bioconductor: ArrayExpress | Projects

10.1038/s41598-019-43795-2

Replication termination without a replication fork trap
Cited by: 20
Author(s): Elisa Galli, Jean-Luc Ferat, Jean-Michel Desfontaines, Marie-Eve Val, Ove Skovgaard, François‐Xavier Barre, Christophe Possoz
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-46664-0

Virus Genotype-Dependent Transcriptional Alterations in Lipid Metabolism and Inflammation Pathways in the Hepatitis C Virus-infected Liver
Cited by: 18
Author(s): W. d’Avigdor, Magdalena A. Budzinska, M Lee, Roselind S. Lam, James G. Kench, Michael Stapelberg, Susan V. McLennan, Geoffrey C. Farrell, Jacob George, Geoffrey W. McCaughan, Thomas Tu, Nicholas Shackel
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-11-150

Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes
Cited by: 41
Author(s): Sigrid Rouam, Thierry Moreau, Philippe Broët
Software Mentions: 1
Published: almost 16 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

10.1186/1471-2105-9-183

Data capture in bioinformatics: requirements and experiences with Pedro
Cited by: 16
Author(s): Daniel Jameson, Kevin Garwood, Christopher Garwood, Tim Booth, Pinar Alper, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: almost 18 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

10.1186/1471-2164-14-376

Time-dependent changes in gene expression induced by secreted amyloid precursor protein-alpha in the rat hippocampus
Cited by: 35
Author(s): Margaret M. Ryan, Gary P. Morris, Bruce G. Mockett, Katie Bourne, Wickliffe C. Abraham, Warren P. Tate, Joanna M. Williams
Software Mentions: 1
Published: about 13 years ago

10.1038/s41598-019-49124-x

Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis
Cited by: 8
Author(s): Perumal Gnanakkumaar, Ram Murugesan, Shiek S. S. J. Ahmed
Software Mentions: 1
Published: over 6 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

10.1186/1471-2164-14-336

A simple and reproducible breast cancer prognostic test
Cited by: 47
Author(s): Luigi Marchionni, Bahman Afsari, Donald Geman, Jeffrey T. Leek
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-10-S12-S10

Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data
Cited by: 4
Author(s): Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano, Ulrich Pfeffer
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-14-8

XperimentR: painless annotation of a biological experiment for the laboratory scientist
Cited by: 7
Author(s): Christopher Tomlinson, Geraint Barton, Mark Woodbridge, Sarah Butcher
Software Mentions: 1
Published: about 13 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

10.1186/1471-2164-16-S1-S11

Transcriptomics profiling study of breast cancer from Kingdom of Saudi Arabia revealed altered expression of Adiponectin and Fatty Acid Binding Protein4: Is lipid metabolism associated with breast cancer?
Cited by: 25
Author(s): Adnan Merdad, Sajjad Karim, Hans-Juergen Schulten, Jayapal Manikandan, Ashraf Dallol, Abdelbaset Buhmeida, Fatima Al-Thubaity, Mamdooh A GariI, Adeel Chaudhary, Adel M. Abuzenadah, Mohammed Al‐Qahtani
Software Mentions: 1
Published: about 11 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

10.1186/s12864-016-2537-1

On the genome base composition of teleosts: the effect of environment and lifestyle
Cited by: 14
Author(s): Andrea Tarallo, Claudia Angelini, Remo Sanges, Mitsuharu Yagi, Claudio Agnisola, Giuseppe D’Onofrio
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-15-315

Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach
Cited by: 66
Author(s): Tommy Bengtsson, Deborah Weighill, Estelle Proux‐Wéra, Fredrik Levander, Svante Resjö, Dharani Dhar Burra, Laith Ibrahim Moushib, Pete E. Hedley, Erland Liljeroth, Dan Jacobson, Erik Alexandersson, Erik Andréasson
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-8-208

Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits
Cited by: 22
Author(s): Carl-Johan Rubin, Johan Lindberg, Carolyn Fitzsimmons, Peter Savolainen, Per Jensen, Joakim Lundeberg, Leif C. Andersson, Andreas Kindmark
Software Mentions: 1
Published: over 18 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

10.1186/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

10.1111/acel.12080

<scp>TORC</scp>1 signaling inhibition by rapamycin and caffeine affect lifespan, global gene expression, and cell proliferation of fission yeast
Cited by: 113
Author(s): Charalampos Rallis, Sandra Codlin, Jürg Bähler
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-016-2814-z

A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease
Cited by: 20
Author(s): Helgi B. Schiöth, Adrian Boström, Susan K. Murphy, Wiebke Erhart, Jochen Hampe, Cynthia A. Moylan, Jessica Mwinyi
Software Mentions: 1
Published: over 9 years ago

10.1111/acel.12160

Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging
Cited by: 40
Author(s): Erik B. van den Akker, Willemijn M. Passtoors, Ritsert C. Jansen, Erik W. van Zwet, Jelle J. Goeman, Marc Hulsman, Valur Emilsson, Markus Perola, Gonneke Willemsen, Brenda W. J. H. Penninx, B.T. Heijmans, Andrea B. Maier, Dorret I. Boomsma, Joost N. Kok, P. Eline Slagboom, Marcel J. T. Reinders, Marian Beekman
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-8-210

Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state
Cited by: 1
Author(s): Daniel Y L Yap, David K. Smith, Xue W Zhang, Jeffrey Hill
Software Mentions: 1
Published: about 19 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

10.1186/1471-2164-7-78

Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity
Cited by: 34
Author(s): Vattipally B Sreenu, Pankaj Kumar, Javaregowda Nagaraju, Hampapathalu A. Nagarajaram
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2105-8-360

Linking microarray reporters with protein functions
Cited by: 12
Author(s): Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. Evelo
Software Mentions: 1
Published: over 18 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

10.1186/1471-2164-10-560

ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles
Cited by: 1
Author(s): Weizhong Li, Andrew Y. Gracey, Luciane V. Mello, Andy Brass, Andrew R. Cossins
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-10-153

Learning from microarray interlaboratory studies: measures of precision for gene expression
Cited by: 9
Author(s): David L. Duewer, Wendell Jones, Laura Reid, Marc Salit
Software Mentions: 1
Published: about 17 years ago

10.1186/ar1903

Cited by: 51
Author(s): Johan Lindberg, Erik af Klint, Ann‐Kristin Ulfgren, André Stark, T. Andersson, Peter Nilsson, Lars Klareskog, Joakim Lundeberg
Software Mentions: 1
Published: about 20 years ago

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 16 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: about 19 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: over 5 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: about 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: about 14 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

10.1186/1471-2164-9-340

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: over 17 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

10.1098/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 13 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: about 16 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

10.1186/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: about 19 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: about 20 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 17 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

10.1186/1471-2164-13-33

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: about 14 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: about 16 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: about 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: about 19 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: about 18 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: about 19 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: about 20 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: about 13 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: about 19 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: over 18 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: about 20 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

10.1186/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: almost 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: over 7 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

10.1186/1471-2164-7-113

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: almost 20 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: 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: about 18 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: over 16 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: about 13 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: over 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: about 6 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 12 years ago

10.1371/journal.pgen.1004243

The Membrane-Associated Transcription Factor NAC089 Controls ER-Stress-Induced Programmed Cell Death in Plants
Cited by: 160
Author(s): Zhenle Yang, Mei-Jing Wang, Ling Sun, Sun-Jie Lu, Dongling Bi, Li‐Zhong Sun, Ze‐Ting Song, Shuang-Shuang Zhang, Shun-Fan Zhou, Jian‐Xiang Liu
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pcbi.1002126

Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach
Cited by: 80
Author(s): Tim D. Williams, Nahid Turan, Amer Diab, Huifeng Wu, Carolynn Mackenzie, Kerry L. Bartie, Olga Hrydziuszko, Brett P. Lyons, Grant D. Stentiford, John Herbert, Kuruvilla Joseph Abraham, Ioanna Katsiadaki, Michael J. Leaver, John B. Taggart, Stephen George, Mark R. Viant, Kevin Chipman, Francesco Falciani
Software Mentions: 1
Published: over 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: almost 16 years ago

10.1371/journal.pcbi.1000851

Large-Scale Analysis of Network Bistability for Human Cancers
Cited by: 75
Author(s): Tetsuya Shiraishi, Shinako Matsuyama, Hiroaki Kitano
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1000940

Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions
Cited by: 63
Author(s): Rong Chen, Tara K. Sigdel, Li Li, Neeraja Kambham, Joel T. Dudley, Szu Chuan Hsieh, R. Bryan Klassen, Amery Chen, Tuyen Caohuu, Alexander A. Morgan, Hannah A. Valantine, Kiran K. Khush, Minnie M. Sarwal, Atul J. Butte
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1003597

Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation
Cited by: 10
Author(s): Marcus J. Tindall, Angela Clerk
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pcbi.1002278

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
Cited by: 65
Author(s): Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu, Mark Gerstein
Software Mentions: 1
Published: about 14 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: almost 17 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: almost 17 years ago

10.1371/journal.pbio.3001311

MHC class I H2-Kb negatively regulates neural progenitor cell proliferation by inhibiting FGFR signaling
Cited by: 12
Author(s): Karin Lin, Gregor Bieri, Géraldine Gontier, Sören Müller, Lucas K. Smith, Cedric E Snethlage, Charles White, Sun Y. Maybury-Lewis, Saul Villeda
Software Mentions: 1
Published: over 4 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: over 12 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 9 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: about 13 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: almost 6 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: over 8 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 5 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: about 14 years ago

10.1371/journal.pbio.0030297

Bioinformatics and Data Management Support for Environmental Genomics
Cited by: 23
Author(s): Dawn Field, Bela Tiwari, Jason Snape
Software Mentions: 1
Published: over 20 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: almost 11 years ago

10.1371/journal.pbio.0030384

Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning
Cited by: 394
Author(s): Benoît Guillemette, Alain R. Bataille, Nicolas Gévry, Maryse Adam, Mathieu Blanchette, François Robert, Luc Gaudreau
Software Mentions: 1
Published: over 20 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962