barbara B. Doonan, Erxi Wu, Joseph M. Wu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0032150

Identification of Candidate Susceptibility and Resistance Genes of Mice Infected with Streptococcus suis Type 2
Cited by: 12
Author(s): Jie Rong, Wei Zhang, Xiaohui Wang, Hongjie Fan, Lu Chen, Huochun Yao
Software Mentions: 1
Published: almost 14 years ago

10.18632/oncotarget.13989

Endometrial cancer cells exhibit high expression of p110β and its selective inhibition induces variable responses on PI3K signaling, cell survival and proliferation
Cited by: 14
Author(s): Thomas Karlsson, Camilla Krakstad, Ingvild L. Tangen, Erling A. Høivik, Pamela M. Pollock, Helga B. Salvesen, Aurélia E. Lewis
Software Mentions: 1
Published: about 9 years ago

10.1186/gb-2007-8-7-r148

Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres
Cited by: 74
Author(s): Alicia Alonso, Björn Fritz, Dan Hasson, György Abrusán, Fanny Cheung, Kinya Yoda, Bernhard Radlwimmer, Andreas G. Ladurner, Peter E. Warburton
Software Mentions: 1
Published: about 19 years ago

10.1186/gb-2008-9-2-r32

Temporal regulation of expression of immediate early and second phase transcripts by endothelin-1 in cardiomyocytes
Cited by: 47
Author(s): Timothy E. Cullingford, Thomais Markou, Stephen J. Fuller, Alejandro Giraldo, Sampsa Pikkarainen, Georgia Zoumpoulidou, Ali Alsafi, Collins Ekere, Timothy J. Kemp, Jayne L. Dennis, Laurence Gamé, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: about 18 years ago

10.1186/gb-2007-8-9-r179

Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere
Cited by: 190
Author(s): Miguel A. Matilla, Manuel Espinosa‐Urgel, José J. Rodríguez‐Herva, Juan L. Ramos, Marı́a Isabel Ramos-González
Software Mentions: 1
Published: about 19 years ago

10.1186/gb-2007-8-9-r200

Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis
Cited by: 212
Author(s): Robert Kleemann, Lars Verschuren, Marjan J. van Erk, Yuri Nikolsky, N.H.P. Cnubben, Elwin Verheij, Age K. Smilde, H. Hendriks, Susanne Zadelaar, Graham J. Smith, Valery Kaznacheev, Tatiana Nikolskaya, А. С. Мельников, Eva Hurt-Camejo, J. van der Greef, Ben van Ommen, Teake Kooistra
Software Mentions: 1
Published: about 19 years ago

10.1186/gb-2008-9-1-r19

Translational control plays a prominent role in the hepatocytic differentiation of HepaRG liver progenitor cells
Cited by: 33
Author(s): Romain Parent, Laura Beretta
Software Mentions: 1
Published: about 18 years ago

10.1186/gb-2008-9-5-r82

Individual mRNA expression profiles reveal the effects of specific microRNAs
Cited by: 47
Author(s): Amit Arora, David Simpson
Software Mentions: 1
Published: about 18 years ago

10.18632/oncotarget.13414

E-cadherin downregulation sensitizes PTEN-mutant tumors to PI3Kβ silencing
Cited by: 10
Author(s): África Millán-Uclés, Susana Zuluaga, Miriam Marqués, Jesús Vallejo-Díaz, Luis Sanz, Ariel Cariaga-Martínez, Francisco X. Real, Ana C. Carrera
Software Mentions: 1
Published: about 9 years ago

10.1186/gb-2009-10-8-r87

Depletion of T-cell intracellular antigen proteins promotes cell proliferation
Cited by: 47
Author(s): Raquel Ruz Reyes, José Alcalde, José M. Izquierdo
Software Mentions: 1
Published: about 17 years ago

10.1186/s13148-018-0542-8

Epigenetic regulation of ID4 in breast cancer: tumor suppressor or oncogene?
Cited by: 20
Author(s): Daniela Nasif, Emanuel Campoy, Sergio Laurito, Richard L. Branham, Guillermo Urrutia, María Roqué, Marı́a Teresita Branham
Software Mentions: 1
Published: over 7 years ago

10.1186/1479-5876-8-6

Robust TLR4-induced gene expression patterns are not an accurate indicator of human immunity
Cited by: 4
Author(s): Kelly L. Brown, Reza Falsafi, Winnie W. S. Kum, Pamela Hamill, Jennifer L. Gardy, Donald J. Davidson, Stuart E. Turvey, B. Brett Finlay, David P. Speert, Robert E. W. Hancock
Software Mentions: 1
Published: about 16 years ago

10.1186/gb-2009-10-12-r139

Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods
Cited by: 136
Author(s): Priit Adler, Raivo Kolde, Meelis Kull, Александр Георгиевич Ткаченко, Hedi Peterson, Jüri Reimand, Jaak Vilo
Software Mentions: 1
Published: about 17 years ago

10.3390/cells10030674

Acyl–Acyl Carrier Protein Desaturases and Plant Biotic Interactions
Cited by: 11
Author(s): Sami Kazaz, Romane Miray, Sébastien Baud
Software Mentions: 1
Published: almost 5 years ago

10.18632/oncotarget.16064

Integrated analysis of genes associated with poor prognosis of patients with colorectal cancer liver metastasis
Cited by: 30
Author(s): Zhenyuan Qian, Guobing Zhang, Guangyuan Song, Jing Shi, Lijie Gong, Yiping Mou, Yong Han
Software Mentions: 1
Published: almost 9 years ago

10.18632/oncotarget.20284

Downregulation of microRNA-31 inhibits proliferation and induces apoptosis by targeting HIF1AN in human keloid
Cited by: 21
Author(s): Juan Zhang, Dan Xu, Na Li, Yan Li, Yongjing He, Xingbo Hu, Lechun Lyu, Li He
Software Mentions: 1
Published: over 8 years ago

10.1186/gb-2009-10-11-r125

High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians
Cited by: 55
Author(s): Hajime Matsuzaki, Peihua Wang, Jing Hu, Rich Rava, Glenn K. Fu
Software Mentions: 1
Published: about 17 years ago

10.1186/gb-2011-12-6-r53

Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa
Cited by: 141
Author(s): Wei Li, Long Yan, Tai Wang
Software Mentions: 1
Published: over 14 years ago

10.3390/cells8121554

Transcriptional Characterization of Stage I Epithelial Ovarian Cancer: A Multicentric Study
Cited by: 9
Author(s): Enrica Calura, Matteo Ciciani, Andrea Sambugaro, Lara Paracchini, Giuseppe Benvenuto, Salvatore Milite, Paolo Martini, Luca Beltrame, Flaminia Zane, Robert Fruscio, Martina Delle Marchette, Fulvio Borella, Germana Tognon, Antonella Ravaggi, Dionyssios Katsaros, Eliana Bignotti, Franco Odicino, Maurizio D’Incalci, Sergio Marchini, Chiara Romualdi
Software Mentions: 1
Published: about 6 years ago

10.1186/gb-2011-12-8-r82

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast
Cited by: 39
Author(s): Brian T. Wilhelm, Samuel Marguerat, Sofia Aligianni, Sandra Codlin, Stephen Watt, Jürg Bähler
Software Mentions: 1
Published: about 15 years ago

10.1186/gb-2011-12-12-r127

Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera
Cited by: 31
Author(s): Tom A. Mendum, Jane Newcombe, Ahmad A. Mannan, Andrzej M. Kierzek, Johnjoe McFadden
Software Mentions: 1
Published: about 15 years ago

10.3390/cells9010142

Dissecting Mechanisms of Melanoma Resistance to BRAF and MEK Inhibitors Revealed Genetic and Non-Genetic Patient- and Drug-Specific Alterations and Remarkable Phenotypic Plasticity
Cited by: 41
Author(s): Mariusz L. Hartman, Małgorzata Sztiller-Sikorska, Anna Gajos-Michniewicz, Małgorzata Czyż
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0030269

Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer
Cited by: 99
Author(s): Stefan Bentink, Benjamin Haibe‐Kains, Thomas S. Risch, Jian–Bing Fan, Michelle S. Hirsch, Kristina M. Holton, Renee Rubio, Craig April, Jing Chen, Eliza Wickham-Garcia, Joyce F. Liu, Aedín C. Culhane, Ronny Drapkin, John Quackenbush, Ursula A. Matulonis
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0065034

Cholecalciferol (Vitamin D3) Improves Myelination and Recovery after Nerve Injury
Cited by: 102
Author(s): Jean-François Chabas, Delphine Stephan, Tanguy Marqueste, Stéphane García, Marie‐Noëlle Lavaut, Catherine Nguyen, R. Legré, Michel Khrestchatisky, Patrick Decherchi, François Féron
Software Mentions: 1
Published: over 12 years ago

10.18632/oncotarget.11215

Frequency of expression and generation of T-cell responses against antigens on multiple myeloma cells in patients included in the GMMG-MM5 trial
Cited by: 5
Author(s): Michael Schmitt, Angela Hückelhoven, Michael Hundemer, Anita Schmitt, Susanne Lipp, Martina Emde, Hans Salwender, Mathias Hänel, Katja Weisel, Uta Bertsch, Jan Dürig, Anthony D. Ho, Igor Wolfgang Blau, Hartmut Goldschmidt, Anja Seckinger, Dirk Hose
Software Mentions: 1
Published: over 9 years ago

10.1186/gb-2013-14-12-r132

Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B
Cited by: 133
Author(s): Elinor K. Karlsson, Snaevar Sigurðsson, Emma Ivansson, Rachael Thomas, Ingegerd Elvers, Jason Wright, Cédric Howald, Noriko Tonomura, Michele Perloski, Ross Swofford, Tara Biagi, Sarah Fryc, Nathan Anderson, Céline Courtay-Cahen, Lisa Youell, Sally L. Ricketts, Sarah Mandlebaum, Patricio Rivera, Henrik von Euler, William C. Kisseberth, Cheryl A. London, Eric S. Lander, Guillermo Couto, Kenine E. Comstock, Mike Starkey, Jaime F. Modiano, Matthew Breen, Kerstin Lindblad‐Toh
Software Mentions: 1
Published: about 13 years ago

10.18632/oncotarget.17926

Increased transcriptional and metabolic capacity for lipid metabolism in the peripheral zone of the prostate may underpin its increased susceptibility to cancer
Cited by: 11
Author(s): Omar Al Kadhi, Μαρία Τράκα, Antonietta Melchini, Perla Troncoso‐Rey, Wiktor Jurkowski, Marianne Defernez, Purnima Pachori, Robert Mills, Richard Y. Ball, Richard Mithen
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0218934

Ticagrelor induces paraoxonase-1 (PON1) and better protects hypercholesterolemic mice against atherosclerosis compared to clopidogrel
Cited by: 10
Author(s): Hasseri Halim, Decha Pinkaew, Preedakorn Chunhacha, Patuma Sinthujaroen, Perumal Thiagarajan, Kenichi Fujise
Software Mentions: 1
Published: over 6 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: almost 17 years ago

10.1371/annotation/121b04a1-0cbb-4e24-8a63-fc9cdd31ec76

Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)
Cited by: 24
Author(s): Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Software Mentions: 1
Published: over 12 years ago

10.1186/gb-2014-15-4-r54

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns
Cited by: 314
Author(s): Kaie Lokk, Vijayachitra Modhukur, Balaji Rajashekar, Kaspar Märtens, Reedik Mägi, Raivo Kolde, Marina Koltšina, Torbjörn Nilsson, Jaak Vilo, Andres Salumets, Neeme Tõnisson
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0006554

Genome-Wide Profile of Pleural Mesothelioma versus Parietal and Visceral Pleura: The Emerging Gene Portrait of the Mesothelioma Phenotype
Cited by: 63
Author(s): Oluf Dimitri Røe, Endre Anderssen, E. Helge, Caroline Hild Pettersen, Anja Olsen, Helmut Sandeck, Rune Haaverstad, Steinar Lundgren, Erik G. Larsson
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0004285

Rapid Changes in Transcription Profiles of the Plasmodium yoelii yir Multigene Family in Clonal Populations: Lack of Epigenetic Memory?
Cited by: 25
Author(s): Deirdre Cunningham, Jannik Fonager, William Jarra, Céline Carret, Peter R. Preiser, Jean Langhorne
Software Mentions: 1
Published: about 17 years ago

10.1186/gb-2014-15-1-r13

Constitutive patterns of gene expression regulated by RNA-binding proteins
Cited by: 34
Author(s): Davide Cirillo, Domenica Marchese, Antonella Federico, Carmen Maria Livi, Teresa Botta-Orfila, Gian Gaetano Tartaglia
Software Mentions: 1
Published: about 12 years ago

10.1186/gb-2013-14-6-r63

Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle
Cited by: 106
Author(s): Julietta Jupe, Remco Stam, Andrew J. M. Howden, Jenny Morris, Runxuan Zhang, Pete E. Hedley, Edgar Huitema
Software Mentions: 1
Published: over 12 years ago

10.1186/gb-2013-14-6-r65

Thermal stress effects on grain yield in Brachypodium distachyon occur via H2A.Z-nucleosomes
Cited by: 71
Author(s): Scott A. Boden, Monika Kavanová, E. Jean Finnegan, Philip A. Wigge
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0006576

Genome-Scale Identification Method Applied to Find Cryptic Aminoglycoside Resistance Genes in Pseudomonas aeruginosa
Cited by: 17
Author(s): Julie M. Struble, Ryan T. Gill
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0067802

Insulin Receptor-Overexpressing β-Cells Ameliorate Hyperglycemia in Diabetic Rats through Wnt Signaling Activation
Cited by: 14
Author(s): Mi‐Hyun Kim, Seung-Hyun Hong, Moon‐Kyu Lee
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0045744

Transcriptome Analysis of Responses to Rhodomyrtone in Methicillin-Resistant Staphylococcus aureus
Cited by: 29
Author(s): Wipawadee Sianglum, Potjanee Srimanote, Peter W. Taylor, Helena Rosado, Supayang Piyawan Voravuthikunchai
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0084428

DACH1: Its Role as a Classifier of Long Term Good Prognosis in Luminal Breast Cancer
Cited by: 24
Author(s): Desmond G. Powe, Gopal Krishna Dhondalay, Christophe Lemetre, Tony Allen, Hany Onsy Habashy, Ian O. Ellis, Robert C. Rees, Graham Ball
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0037646

Stromal Genes Add Prognostic Information to Proliferation and Histoclinical Markers: A Basis for the Next Generation of Breast Cancer Gene Signatures
Cited by: 17
Author(s): Dwain Mefford, Joel Mefford
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0198555

The immunosuppressive face of sepsis early on intensive care unit—A large-scale microarray meta-analysis
Cited by: 29
Author(s): Dominik Schaack, Benedikt Hermann Siegler, Sandra Tamulyte, Markus Weigand, Florian Uhle
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0089318

Global Meta-Analysis of Transcriptomics Studies
Cited by: 11
Author(s): José Caldas, Susana Vinga
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0054717

Global Transcriptional Profiling of Longitudinal Clinical Isolates of Mycobacterium tuberculosis Exhibiting Rapid Accumulation of Drug Resistance
Cited by: 43
Author(s): Anirvan Chatterjee, Dhananjaya Saranath, Purva Bhatter, Nerges Mistry
Software Mentions: 1
Published: about 13 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 9 years ago

10.1371/journal.pone.0181231

CSmiRTar: Condition-Specific microRNA targets database
Cited by: 20
Author(s): Wei Wu, Bor Wen Tu, Tsung Te Chen, Shang Wei Hou, Joseph T. Tseng
Software Mentions: 1
Published: over 8 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: over 9 years ago

10.1371/journal.pone.0112655

Identification of Modulators of the Nuclear Receptor Peroxisome Proliferator-Activated Receptor α (PPARα) in a Mouse Liver Gene Expression Compendium
Cited by: 58
Author(s): Keiyu Oshida, Naresh Vasani, Russell S. Thomas, Dawn Applegate, Mitchell B. Rosen, Barbara D. Abbott, Christopher Lau, Grace L. Guo, Lauren M. Aleksunes, Curtis D. Klaassen, J. Christopher Corton
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0064880

The Elongation Complex Components BRD4 and MLLT3/AF9 Are Transcriptional Coactivators of Nuclear Retinoid Receptors
Cited by: 14
Author(s): Sébastien Flajollet, Christophe Rachez, Maheul Ploton, Céline Schulz, Rozenn Gallais, Raphaël Métivier, Michał Pawlak, Aymeric Leray, Al Amine Issulahi, Laurent Héliot, Bart Staels, Gilles Salbert, Philippe Lefèbvre
Software Mentions: 1
Published: over 12 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: about 22 years ago

10.1371/journal.pone.0116973

A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network
Cited by: 39
Author(s): Felipe Leal Valentim, S. van Mourik, David Posé, Min C. Kim, Markus Schmid, Roeland C. H. J. van Ham, Marco Busscher, Gabino F. Sánchez-Pérez, Jaap Molenaar, Gerco C. Angenent, Richard G. H. Immink, Aalt D. J. van Dijk
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0109745

Mg2+ Effect on Argonaute and RNA Duplex by Molecular Dynamics and Bioinformatics Implications
Cited by: 9
Author(s): Seungyoon Nam, Hyojung Ryu, Won Son, Yon Hui Kim, Young Ho Kim, Curt Balch, Kenneth P. Nephew, Jinhyuk Lee
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0053478

Genome-Wide Alteration of Histone H3K9 Acetylation Pattern in Mouse Offspring Prenatally Exposed to Arsenic
Cited by: 83
Author(s): Andrea A. Cronican, Nicholas F. Fitz, Alexis B. Carter, Muzamil Saleem, Sruti Shiva, Aaron Barchowsky, Radosveta Koldamova, Jonathan Schug, Iliya Lefterov
Software Mentions: 1
Published: about 13 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: over 7 years ago

10.1371/journal.pone.0109978

Life without Oxygen: Gene Regulatory Responses of the Crucian Carp (Carassius carassius) Heart Subjected to Chronic Anoxia
Cited by: 11
Author(s): Kåre‐Olav Stensløkken, Stian Ellefsen, Olga Vasieva, Yongxiang Fang, Anthony P. Farrell, Lisa Olohan, Jarle Vaage, Göran Nilsson, Andrew R. Cossins
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0020063

Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
Cited by: 72
Author(s): Masayuki Murata, Hiroko Fujimoto, Kaori Nishimura, Kannikar Charoensuk, Hiroshi Nagamitsu, Satish Raina, Tomoyuki Kosaka, Taku Oshima, Nagahisa Ogasawara, Mamoru Yamada
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0008939

The Transcriptional Programme of Human Heart Valves Reveals the Natural History of Infective Endocarditis
Cited by: 29
Author(s): Marie Benoit, Franck Thuny, Yannick Le Priol, Hubert Lépidi, Sonia Bastonero, Jean‐Paul Casalta, Frédéric Collart, Christian Capo, Didier Raoult, Jean‐Louis Mège
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0062456

Age-Mediated Transcriptomic Changes in Adult Mouse Substantia Nigra
Cited by: 12
Author(s): Lin Gao, María Hidalgo-Figueroa, Luis Escudero, Juan Díaz‐Martín, José López‐Barneo, Alberto Pascual
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0177278

The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.)
Cited by: 23
Author(s): Bart Verwaaijen, Daniel Wibberg, Magdalena Kröber, Anderson M. Winkler, Rita Zrenner, Hanna Bednarz, Karsten Niehaus, Rita Grosch, Alfred Pühler, Andreas Schlüter
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0057329

Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)
Cited by: 116
Author(s): Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Software Mentions: 1
Published: almost 13 years ago

10.18632/oncotarget.24644

MiR-21 over-expression and Programmed Cell Death 4 down-regulation features malignant pleural mesothelioma
Cited by: 12
Author(s): Lorenzo Nicolè, Rocco Cappellesso, Tiziana Sanavia, Vincenza Guzzardo, Ambrogio Fassina
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0073817

Wild Type p53 Transcriptionally Represses the SALL2 Transcription Factor under Genotoxic Stress
Cited by: 10
Author(s): Carlos Farkas, Carla P. Martins, D. E. Escobar, Matías I. Hepp, David B. Donner, Ariel F. Castro, Gérard I. Evan, José L. Gutiérrez, Robert S. Warren, Roxana Pincheira
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0017259

GTI: A Novel Algorithm for Identifying Outlier Gene Expression Profiles from Integrated Microarray Datasets
Cited by: 27
Author(s): John Patrick Mpindi, Henri Sara, Saija Haapa-Paananen, Sami Kilpinen, Tommi Pisto, Elmar Bucher, K. Ojala, Kristiina Iljin, Paula Vainio, Mari Björkman, Santosh Gupta, Pekka Kohonen, Matthias Nees, Olli Kallioniemi
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0145696

Correction: Lung Transcriptomics during Protective Ventilatory Support in Sepsis-Induced Acute Lung Injury
Cited by: 3
Author(s): Marialbert Acosta‐Herrera, Fabián Lorenzo-Díaz, Maria Pino‐Yanes, Almudena Corrales, Francisco Valladares, Tilman E. Klassert, Basilio Valladares, Hortense Slevogt, Shwu‐Fan Ma, Jesús Villar, Carlos Flores
Software Mentions: 1
Published: about 10 years ago

10.18632/oncotarget.25736

A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing’s family of tumors
Cited by: 3
Author(s): Andrew J. Annalora, Shawn T. O’Neil, Jeremy D Bushman, James Summerton, Carol S. Marcus, Patrick L. Iversen
Software Mentions: 1
Published: over 7 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: over 9 years ago

10.1371/journal.pone.0106706

Research Resources: Comparative MicroRNA Profiles in Human Corona Radiata Cells and Cumulus Oophorus Cells Detected by Next-Generation Small RNA Sequencing
Cited by: 23
Author(s): Xianhong Tong, Bo Xu, Yuan‐Wei Zhang, Yusheng Liu, Chao Ma
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0014672

Estrogen-Dependent Gene Expression in the Mouse Ovary
Cited by: 9
Author(s): Seng H. Liew, Mai A. Sarraj, Ann E. Drummond, Jock K. Findlay
Software Mentions: 1
Published: about 15 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: about 6 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: almost 11 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: over 12 years ago

10.1371/journal.pone.0200716

Identification of serum miR-1915-3p and miR-455-3p as biomarkers for breast cancer
Cited by: 45
Author(s): Jian Guo, Chen Liu, Wei Wang, Yan Liu, Huiwen He, Chong Chen, Rong Xiang, Yunping Luo
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0044206

MiR-214 Targets β-Catenin Pathway to Suppress Invasion, Stem-Like Traits and Recurrence of Human Hepatocellular Carcinoma
Cited by: 142
Author(s): Hongping Xia, London Lucien Ooi, Kam M. Hui
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0019077

miR-132 Mediates the Integration of Newborn Neurons into the Adult Dentate Gyrus
Cited by: 140
Author(s): Bryan W. Luikart, Ae Soon L. Bensen, Eric K. Washburn, Julia V. Perederiy, Kimmy Su, Yun Li, Steven G. Kernie, Luis F. Parada, Gary L. Westbrook
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0011429

Revealing New Mouse Epicardial Cell Markers through Transcriptomics
Cited by: 59
Author(s): Lars Bochmann, Padmini Sarathchandra, Frederica Mori, Enrique Lara‐Pezzi, Domenico Lazzaro, Nadia Rosenthal
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0084611

TFPI1 Mediates Resistance to Doxorubicin in Breast Cancer Cells by Inducing a Hypoxic-Like Response
Cited by: 14
Author(s): Gerald F. Davies, Arnie Berg, Spike D. L. Postnikoff, Heather L. Wilson, Terra Arnason, Anthony Kusalik, Troy A. A. Harkness
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0052232

Interaction of Salmonella Typhimurium with Dendritic Cells Derived from Pluripotent Embryonic Stem Cells
Cited by: 10
Author(s): Raffaella Rossi, Christine Hale, David Goulding, Robert Andrews, Zarah Abdellah, Paul J. Fairchild, Gordon Dougan
Software Mentions: 1
Published: about 13 years ago

10.18632/oncotarget.26330

Whole genome duplication is an early event leading to aneuploidy in IDH-wild type glioblastoma
Cited by: 15
Author(s): Blandine Boisselier, Frédéric Dugay, Marc‐Antoine Belaud‐Rotureau, Anne Coutolleau, Emmanuel Garcion, Philippe Meneï, Philippe Guardiola, Audrey Rousseau
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0112399

Protein Interaction Networks Reveal Novel Autism Risk Genes within GWAS Statistical Noise
Cited by: 15
Author(s): Catarina Correia, Guiomar Oliveira, Astrid M. Vicente
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0030960

Role of Position 627 of PB2 and the Multibasic Cleavage Site of the Hemagglutinin in the Virulence of H5N1 Avian Influenza Virus in Chickens and Ducks
Cited by: 61
Author(s): K. A. Schat, John Bingham, Jeff Butler, Li Mei Chen, Sue Lowther, Tamsyn M. Crowley, Robert J. Moore, Ruben O. Donis, John W. Lowenthal
Software Mentions: 1
Published: almost 14 years ago

10.1002/path.5335

Overactivity or blockade of transforming growth factor‐β each generate a specific ureter malformation
Cited by: 11
Author(s): Filipa Lopes, Neil Roberts, Leo Zeef, Natalie J. Gardiner, Adrian S. Woolf
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0011066

Contrasting Transcriptional Responses of a Virulent and an Attenuated Strain of Mycobacterium tuberculosis Infecting Macrophages
Cited by: 43
Author(s): Alice H. Li, Simon J. Waddell, Jason Hinds, Chad A. Malloff, Manjeet Bains, Robert E. W. Hancock, Wan L. Lam, Philip D. Butcher, Richard W. Stokes
Software Mentions: 1
Published: over 15 years ago

10.1172/jci.insight.143643

CMTM6 drives cisplatin resistance by regulating Wnt signaling through ENO-1/AKT/GSK3β axis
Cited by: 21
Author(s): Pallavi Mohapatra, Omprakash Shriwas, Sibasish Mohanty, Arup Ghosh, Shuchi Smita, Sandeep Rai Kaushik, Rakesh Arya, Rachna Rath, Saroj Kumar Das Majumdar, Dillip Kumar Muduly, Sunil K. Raghav, Ranjan Kumar Nanda, Rupesh Dash
Software Mentions: 1
Published: about 5 years ago

10.1002/cjp2.138

High immune cytolytic activity in tumor‐free tongue tissue confers better prognosis in patients with squamous cell carcinoma of the oral tongue
Cited by: 13
Author(s): Xiaolian Gu, Linda Boldrup, Philip J. Coates, Robin Fåhræus, Lixiao Wang, Torben Wilms, Lena Norberg‐Spaak, Nicola Sgaramella, Karin Nylander
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0017359

The PI3K p110δ Regulates Expression of CD38 on Regulatory T Cells
Cited by: 71
Author(s): Daniel T. Patton, Marcus D. Wilson, Wendy C. Rowan, Dalya R. Soond, Klaus Okkenhaug
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0063296

Efferocytosis Promotes Suppressive Effects on Dendritic Cells through Prostaglandin E2 Production in the Context of Autoimmunity
Cited by: 23
Author(s): Irma Pujol‐Autonell, Rosa-Maria Ampudia, Raquel Planas, Sílvia Marín-Gallén, Jorge Carrascal, Álex Sánchez, Ana V. Marín, Manel Puig-Domingo, Ricardo Pujol-Borrell, Joan Verdaguer, Marta Vives-Pi
Software Mentions: 1
Published: over 12 years ago

10.1128/JB.00473-13

The agr Locus Regulates Virulence and Colonization Genes in Clostridium difficile 027
Cited by: 95
Author(s): Melissa J. Martin, Simon Clare, David Goulding, Alexandra Faulds-Pain, Lars Barquist, Hilary P. Browne, Laura J. Pettit, Gordon Dougan, Trevor D. Lawley, Brendan W. Wren
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0171508

A distal intergenic region controls pancreatic endocrine differentiation by acting as a transcriptional enhancer and as a polycomb response element
Cited by: 12
Author(s): Joris van Arensbergen, Sébastien Dussaud, Corinne Pardanaud-Glavieux, Javier García-Hurtado, Claire Sauty, Aline Guerci, Jorge Ferrer, Philippe Ravassard
Software Mentions: 1
Published: almost 9 years ago

10.1186/jbiol54

Growth control of the eukaryote cell: a systems biology study in yeast
Cited by: 244
Author(s): Juan I. Castrillo, Leo Zeef, David C. Hoyle, Nianshu Zhang, Andrew Hayes, David C. Gardner, Michael Cornell, June Petty, Luke Hakes, Leanne Wardleworth, Bharat Rash, Marie Brown, Warwick B. Dunn, David Broadhurst, Kerry O'Donoghue, Svenja Hester, Tom Dunkley, Sarah R. Hart, Neil Swainston, Peter Li, Simon J. Gaskell, Norman W. Paton, Kathryn S. Lilley, Douglas B. Kell, Stephen G. Oliver
Software Mentions: 1
Published: about 19 years ago

10.1074/jbc.M114.598300

Cross-talk between Two Nucleotide-signaling Pathways in Staphylococcus aureus
Cited by: 103
Author(s): Rebecca M. Corrigan, Lisa Bowman, Alexandra R. Willis, Volkhard Kaever, Angelika Gründling
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0114627

Altered MicroRNA Expression Profile in Exosomes during Osteogenic Differentiation of Human Bone Marrow-Derived Mesenchymal Stem Cells
Cited by: 184
Author(s): Jiajie Xu, Guangxiao Yang, Xiaohong Pan, Shuijun Zhang, Chen Zhao, Bin-Song Qiu, Haifeng Gu, Jian-fei Hong, Li Cao, Yu Chen, Bing Xia, Qinsheng Bi, Yaping Wang
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0177701

SiGNet: A signaling network data simulator to enable signaling network inference
Cited by: 7
Author(s): Elizabeth A. Coker, Costas Mitsopoulos, Paul Workman, Bissan Al‐Lazikani
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0001973

Genomic Diversity among Beijing and non-Beijing Mycobacterium tuberculosis Isolates from Myanmar
Cited by: 20
Author(s): Ruth Stavrum, Håvard Valvatne, Trond Hellem Bø, Inge Jonassen, Jason Hinds, Philip D. Butcher, Harleen M. S. Grewal
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0055764

Simultaneous Quantification of Multiple Bacteria by the BactoChip Microarray Designed to Target Species-Specific Marker Genes
Cited by: 17
Author(s): Annalisa Ballarini, Nicola Segata, Curtis Huttenhower, Olivier Jousson
Software Mentions: 1
Published: almost 13 years ago

10.1186/2041-1480-1-S1-S1

Building a biomedical ontology recommender web service
Cited by: 68
Author(s): Clément Jonquet, Mark A. Musen, Nigam H. Shah
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0087665

Genome-Wide Screening Identified That miR-134 Acts as a Metastasis Suppressor by Targeting Integrin β1 in Hepatocellular Carcinoma
Cited by: 69
Author(s): Rujing Zha, Weijie Guo, Zhenfeng Zhang, Zhaoping Qiu, Qifeng Wang, Jie Ding, Shenglin Huang, Taoyang Chen, Jianren Gu, Ming Yao, Xianghuo He
Software Mentions: 1
Published: about 12 years ago

10.1186/2041-1480-5-25

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
Cited by: 60
Author(s): James Malone, Andy Brown, Allyson L. Lister, Jon C. Ison, Duncan Hull, Helen Parkinson, Robert Stevens
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0176353

Intracellular signaling entropy can be a biomarker for predicting the development of cervical intraepithelial neoplasia
Cited by: 4
Author(s): Masakazu Sato, Kei Kawana, Katsuyuki Adachi, Asaha Fujimoto, Midori Yoshida, Hitomi Nakamura, Hidetoshi Nishida, Tatsuo Inoue, Ayumi Taguchi, Juri Ogishima, Shuichiro Eguchi, Aki Yamashita, Kensuke Tomio, Osamu Wada-Hiraike, Katsutoshi Oda, Takeshi Nagamatsu, Yutaka Osuga, Tomoyuki Fujii
Software Mentions: 1
Published: almost 9 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962