bioconductor: ArrayExpress | Projects

10.1038/s41598-017-12498-x

A dual targeted β-defensin and exome sequencing approach to identify, validate and functionally characterise genes associated with bull fertility
Cited by: 21
Author(s): Ronan Whiston, Emma K. Finlay, Matthew S. McCabe, Paul Cormican, Paul Flynn, A.R. Cromie, P. J. Hansen, A. Bruce Lyons, Seán Fair, Patrick Lonergan, Cliona O’ Farrelly, Kieran G. Meade
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.devcel.2016.10.015

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances
Cited by: 188
Author(s): Orsolya Symmons, Leslie Pan, Silvia Remeseiro, Tuğçe Aktaş, Felix A. Klein, Wolfgang Huber, François Spitz
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-016-2771-6

Transcriptomic response of yeast cells to ATX1 deletion under different copper levels
Cited by: 12
Author(s): Ayca Cankorur-Cetinkaya, Serpil Eraslan, Betül Kırdar
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2105-8-447

Application of a correlation correction factor in a microarray cross-platform reproducibility study
Cited by: 7
Author(s): Kellie J. Archer, Catherine I. Dumur, G. Scott Taylor, Michael D. Chaplin, Anthony Guiseppi‐Elie, Geraldine M. Grant, Andrea Ferreira‐Gonzalez, Carleton T. Garrett
Software Mentions: 1
Published: over 18 years ago

10.1016/j.devcel.2014.12.024

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State
Cited by: 70
Author(s): Shilu Amin, Ian J. Donaldson, Denise A. Zannino, James Hensman, Magnus Rattray, Marta Losa, François Spitz, Franck Ladam, Charles G. Sagerström, Nicoletta Bobola
Software Mentions: 1
Published: over 11 years ago

10.1242/dev.168146

Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes
Cited by: 17
Author(s): Toru Suzuki, Chisato Kikuguchi, Saori Nishijima, Takeshi Nagashima, Akinori Takahashi, Mariko Okada, Tadashi Yamamoto
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-10-215

Dynamic changes in transcripts during regeneration of the secondary vascular system in Populus tomentosa Carr. revealed by cDNA microarrays
Cited by: 29
Author(s): Minjie Wang, Xiaoli Qi, Shutang Zhao, Shougong Zhang, Mengzhu Lu
Software Mentions: 1
Published: over 17 years ago

10.1186/s12859-015-0854-z

Evaluation of O2PLS in Omics data integration
Cited by: 91
Author(s): Said el Bouhaddani, Jeanine J. Houwing-Duistermaat, Perttu Salo, Markus Perola, Geurt Jongbloed, Hae‐Won Uh
Software Mentions: 1
Published: over 10 years ago

10.1242/dev.112623

Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo
Cited by: 53
Author(s): Isabel Olivera-Martínez, Nicholas J. Schurch, Roman A. Li, Junfang Song, Pamela A. Halley, Raman M Das, David W. Burt, Geoffrey J. Barton, Kate G. Storey
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-8-343

Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model
Cited by: 12
Author(s): Ryoko Morioka, Shigehiko Kanaya, Masami Yokota Hirai, Mitsuru Yano, Nagahisa Ogasawara, Kazuki Saito
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2164-11-682

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
Cited by: 40
Author(s): Richard A. Lewis, Emma Laing, Nicholas E. E. Allenby, Giselda Bucca, Volker Brenner, Marcus Harrison, Andrzej M. Kierzek, Colin P. Smith
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2105-12-S10-S2

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses
Cited by: 14
Author(s): Mikhail G. Dozmorov, Jonathan D. Wren
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-9-208

RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina
Cited by: 14
Author(s): Ravi Kiran Reddy Kalathur, Nicolas Gagnière, Guillaume Berthommier, Laetitia Poidevin, Wolfgang Raffelsberger, Raymond Ripp, Thierry Léveillard, Olivier Poch
Software Mentions: 1
Published: over 18 years ago

10.1242/dmm.021626

Pulmonary transcriptome analysis in the rabbit model of surgically-induced diaphragmatic hernia treated with fetal tracheal occlusion
Cited by: 17
Author(s): Alexander C. Engels, Paul Brady, Molka Kammoun, Julio Finalet Ferreiro, Philip DeKoninck, Masayuki Endo, Jaan Toelen, Joris Robert Vermeesch, Jan Deprest
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-10-575

Using transcriptome profiling to characterize QTL regions on chicken chromosome 5
Cited by: 13
Author(s): Guillaume Le Mignon, Colette Désert, Frédérique Pitel, Sophie Leroux, Olivier Demeure, Grégory Guernec, Behnam Abasht, Madeleine Douaire, Pascale Le Roy, Sandrine Lagarrigue
Software Mentions: 1
Published: over 16 years ago

10.1016/j.drudis.2012.07.014

Transcriptional data: a new gateway to drug repositioning?
Cited by: 193
Author(s): Francesco Iorio, Timothy Rittman, Hong Ge, Michael P. Menden, Julio Sáez-Rodríguez
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-5-68

PEDRo: A database for storing, searching and disseminating experimental proteomics data
Cited by: 66
Author(s): Kevin Garwood, Thomas J. McLaughlin, Chris Garwood, Scott Joens, Norman Morrison, Christopher F Taylor, Kathleen M. Carroll, Caroline A. Evans, Anthony D. Whetton, Sarah R. Hart, David Stead, Zhikang Yin, Alistair J. P. Brown, Andrew Hesketh, Keith F. Chater, Lena Hansson, Muriel Mewissen, Peter Ghazal, Julie A. Howard, Kathryn S. Lilley, Simon J. Gaskell, Andy Brass, Simon J. Hubbard, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: almost 22 years ago

10.1186/1471-2164-16-S1-S2

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data
Cited by: 41
Author(s): Anna L Swan, Dov J. Stekel, Charlie Hodgman, David Allaway, Mohammed Hussein Al-Qahtani, Ali Mobasheri, Jaume Bacardit
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-11-S1-S6

Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha
Cited by: 116
Author(s): Winston Koh, Chen Tian Sheng, Betty Tan, Qian Yi Lee, Vladimir A. Kuznetsov, Lim Sai Kiang, Vivek Tanavde
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-9-291

Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium
Cited by: 66
Author(s): Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens, Salvatore Bozzaro
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2164-11-478

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes
Cited by: 11
Author(s): Michael Klutstein, Zahava Siegfried, Ariel Gispan, Shlomit Farkash-Amar, Guy Zinman, Ziv Bar‐Joseph, Giora Simchen, Itamar Simon
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-9-285

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
Cited by: 78
Author(s): Michael Boedigheimer, Russell D. Wolfinger, Michael Bass, Pierre R. Bushel, Jeff W. Chou, Matthew N. Cooper, J. Christopher Corton, Jennifer Fostel, Susan Hester, Janice S. Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit, Karol L. Thompson
Software Mentions: 1
Published: about 18 years ago

10.15252/emmm.201708163

An <scp>FGFR</scp> 3/ <scp>MYC</scp> positive feedback loop provides new opportunities for targeted therapies in bladder cancers
Cited by: 40
Author(s): Mélanie Mahé, Florent Dufour, Hélène Neyret–Kahn, Aura Ileana Moreno-Vega, C Béraud, Ming Shi, Iméne Hamaidi, Virginia Sánchez-Quiles, Clémentine Krucker, Marion Dorland‐Galliot, Élodie Chapeaublanc, Rémy Nicolle, Hervé Lang, Célio Pouponnot, Thierry Massfelder, François Radvanyi, Isabelle Bernard‐Pierrot
Software Mentions: 1
Published: over 8 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: about 8 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: almost 8 years ago

10.1080/22221751.2019.1645572

Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity
Cited by: 19
Author(s): Natalie D. Collins, Steven G. Widen, Li Li, Daniele M. Swetnam, Pei–Yong Shi, Robert B. Tesh, Vanessa V. Sarathy
Software Mentions: 1
Published: over 7 years ago

10.1530/ERC-13-0098

Clinical and functional impact of TARBP2 over-expression in adrenocortical carcinoma
Cited by: 51
Author(s): Stefano Caramuta, Linkiat Lee, Deniz M. Özata, Pınar Akçakaya, Hong Xie, Anders Höög, Jan Zedenius, Martin Bäckdahl, Catharina Larsson, Weng‐Onn Lui
Software Mentions: 1
Published: over 13 years ago

10.1530/ERC-17-0399

GnRH antagonist treatment of malignant adrenocortical tumors
Cited by: 14
Author(s): Milena Doroszko, Marcin Chruściel, Joanna Stelmaszewska, T. Ślęzak, Sławomir Anisimowicz, Ursula Plöckinger, Marcus Quinkler, Marco Bonomi, Sławomir Wołczyński, Ilpo Huhtaniemi, Jorma Toppari, Nafis Rahman
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-21915-8

Morphine induces changes in the gut microbiome and metabolome in a morphine dependence model
Cited by: 144
Author(s): Fuyuan Wang, Jingjing Meng, Li Zhang, Timothy J. Johnson, Chi Chen, Sabita Roy
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-12-137

Assessing affymetrix GeneChip microarray quality
Cited by: 70
Author(s): Matthew N. McCall, Peter Murakami, Margus Lukk, Wolfgang Huber, Rafael A. Irizarry
Software Mentions: 1
Published: over 15 years ago

10.1111/1462-2920.12726

Adaptation of anaerobic cultures ofEscherichia coli K-12 in response to environmental trimethylamine-N-oxide
Cited by: 9
Author(s): Katie J. Denby, Matthew D. Rolfe, Ellen Crick, Guido Sanguinetti, Robert K. Poole, Jeffrey Green
Software Mentions: 1
Published: over 11 years ago

10.1111/j.1462-2920.2011.02461.x

Genomic variations define divergence of water/wildlife‐associated Campylobacter jejuni niche specialists from common clonal complexes
Cited by: 54
Author(s): Philip J. Hepworth, Kevin E. Ashelford, Jason Hinds, Katherine A. Gould, Adam A. Witney, Nicola Williams, Howard Leatherbarrow, Nigel P. French, Richard J. Birtles, Chriselle Mendonca, Nick Dorrell, Brendan W. Wren, Paul Wigley, Neil Hall, Craig Winstanley
Software Mentions: 1
Published: over 15 years ago

10.1038/s41598-018-24437-5

Deviations of the immune cell landscape between healthy liver and hepatocellular carcinoma
Cited by: 130
Author(s): Nataliya Rohr-Udilova, Florian Klinglmüller, Rolf Schulte‐Hermann, Judith Stift, Merima Herac, Martina Salzmann, Francesca Finotello, Gerald Timelthaler, Georg Oberhuber, Matthias Pinter, Thomas Reiberger, Erika Jensen‐Jarolim, Robert Eferl, Michael Trauner
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-9-171

Transcriptional regulation by Poly(ADP-ribose) polymerase-1 during T cell activation
Cited by: 41
Author(s): Luis Sáenz, Juan José Lozano, Rut Valdor, Alberto Baroja‐Mazo, Pablo Ramı́rez, Pascual Parrilla, Pedro Aparicio, Lauro Sumoy, José Yélamos
Software Mentions: 1
Published: over 18 years ago

10.1038/s41598-018-24769-2

Profiling of 179 miRNA Expression in Blood Plasma of Lung Cancer Patients and Cancer-Free Individuals
Cited by: 32
Author(s): Ivan A. Zaporozhchenko, Evgeny S. Morozkin, Anastasia A. Ponomaryova, Elena Y. Rykova, Н. В. Чердынцева, А. А. Жеравин, O. A. Pashkovskaya, Evgeny Pokushalov, Valentin V. Vlassov, Pavel P. Laktionov
Software Mentions: 1
Published: over 8 years ago

10.1186/s13072-015-0018-4

Role of Ccr4-Not complex in heterochromatin formation at meiotic genes and subtelomeres in fission yeast
Cited by: 40
Author(s): Cristina Cotobal, María Rodríguez-López, Caia D. S. Duncan, Ayesha Hasan, Akira Yamashita, Masayuki Yamamoto, Jürg Bähler, Juan Mata
Software Mentions: 1
Published: about 11 years ago

10.1186/s13072-016-0078-0

Chromatin variation associated with liver metabolism is mediated by transposable elements
Cited by: 30
Author(s): Juan Du, Amy Leung, Candi Trac, Michael Lee, Brian W. Parks, Aldons J. Lusis, Rama Natarajan, Dustin E. Schones
Software Mentions: 1
Published: about 10 years ago

10.1186/1756-8935-3-6

A paucity of heterochromatin at functional human neocentromeres
Cited by: 86
Author(s): Alicia Alonso, Dan Hasson, Fanny Cheung, Peter E. Warburton
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-10-350

Type I interferon receptor-independent and -dependent host transcriptional responses to mouse hepatitis coronavirus infection in vivo
Cited by: 17
Author(s): Matthijs Raaben, Marian J. A. Groot Koerkamp, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-13-323

Flexible and efficient genome tiling design with penalized uniqueness score
Cited by: 3
Author(s): Yang Du, Eduard Muráni, Siriluck Ponsuksili, Klaus Wimmers
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-15-S10-S4

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation
Cited by: 2
Author(s): Alexis Vandenbon, Shunsuke Teraguchi, Osamu Takeuchi, Yutaka Suzuki, Daron M. Standley
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-12-113

Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns
Cited by: 21
Author(s): Daniel Báron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péreón, Reiner A. Veitia, Frédérique Savagner, Gérard Ramstein, Rémi Houlgatte
Software Mentions: 1
Published: over 15 years ago

10.1016/j.exer.2021.108553

ON-bipolar cell gene expression during retinal degeneration: Implications for optogenetic visual restoration
Cited by: 13
Author(s): Michael James Gilhooley, Doron Hickey, Moritz Lindner, Teele Palumaa, Steven Hughes, Stuart N. Peirson, Robert E. MacLaren, Mark W. Hankins
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-8-22

Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population
Cited by: 73
Author(s): Chun Shi, Anna Użarowska, Milena Ouzunova, Matthias Landbeck, G. Wenzel, Thomas Lübberstedt
Software Mentions: 1
Published: over 19 years ago

10.1038/s12276-018-0162-6

The E3 ubiquitin ligase TRIM25 regulates adipocyte differentiation via proteasome-mediated degradation of PPARγ
Cited by: 17
Author(s): Jae Min Lee, Sun Sil Choi, Yo Han Lee, Keon Woo Khim, Susan A. Yoon, Byung-gyu Kim, Dougu Nam, Pann‐Ghill Suh, Kyungjae Myung, Jang Hyun Choi
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-13-146

Meta-analysis of Chicken – Salmonella infection experiments
Cited by: 11
Author(s): M.F.W. te Pas, Ina Hulsegge, Dirkjan Schokker, M.A. Smits, Mark Fife, Rima Zoorob, Marie-Laure Endale, Johanna M.J. Rebel
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-9-324

Topoisomerase II inhibition involves characteristic chromosomal expression patterns
Cited by: 7
Author(s): Susanne Reymann, Jürgen Borlak
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-15-333

MicroRNA profiling of rats with ochratoxin A nephrotoxicity
Cited by: 47
Author(s): Dai Qiu, Jingbo Zhao, Xiaozhe Qi, Wentao Xu, Xiaoyun He, Mingzhang Guo, Harsh Dweep, Wen‐Hsing Cheng, Yunbo Luo, Kai Xia, Norbert Gretz, Kunlun Huang
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-10-119

Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes
Cited by: 58
Author(s): José Osorio y Fortéa, Emilie de La Llave, Béatrice Regnault, Jean‐Yves Coppée, Geneviève Milon, Thierry Lang, Éric Prina
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-6-174

Bacterial genome adaptation to niches: Divergence of the potential virulence genes in three Burkholderia species of different survival strategies
Cited by: 137
Author(s): Heenam Stanley Kim, Mark A. Schell, Yan Yu, Ricky L. Ulrich, Saul Sarria, William C. Nierman, David DeShazer
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2164-14-799

Chronic parasitization by Nosema microsporidia causes global expression changes in core nutritional, metabolic and behavioral pathways in honey bee workers (Apis mellifera)
Cited by: 85
Author(s): Holly L. Holt, Katherine A. Aronstein, Christina M. Grozinger
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-10-S1-S54

Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data
Cited by: 3
Author(s): Dongxiao Zhu
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-9-628

Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality
Cited by: 13
Author(s): Adam Ertel, Aydın Tözeren
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2105-8-52

PASSIM – an open source software system for managing information in biomedical studies
Cited by: 23
Author(s): Juris Vīksna, Edgars Celms, Mārtiņš Opmanis, Kārlis Podnieks, Pēteris Ručevskis, Andris Zarins, Amy Barrett, Sudeshna Guha Neogi, Maria Krestyaninova, Mark I. McCarthy, Alvis Brāzma, Ugis Sarkans
Software Mentions: 1
Published: over 19 years ago

10.12688/f1000research.7911.1

Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources
Cited by: 14
Author(s): David Bousfield, Johanna McEntyre, Sameer Velankar, George Papadatos, Alex Bateman, Guy Cochrane, Jee-Hyub Kim, Florian Graef, Vid Vartak, Blaise T. F. Alako, Niklas Blomberg
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-11-714

Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources
Cited by: 22
Author(s): Camille Rustenholz, Pete E. Hedley, Jenny Morris, Frédéric Choulet, Catherine Feuillet, Robbie Waugh, Etienne Paux
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-12-452

Histological and global gene expression analysis of the 'lactating' pigeon crop
Cited by: 43
Author(s): Meagan J Gillespie, Volker Häring, Kenneth A. McColl, Paul Monaghan, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-13-407

Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins
Cited by: 75
Author(s): David Peris, Christian A. Lopes, Carmela Belloch, Amparo Querol, Eladio Barrio
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-15-649

Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation
Cited by: 28
Author(s): Alison F. Richard, Paul Lyons, James E. Peters, Daniele Biasci, Shaun Flint, James C. Lee, Eoín McKinney, Richard M. Siegel, Kenneth G. C. Smith
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-11-142

TobEA: an atlas of tobacco gene expression from seed to senescence
Cited by: 61
Author(s): Kieron D. Edwards, Aureliano Bombarely, Geraint W. Story, F H Allen, Lukas A. Mueller, Steve Coates, Louise Jones
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-9-S6-S18

ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses
Cited by: 29
Author(s): Todd H. Stokes, J.T. Torrance, Henry Li, May D. Wang
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2105-10-441

The Medicago truncatula gene expression atlas web server
Cited by: 172
Author(s): Ji He, Vagner A. Benedito, Mingyi Wang, J. D. Murray, Patrick Xuechun Zhao, Yuhong Tang, Michael K. Udvardi
Software Mentions: 1
Published: over 16 years ago

10.1002/2211-5463.12082

Cryptochrome 2 extensively regulates transcription of the chloroplast genome in tomato
Cited by: 14
Author(s): Paolo Facella, Fabrizio Carbone, Antonio Placido, Gaetano Perrotta
Software Mentions: 1
Published: over 9 years ago

10.1111/1574-6968.12230

An attenuated mutant of the Rv1747 ATP-binding cassette transporter ofMycobacterium tuberculosisand a mutant of its cognate kinase, PknF, show increased expression of the efflux pump-relatediniBACoperon
Cited by: 6
Author(s): Vicky L. Spivey, Rachael H. Whalan, Elizabeth Hirst, Stephen J. Smerdon, Roger S. Buxton
Software Mentions: 1
Published: about 13 years ago

10.3389/fnbeh.2019.00103

Autonomic and Redox Imbalance Correlates With T-Lymphocyte Inflammation in a Model of Chronic Social Defeat Stress
Cited by: 23
Author(s): Cassandra Moshfegh, Safwan Elkhatib, Christopher W. Collins, Allison J. Kohl, Adam J. Case
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-11-610

BiologicalNetworks 2.0 - an integrative view of genome biology data
Cited by: 21
Author(s): Sergey Kozhenkov, Yulia Dubinina, Mayya Sedova, Amarnath Gupta, Julia Ponomarenko, Michael Baitaluk
Software Mentions: 1
Published: over 15 years ago

10.3389/fbioe.2015.00058

SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human
Cited by: 13
Author(s): Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-11-343

Regulation of the cardiomyocyte transcriptome vs translatome by endothelin-1 and insulin: translational regulation of 5' terminal oligopyrimidine tract (TOP) mRNAs by insulin
Cited by: 15
Author(s): Thomais Markou, Andrew Keith Marshall, Timothy E. Cullingford, El Li Tham, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-11-709

Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans
Cited by: 62
Author(s): Jessica Cleiss-Arnold, Sandrine Koechler, Caroline Proux, Marie‐Laure Fardeau, Marie‐Agnès Dillies, Jean‐Yves Coppée, Florence Arsène-Ploetze, Philippe Bertin
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2105-10-226

Information management for high content live cell imaging
Cited by: 4
Author(s): Daniel Jameson, David A. Turner, John Ankers, Stephnie Kennedy, Sheila Ryan, Neil Swainston, Tony Griffiths, David G. Spiller, Stephen G. Oliver, Mike White, Douglas B. Kell, Norman W. Paton
Software Mentions: 1
Published: about 17 years ago

10.3390/genes9060275

Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson’s Disease Data
Cited by: 16
Author(s): Elisa Mariani, Lorenza Lombardini, Federica Facchin, Fabrizio Pizzetti, Flavia Frabetti, Andrea Tarozzi, Raffaella Casadei
Software Mentions: 1
Published: about 8 years ago

10.3390/genes10050341

Genetical Genomics of Tonic Immobility in the Chicken
Cited by: 19
Author(s): Jesper Fogelholm, Samuel Eguasi Inkabi, Andrey Höglund, Robin N. Abbey-Lee, Martin Johnsson, Per Jensen, Rie Henriksen, I. A. Wright
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-10-151

MIMAS 3.0 is a Multiomics Information Management and Annotation System
Cited by: 16
Author(s): Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig
Software Mentions: 1
Published: about 17 years ago

10.1186/s12859-019-2651-6

Identification of trans-eQTLs using mediation analysis with multiple mediators
Cited by: 31
Author(s): Nayang Shan, Zuoheng Wang, Lin Hou
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-37591-7

Author Correction: Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 1
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Connor Rogerson, Christopher W. Bleaney, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-42750-5

Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation
Cited by: 5
Author(s): Michael Laimighofer, Ramona Lickert, R. Fuerst, Fabian J. Theis, Christiane Winkler, Ezio Bonifacio, Anette‐Gabriele Ziegler, Jan Krumsiek
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-8-70

Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation
Cited by: 338
Author(s): Birgit Kulterer, Gerald Friedl, Anita Jandrositz, Fátima Sánchez‐Cabo, Andreas Prokesch, Christine Paar, Marcel Scheideler, Reinhard Windhager, Karl‐Heinz Preisegger, Zlatko Trajanoski
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2105-7-489

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Cited by: 197
Author(s): Tim Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert, Joseph A. White, Patricia L. Whetzel, Farrell Wymore, Helen Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brāzma
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-9-375

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability
Cited by: 76
Author(s): Martin H. van Vliet, Fabien Reyal, Hugo M. Horlings, Marc J. van de Vijver, Marcel J. T. Reinders, Lodewyk Wessels
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-10-324

Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues
Cited by: 28
Author(s): Anita Grigoriadis, Gavin R. Oliver, Austin Tanney, Howard Kendrick, Matthew J. Smalley, Parmjit Jat, A. Munro Neville
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-9-121

Transcriptome analysis of grain development in hexaploid wheat
Cited by: 183
Author(s): Yongfang Wan, Rebecca L Poole, Alison K. Huttly, C. Toscano-Underwood, Kevin A. Feeney, S. J. Welham, M. J. Gooding, Clare Mills, Keith J. Edwards, Peter R. Shewry, R. A. C. Mitchell
Software Mentions: 1
Published: over 18 years ago

10.1038/s41436-018-0015-7

A homozygous FANCM frameshift pathogenic variant causes male infertility
Cited by: 61
Author(s): Hong Yin, Hui Ma, Sajjad Hussain, Huan Zhang, Xuefeng Xie, Long Jiang, Xiaohua Jiang, Furhan Iqbal, Ihtisham Bukhari, Hanwei Jiang, Asim Ali, Liangwen Zhong, Tao Li, Suixing Fan, Beibei Zhang, Jianing Gao, Yang Li, Nazish Jabeen, Teka Khan, Manan Khan, Muhammad Zubair, Qiaomei Hao, Hui Fang, Jun Huang, Mahmoud Huleihel, Jiahao Sha, Tej K. Pandita, Yuanwei Zhang, Qinghua Shi
Software Mentions: 1
Published: over 7 years ago

10.1186/s12711-020-00587-x

Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)
Cited by: 8
Author(s): Hanne Dvergedal, Thomas Nelson Harvey, Yang Jin, Jørgen Ødegård, Lars Grønvold, Simen Rød Sandve, Dag Inge Våge, Thomas Moen, G. Klemetsdal
Software Mentions: 1
Published: almost 6 years ago

10.1534/genetics.116.197376

Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function
Cited by: 11
Author(s): Tai‐Di Chen, Maxime Rotival, Ling-Yin Chiu, Marta Bagnati, Jeong‐Hun Ko, Prashant K. Srivastava, Enrico Petretto, Charles D. Pusey, Ping-Chin Lai, Timothy J. Aitman, H. Terence Cook, Jacques Behmoaras
Software Mentions: 1
Published: about 9 years ago

10.1534/genetics.119.302493

Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies
Cited by: 28
Author(s): Ana Catalán, Adriana D. Briscoe, Sebastian Höhna
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.gdata.2014.10.016

Transcriptional ontogeny of first trimester human fetal and placental mesenchymal stem cells: Gestational age versus niche
Cited by: 5
Author(s): Jennifer Ryan, Nicholas Matigian, Rebecca A. Pelekanos, Samuel Jesuadian, Christine A. Wells, Nicholas M. Fisk
Software Mentions: 1
Published: over 11 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: almost 7 years ago

10.1186/gb-2005-6-11-r94

Cited by: 155
Author(s): Bregje Wertheim, Alex R. Kraaijeveld, Eugene F. Schuster, Eric Blanc, Meirion Hopkins, Scott D. Pletcher, Michael R. Strand, Linda Partridge, H. C. J. Godfray
Software Mentions: 1
Published: over 21 years ago

10.1186/1471-2164-7-266

Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray™
Cited by: 14
Author(s): Carole L. Yauk, Andrew Williams, Sherri E. Boucher, Lynn Berndt, Gu Zhou, Jiangxia Zheng, Andrea Rowan-Carroll, Hongyan Dong, Iain B. Lambert, George R. Douglas, Craig L.J. Parfett
Software Mentions: 1
Published: almost 20 years ago

10.1186/gb-2005-6-7-r56

Cited by: 41
Author(s): Shiri Freilich, Tim Massingham, Sumit Bhattacharyya, Hannes Ponstingl, Paul Lyons, Tom C. Freeman, Janet M. Thornton
Software Mentions: 1
Published: over 21 years ago

10.1186/s12864-015-1342-6

The recent escalation in strength of pyrethroid resistance in Anopheles coluzzi in West Africa is linked to increased expression of multiple gene families
Cited by: 80
Author(s): Hyacinthe K. Toé, N’Falé Sagnon, Roch K. Dabiré, Hilary Ranson, Christopher M. Jones
Software Mentions: 1
Published: over 11 years ago

10.1186/gb-2006-7-3-r26

Cited by: 40
Author(s): Colin C. Pritchard, David A. Coil, Sarah Hawley, Li Hsu, Peter S. Nelson
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-6-r46

Cited by: 39
Author(s): Emma Laing, Vassilis Mersinias, Colin P. Smith, Simon J. Hubbard
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-12-r114

Cited by: 56
Author(s): Hanni Willenbrock, Carsten Friis, Agnieszka Sierakowska Juncker, David W. Ussery
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-9-r84

Cited by: 140
Author(s): Katleen De Preter, Jo Vandesompele, Pierre Heimann, Nurten Yigit, Siv Beckman, Alexander Schramm, Angelika Eggert, Raymond L. Stallings, Yves Benoît, Marleen Renard, Anne De Paepe, Geneviève Laureys, Sven Påhlman, Franki Speleman
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-10-r99

Cited by: 78
Author(s): Anders F. Andersson, Magnus Lundgren, Stefan Eriksson, Magnus Rosenlund, Rolf Bernander, Peter Nilsson
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-10-r89

Cited by: 25
Author(s): Shiri Freilich, Tim Massingham, Eric Blanc, Leon Goldovsky, Janet M. Thornton
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-11-r107

Cited by: 211
Author(s): Birgitte Regenberg, Thomas Grotkjær, Ole Winther, Anders Fausbøll, Mats Åkesson, Christoffer Bro, Lars Kai Hansen, Søren Brunak, Jens Nielsen
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2007-8-5-r74

Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies
Cited by: 23
Author(s): Björn Nilsson, Petra Håkansson, Mikael Johansson, Sven Nelander, Thoas Fioretos
Software Mentions: 1
Published: over 19 years ago

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: over 19 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962