bioconductor: ArrayExpress | Projects

10.1186/1471-2407-12-426

Stress associated gene expression in blood cells is related to outcome in radiotherapy treated head and neck cancer patients
Cited by: 5
Author(s): Siv Kjølsrud Bøhn, Kjell Magne Russnes, Amrit Kaur Sakhi, Magne Thoresen, Matthew T. G. Holden, Jan Øivind Moskaug, Mari Myhrstad, Ole Kristoffer Olstad, Sigbjørn Smeland, Rune Blomhoff
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2407-11-450

Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
Cited by: 30
Author(s): Stefan Enroth, Alvaro Rada-Iglesisas, Robin Andersson, Ola Wallerman, Alkwin Wanders, Lars Påhlman, Jan Komorowski, Claes Wadelius
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0234299

Yellow sea mediated segregation between North East Asian Dryophytes species
Cited by: 18
Author(s): Amaël Borzée, Kevin R. Messenger, Shinhyeok Chae, Desiree Andersen, Jordy Groffen, Ye Inn Kim, Junghwa An, Siti N. Othman, Kyongsin Ri, Tu Yong Nam, Yoonhyuk Bae, Jin Ren, Jia Tang Li, Ming‐Feng Chuang, Yoonjung Yi, Yucheol Shin, Taejoon Kwon, Yikweon Jang, Mi Sook Min
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-015-0510-7

Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia
Cited by: 12
Author(s): Xinan Yang, Meiyi Li, Bin Wang, Wei Zhu, Aurelie Desgardin, Kenan Onel, Jill de Jong, Jianjun Chen, Luonan Chen, John M. Cunningham
Software Mentions: 3
Published: about 11 years ago

10.1523/ENEURO.0226-19.2019

Mega-Analysis of Gene Expression in Mouse Models of Alzheimer’s Disease
Cited by: 6
Author(s): Beryl Zhuang, B. Ogan Mancarci, Lilah Toker, Paul Pavlidis
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-10-26

A novel regulatory event-based gene set analysis method for exploring global functional changes in heterogeneous genomic data sets
Cited by: 8
Author(s): Chien Yi Tung, Chih Hung Jen, Ming Hsu, Hsei Wei Wang, Chi Lin
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-11-104

Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements
Cited by: 32
Author(s): Jakub Mieczkowski, Magdalena E. Tyburczy, Michał Dąbrowski, Piotr Pokarowski
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2105-10-138

PCOPGene-Net: Holistic Characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships
Cited by: 4
Author(s): Mario Huerta, Juan Cedano, Darío Yesid Peña Ballesteros, A. Laborda Rodríguez, Enrique Querol
Software Mentions: 3
Published: about 17 years ago

10.1186/s12885-016-2453-4

Context dependent regulatory patterns of the androgen receptor and androgen receptor target genes
Cited by: 26
Author(s): Jan Roger Olsen, Waqas Azeem, Margrete R. Hellem, Kristo Marvyin, Yaping Hua, Yi Qu, Lisha Li, Biaoyang Lin, Xiaoting Ke, Anne Margrete Øyan, Karl H. Kalland
Software Mentions: 3
Published: almost 10 years ago

10.3390/nu13082521

A Convergent Functional Genomics Analysis to Identify Biological Regulators Mediating Effects of Creatine Supplementation
Cited by: 5
Author(s): Diego A. Bonilla, Yurany Moreno, Eric S. Rawson, Diego A. Forero, Jeffrey R. Stout, Chad M. Kerksick, Michael D. Roberts, Richard B. Kreider
Software Mentions: 3
Published: almost 5 years ago

10.3390/microarrays5030023

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories
Cited by: 9
Author(s): Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms21082818

Identification of the Key Molecular Drivers of Phosphorus Utilization Based on Host miRNA-mRNA and Gut Microbiome Interactions
Cited by: 14
Author(s): Siriluck Ponsuksili, Henry Reyer, Frieder Hadlich, Frank Weber, Nares Trakooljul, Michael Oster, Puntita Siengdee, Eduard Muráni, M. Rodehutscord, Amélia Camarinha‐Silva, Jörn Bennewitz, Klaus Wimmers
Software Mentions: 3
Published: about 6 years ago

10.1186/s13326-016-0079-8

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease
Cited by: 16
Author(s): Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann‐Apitius, Philipp Senger
Software Mentions: 3
Published: almost 10 years ago

10.1186/1471-2105-10-147

Effects of sample size on robustness and prediction accuracy of a prognostic gene signature
Cited by: 79
Author(s): Seon‐Young Kim
Software Mentions: 3
Published: about 17 years ago

10.1074/jbc.M117.784629

The transcription factor Pax6 is required for pancreatic β cell identity, glucose-regulated ATP synthesis, and Ca2+ dynamics in adult mice
Cited by: 48
Author(s): Ryan K. Mitchell, Marie‐Sophie Nguyen‐Tu, Pauline Chabosseau, Rebecca Callingham, Timothy J. Pullen, Rebecca Cheung, Isabelle Leclerc, David J. Hodson, Guy A. Rutter
Software Mentions: 3
Published: about 9 years ago

10.1074/jbc.RA119.010302

Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription
Cited by: 51
Author(s): Leonie Kollenstart, Anton J.L. de Groot, George M.C. Janssen, Xue Cheng, Kees Vreeken, Fabrizio Martino, Jacques Côté, Peter A. van Veelen, Haico van Attikum
Software Mentions: 3
Published: over 6 years ago

10.1186/2041-1480-2-S1-S1

Biomedical semantics in the Semantic Web
Cited by: 12
Author(s): Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano, M. Scott Marshall
Software Mentions: 3
Published: over 15 years ago

10.1155/2020/5943014

Bioinformatic Identification of Neuroblastoma Microenvironment-Associated Biomarkers with Prognostic Value
Cited by: 4
Author(s): Yi Wang, Huan Luo, Jing Cao, Chi Ma
Software Mentions: 3
Published: almost 6 years ago

10.1093/ajcn/nqz012

Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention—results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial
Cited by: 61
Author(s): Μαρία Τράκα, Antonietta Melchini, Jack Coode‐Bate, Omar Al Kadhi, Shikha Saha, Marianne Defernez, Perla Troncoso‐Rey, Helen Kibblewhite, Carmel M. O’Neill, Federico Bernuzzi, Laura Mythen, Jackie C. Hughes, Paul W. Needs, J. Dainty, George M. Savva, Robert Mills, Richard Y. Ball, Christopher S. Cooper, Richard Mithen
Software Mentions: 3
Published: about 7 years ago

10.1186/jbiol53

Dosage compensation is less effective in birds than in mammals
Cited by: 300
Author(s): Yuichiro Itoh, Esther Melamed, Xia Yang, Kathy Kampf, Susanna Wang, Nadir Yehya, Atila van Nas, Kirstin Replogle, Mark Band, David F. Clayton, Eric E. Schadt, Aldons J. Lusis, Arthur P. Arnold
Software Mentions: 3
Published: over 19 years ago

10.1186/1471-2164-10-419

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation
Cited by: 32
Author(s): Sergei A. Manakov, Seth G. N. Grant, Anton J. Enright
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2164-7-228

Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts
Cited by: 26
Author(s): Claudia Mabel Terenti Romero, David DeShazer, Tamara Feldblyum, Jacques Ravel, Donald E. Woods, Heenam Stanley Kim, Yan Yu, Catherine M. Ronning, William C. Nierman
Software Mentions: 3
Published: almost 20 years ago

10.1074/jbc.M114.634816

Early Growth Response Genes 2 and 3 Regulate the Expression of Bcl6 and Differentiation of T Follicular Helper Cells
Cited by: 26
Author(s): Ane Ogbe, Tizong Miao, Alistair L. J. Symonds, Becky Omodho, Randeep Singh, Punamdip Bhullar, Suling Li, Ping Wang
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.isci.2021.102848

Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana
Cited by: 10
Author(s): Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Antonia Angelopoulou, C.-L. Jen, William Duddy, Γεράσιμος Δάρας, Polydefkis Hatzopoulos, David Westhead, Ioannis Michalopoulos
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0229467

Discovery of antitumor lectins from rainforest tree root transcriptomes
Cited by: 3
Author(s): Atip Lawanprasert, Caitlin A. Guinan, Erica A. Langford, Carly E. Hawkins, Janna N. Sloand, Howard W. Fescemyer, Matthew R. Aronson, Jacob A. Halle, James H. Marden, Scott H. Medina
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pntd.0005559

MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni
Cited by: 32
Author(s): Anna V. Protasio, Stijn van Dongen, Julie Collins, Leonor Quintais, Diogo M Ribeiro, Florian Sessler, Martin Hunt, Gabriel Rinaldi, James J. Collins, Anton J. Enright, Matthew Berriman
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pntd.0008059

Exposure of Anopheles mosquitoes to trypanosomes reduces reproductive fitness and enhances susceptibility to Plasmodium
Cited by: 10
Author(s): Constentin Dieme, Natalia Marta Zmarlak, Emma Brito-Fravallo, Christelle Travaillé, Adrien Pain, Floriane Cherrier, Corinne Genève, Estefanía Calvo-Álvarez, Michelle M. Riehle, Kenneth D. Vernick, Brice Rotureau, Christian Mitri
Software Mentions: 3
Published: over 6 years ago

10.1002/1878-0261.12522

PARP1 expression in soft tissue sarcomas is a poor‐prognosis factor and a new potential therapeutic target
Cited by: 15
Author(s): François Bertucci, Pascal Finetti, Audrey Monneur, Delphine Perrot, Christine Chevreau, Axel Le Cesne, Jean‐Yves Blay, Olivier Mir, Daniel Birnbaum
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-14-514

Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data
Cited by: 15
Author(s): Leandro Hermida, Carine Poussin, Michael Stadler, Sylvain Gubian, Alain Sewer, Dimos Gaidatzis, Hans-Rudolf Hotz, Florian Martin, Vincenzo Belcastro, Stéphane Cano, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 3
Published: over 13 years ago

10.1186/s13027-021-00357-4

Identification of key genes in hepatitis B associated hepatocellular carcinoma based on WGCNA
Cited by: 6
Author(s): Chang Liu, Qinghai Dai, Qian Ding, Min Wei, Xiaohong Kong
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0223341

Genome wide DNA methylation profiling identifies specific epigenetic features in high-risk cutaneous squamous cell carcinoma
Cited by: 29
Author(s): David Hervás‐Marín, Faatiemah Higgins, O. Sanmartín, José Antonio Löpez‐Guerrero, M. Carmen Bañó, J. Carlos Igual, Inma Quilis, Juan Sandoval
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-10-420

Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation
Cited by: 13
Author(s): Tamara Aid-Pavlidis, Pavlos Pavlidis, Tõnis Timmusk
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2180-8-109

Dictyostelium transcriptional responses to Pseudomonas aeruginosa: common and specific effects from PAO1 and PA14 strains
Cited by: 40
Author(s): Sergio Carilla-Latorre, Javier Calvo‐Garrido, Gareth Bloomfield, Jason Skelton, Robert R. Kay, Alasdair Ivens, José Luis Martínez, Ricardo Escalante
Software Mentions: 3
Published: almost 18 years ago

10.1371/journal.pgen.1003067

CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function
Cited by: 102
Author(s): Jacy L. Wagnon, Michael Briese, Wenzhi Sun, Connie L. Mahaffey, Tomaž Curk, Gregor Rot, Jernej Ule, Wayne N. Frankel
Software Mentions: 3
Published: over 13 years ago

10.1172/jci.insight.97011

Peripheral tissues reprogram CD8+ T cells for pathogenicity during graft-versus-host disease
Cited by: 19
Author(s): Pedro M. Sousa, Séverine Cire, Thomas Conlan, Laura Jardine, Claire Tkacz, Ivana R. Ferrer, C Lomas, Sophie Ward, Heather C. West, Simone Dertschnig, Sven Blobner, Terry K. Means, Stephen Henderson, Daniel H. Kaplan, Matthew Collin, Vincent Plagnol, Clare Bennett, Ronjon Chakraverty
Software Mentions: 3
Published: over 8 years ago

10.1016/j.molmet.2020.101015

The type 2 diabetes gene product STARD10 is a phosphoinositide-binding protein that controls insulin secretory granule biogenesis
Cited by: 20
Author(s): Gaëlle Carrat, Elizabeth Haythorne, Alejandra Tomás, Leena Haataja, Andreas Müller, Peter Arvan, Alexandra Piunti, Kaiying Cheng, Mutian Huang, Timothy J. Pullen, Eleni Georgiadou, Theodoros Stylianides, Nur Shabrina Amirruddin, Victoria Salem, Walter Distaso, Andrew Cakebread, Kate J Heesom, Philip A. Lewis, David J. Hodson, Linford J.B. Briant, Annie Fung, Richard B. Sessions, Fabien Alpy, Alice Pik‐Shan Kong, Peter I. Benke, Federico Torta, Adrian Kee Keong Teo, Isabelle Leclerc, Michele Solimena, Dale B. Wigley, Guy A. Rutter
Software Mentions: 3
Published: over 5 years ago

10.1093/gbe/evw059

Genetic Evidence of Human Adaptation to a Cooked Diet
Cited by: 26
Author(s): Rachel N. Carmody, Michael Dannemann, Adrian W. Briggs, Birgit Nickel, Emily Groopman, Richard W. Wrangham, Janet Kelso
Software Mentions: 3
Published: over 10 years ago

10.1111/mec.13362

Genomewide transcriptional signatures of migratory flight activity in a globally invasive insect pest
Cited by: 60
Author(s): Christopher M. Jones, Alexie Papanicolaou, George K. Mironidis, John Vontas, Yihua Yang, Koeng Su Lim, John G. Oakeshott, Chris Bass, Jason W. Chapman
Software Mentions: 3
Published: over 10 years ago

10.1016/j.mce.2020.111007

Hypoxia regulates GR function through multiple mechanisms involving microRNAs 103 and 107
Cited by: 11
Author(s): Nan Yang, Andrew Berry, Carolin M Sauer, Matthew Baxter, Ian J. Donaldson, Karen Forbes, Rachelle Donn, Laura Matthews, David Ray
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-11-73

BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
Cited by: 11
Author(s): Mark Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini
Software Mentions: 3
Published: over 16 years ago

10.1186/s13059-021-02323-0

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication
Cited by: 46
Author(s): Gareth Benjamin Gillard, Lars Grønvold, Line Lieblein Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F. Koop, Eric B. Rondeau, Manu Kumar Gundappa, J. Mendoza, Daniel J. Macqueen, Rori V. Rohlfs, Simen Rød Sandve, Torgeir R. Hvidsten
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-13-85

DIPSBC - data integration platform for systems biology collaborations
Cited by: 13
Author(s): Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, K. Schellander, Hans Lehrach, Bodo Lange, Ralf Herwig
Software Mentions: 3
Published: about 14 years ago

10.1186/1471-2164-10-98

SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data
Cited by: 26
Author(s): Adriane Menßen, Götz Edinger, Joachim R. Grün, Ulrike Haase, Ria Baumgrass, Andreas Grützkau, Andreas Radbruch, G.-R. Burmester, Thomas Häupl
Software Mentions: 3
Published: over 17 years ago

10.1186/s12943-020-01155-z

Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme
Cited by: 57
Author(s): Mathilde Cheray, Amandine Etcheverry, Camille Jacques, Romain Pacaud, Gwenola Bougras-Cartron, Marc Aubry, Florent Denoual, Pierre Peterlongo, Arulraj Nadaradjane, Joséphine Briand, Farida Akcha, Dominique Heymann, François M. Vallette, Jean Mosser, Benjamin Ory, Pierre-François Cartron
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-127

Genetic analysis of the Trichuris muris-induced model of colitis reveals QTL overlap and a novel gene cluster for establishing colonic inflammation
Cited by: 20
Author(s): Scott Levison, Paul Fisher, Jenny Hankinson, Leo Zeef, Steve Eyre, William Ollier, John McLaughlin, Andy Brass, Richard K. Grencis, Joanne L. Pennock
Software Mentions: 3
Published: over 13 years ago

10.1186/s12943-016-0554-y

Systems analysis identifies miR-29b regulation of invasiveness in melanoma
Cited by: 18
Author(s): Miles C. Andrews, Joseph Cursons, Daniel Hurley, Matthew Anaka, Jonathan Cebon, Andreas Behren, Edmund J. Crampin
Software Mentions: 3
Published: over 9 years ago

10.1186/s13073-016-0335-7

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq
Cited by: 104
Author(s): David Redmond, Asaf Poran, Olivier Elemento
Software Mentions: 3
Published: almost 10 years ago

10.1172/jci.insight.148652

CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking
Cited by: 1
Author(s): Tábata Takahashi França, Ashraf Al-Sbiei, Ghada Bashir, Yassir A. Mohamed, Ranieri Coelho Salgado, Lucila Akune Barreiros, Sarah Maria da Silva Napoleão, Cristiane Seganfredo Weber, Janáira Fernandes Severo Ferreira, Carolina Sánchez Aranda, Carolina Prando, Mayra B. de Barros Dorna, Igor Jurišica, Maria J. Fernández-Cabezudo, Hans D. Ochs, Antônio Condino‐Neto, Basel K. al-Ramadi, Otávio Cabral-Marques
Software Mentions: 3
Published: almost 5 years ago

10.18632/oncotarget.7248

MicroRNA-34a promotes genomic instability by a broad suppression of genome maintenance mechanisms downstream of the oncogene KSHV-vGPCR
Cited by: 14
Author(s): Claudia J. Krause, Oliver Popp, Nanthakumar Thirunarayanan, Gunnar Dittmar, Martin Lipp, Gerd Müller
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2105-15-S14-S4

linkedISA: semantic representation of ISA-Tab experimental metadata
Cited by: 55
Author(s): Alejandra N. González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pgen.1005250

Genetic Regulation of Bone Metabolism in the Chicken: Similarities and Differences to Mammalian Systems
Cited by: 41
Author(s): Martin Johnsson, Kenneth B. Jonsson, Leif C. Andersson, Per Jensen, I. A. Wright
Software Mentions: 3
Published: about 11 years ago

10.1186/gb-2013-14-10-r110

Modeling precision treatment of breast cancer
Cited by: 263
Author(s): Anneleen Daemen, Obi L. Griffith, Laura M. Heiser, Nicholas J. Wang, Oana Enache, Zachary Sanborn, François Pépin, Steffen Durinck, James E. Korkola, Malachi Griffith, Joe S. Hur, Nam Huh, Jongsuk Chung, Leslie Cope, Mary Jo Fackler, Christopher B. Umbricht, Saraswati Sukumar, Pankaj Seth, Vikas P. Sukhatme, Lakshmi R. Jakkula, Yiling Lu, Gordon B. Mills, Raymond J. Cho, Eric A. Collisson, Laura J. van’t Veer, Paul T. Spellman, Joe W. Gray
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pgen.1009679

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
Cited by: 16
Author(s): Enrique Audain, Anna Wilsdon, Jeroen Breckpot, Jose M. G. Izarzugaza, Tomas Fitzgerald, Anne‐Karin Kahlert, Alejandro Sifrim, Florian Wünnemann, Yasset Perez‐Riverol, Hashim Abdul‐Khaliq, Mads Bak, Anne S. Bassett, Woodrow Benson, Felix Berger, Ingo Daehnert, Koenraad Devriendt, Sven Dittrich, Piers E.F. Daubeney, Vidu Garg, Karl Hackmann, Kirstin Hoff, Philipp Hofmann, Gregor Dombrowsky, Thomas Pickardt, Ulrike Bauer, Bernard Keavney, Sabine Klaassen, Hans‐Heiner Kramer, Christian R. Marshall, Dianna M. Milewicz, Scott A. LeMaire, Joseph S. Coselli, Michael E. Mitchell, Aoy Tomita‐Mitchell, Siddharth K. Prakash, Karl Stamm, Alexandre F.R. Stewart, Candice K. Silversides, Reiner Siebert, Brigitte Stiller, Jill A. Rosenfeld, Inga Vater, Alex V. Postma, Almuth Caliebe, J. David Brook, Grégor Andelfinger, Matthew E. Hurles, Bernard Thienpont, Lars Allan Larsen, Marc‐Phillip Hitz
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1006179

Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes
Cited by: 83
Author(s): Kyuha Choi, Carsten Reinhard, Heïdi Serra, Piotr A Ziolkowski, Charles J Underwood, Xiaohui Zhao, Thomas J. Hardcastle, Nataliya E. Yelina, Catherine Griffin, Matthew A. Jackson, Christine Mézard, Gil McVean, Gregory P. Copenhaver, Ian Henderson
Software Mentions: 3
Published: almost 10 years ago

10.1186/gb-2012-13-4-r30

Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium
Cited by: 49
Author(s): Simen M. Kristoffersen, Chad P. Haase, M. Ryan Weil, Karla D. Passalacqua, Faheem Niazi, Stephen Hutchison, Brian Desany, Anne Brit Kolstø, Nicolas J. Tourasse, Timothy D. Read, Ole Andreas Økstad
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pgen.1000574

Alternative Splicing of NURF301 Generates Distinct NURF Chromatin Remodeling Complexes with Altered Modified Histone Binding Specificities
Cited by: 53
Author(s): So Yeon Kwon, Hua Xiao, Carl Wu, Paul Badenhorst
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2105-7-286

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology
Cited by: 53
Author(s): Bruz Marzolf, Eric W. Deutsch, Patrick Moss, D. S. Campbell, Michael H. Johnson, Timothy Galitski
Software Mentions: 3
Published: about 20 years ago

10.1371/journal.pgen.1003868

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection
Cited by: 71
Author(s): Nicholas J. Croucher, Andrea M. Mitchell, Katherine A. Gould, Donald Inverarity, Lars Barquist, Theresa Feltwell, María Fookes, Simon R. Harris, Janina Dordel, Susannah J. Salter, Sarah Browall, Helena Žemličková, Julian Parkhill, Staffan Normark, Birgitta Henriques‐Normark, Jason Hinds, Tim Mitchell, Stephen D. Bentley
Software Mentions: 3
Published: over 12 years ago

10.1186/gb-2010-11-8-r80

Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development
Cited by: 29
Author(s): Noëlle Billon, Raivo Kolde, Jüri Reimand, Miguel Caetano Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian Dani
Software Mentions: 3
Published: over 16 years ago

10.1186/gb-2012-13-4-r31

Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
Cited by: 33
Author(s): Marieke Simonis, Santosh S. Atanur, Sam E.V. Linsen, Victor Guryev, Frans-Paul Ruzius, Laurence Gamé, Nico Lansu, Ewart de Bruijn, Sebastiaan van Heesch, Steven J.M. Jones, Michal Pravenec, Tim Aitman, Edwin Cuppen
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2229-13-147

Grafting with rootstocks induces extensive transcriptional re-programming in the shoot apical meristem of grapevine
Cited by: 79
Author(s): Sarah Jane Cookson, Nathalie Ollat
Software Mentions: 3
Published: over 13 years ago

10.1186/s13059-016-0971-7

Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies
Cited by: 156
Author(s): Björn Bakker, Aaron Taudt, Mirjam E. Belderbos, David Porubský, Diana C.J. Spierings, Tristan de Jong, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Allan Bradley, Eveline S.J.M. de Bont, Anke van den Berg, Victor Guryev, Peter M Lansdorp, Maria Colomé-Tatché, Floris Foijer
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pgen.0030145

Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells
Cited by: 80
Author(s): Marica Grs̆ković, Christina Chaivorapol, Alexandre Gaspar-Maia, Hao Li, Miguel Ramalho-Santos
Software Mentions: 3
Published: almost 19 years ago

10.1007/s12263-014-0439-x

White adipose tissue reference network: a knowledge resource for exploring health-relevant relations
Cited by: 10
Author(s): Thomas Kelder, Georg Summer, Martien P. M. Caspers, Evert M. van Schothorst, Jaap Keijer, Loes P. M. Duivenvoorde, К. Schimrigk, Anja Voigt, Laura Bohnert, Catalina Picó, M. Luisa Bonet, A. Dembińska-Kieć, Małgorzata Malczewska-Malec, Beata Kieć‐Wilk, Josep Maria del Bas, Antoni Caimari, Lluı́s Arola, Marjan van Erk, Ben van Ommen, Marijana Radonjić
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pcbi.1005703

Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
Cited by: 32
Author(s): Lingfei Wang, Tom Michoel
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pcbi.1005157

Fused Regression for Multi-source Gene Regulatory Network Inference
Cited by: 36
Author(s): Kari Y. Lam, Zachary M. Westrick, Christian L. Müller, Lionel Christiaen, Richard Bonneau
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1000311

Developmental Constraints on Vertebrate Genome Evolution
Cited by: 104
Author(s): Julien Roux, Marc Robinson‐Rechavi
Software Mentions: 3
Published: over 17 years ago

10.3389/fbioe.2020.584614

Revisiting the Growth Modulon of Corynebacterium glutamicum Under Glucose Limited Chemostat Conditions
Cited by: 5
Author(s): Michaela Graf, Thorsten Haas, Attila Teleki, André Feith, Martin Cerff, Wolfgang Wiechert, Katharina Nöh, Tobias Busche, Jörn Kalinowski, Ralf Takors
Software Mentions: 3
Published: over 5 years ago

10.3390/metabo11040221

Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling
Cited by: 5
Author(s): Özlem Altay, Cheng Cheng Zhang, Hasan Türkez, Jens Nielsen, Mathias Uhlén, Adil Mardinoğlu
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pcbi.1002568

MC EMiNEM Maps the Interaction Landscape of the Mediator
Cited by: 14
Author(s): Theresa Niederberger, Stefanie Etzold, Michael Lidschreiber, Kerstin Maier, Dietmar E. Martin, Holger Fröhlich, Patrick Cramer, Achim Tresch
Software Mentions: 3
Published: almost 14 years ago

10.1186/gb-2008-9-10-r146

A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection
Cited by: 19
Author(s): Amanda Greenall, Guiyuan Lei, Daniel Swan, Katherine James, Liming Wang, Heiko Peters, Anil Wipat, Darren J. Wilkinson, David Lydall
Software Mentions: 3
Published: over 18 years ago

10.1186/s13059-016-0992-2

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cited by: 330
Author(s): Jonathan Cairns, Paula Freire-Pritchett, Steven W. Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel R. Zerbino, Stefan Schoenfelder, Biola M. Javierre, Cameron S. Osborne, Peter Fraser, Mikhail Spivakov
Software Mentions: 3
Published: almost 10 years ago

10.3390/plants9050591

Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era
Cited by: 20
Author(s): Luca Ambrosino, Chiara Colantuono, Gianfranco Diretto, Alessia Fiore, Maria Luisa Chiusano
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pbio.3001101

Stress and odorant receptor feedback during a critical period after hatching regulates olfactory sensory neuron differentiation in Drosophila
Cited by: 8
Author(s): Shadi Jafari, Johan Henriksson, Hua Yan, Mattias Alenius
Software Mentions: 3
Published: about 5 years ago

10.1002/pld3.123

Identification of gene expression logical invariants in <i>Arabidopsis</i>
Cited by: 8
Author(s): Sonalisa Pandey, Debashis Sahoo
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.103073

MicroRNA-375 exacerbates knee osteoarthritis through repressing chondrocyte autophagy by targeting ATG2B
Cited by: 30
Author(s): Hongxing Li, Zhiling Li, Yigang Pi, Yang Chen, Lin Mei, Yiliao Luo, Jingping Xie, Xinzhan Mao
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-018-5176-x

funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data
Cited by: 5
Author(s): Liis Kolberg, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-494

Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast
Cited by: 2
Author(s): Lucas D. Ward, Junbai Wang, Harmen J. Bussemaker
Software Mentions: 3
Published: almost 12 years ago

10.1098/rstb.2017.0073

Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing
Cited by: 12
Author(s): Clare Pacini, Magdalena J. Koziol
Software Mentions: 3
Published: about 8 years ago

10.7717/peerj.175

Data reuse and the open data citation advantage
Cited by: 358
Author(s): Heather Piwowar
Software Mentions: 3
Published: over 12 years ago

10.1002/cam4.1633

Molecular heterogeneity in human papillomavirus‐dependent and ‐independent vulvar carcinogenesis
Cited by: 16
Author(s): Dorian R.A. Swarts, Quirinus J.M. Voorham, Annina P. van Splunter, Saskia M. Wilting, Daoud Sie, Divera T.M. Pronk, Marc van Beurden, Daniëlle A.M. Heideman, Peter J.F. Snijders, Chris J.L.M. Meijer, Renske D.M. Steenbergen, Maaike Bleeker
Software Mentions: 3
Published: almost 8 years ago

10.1007/s00262-020-02718-1

Immune checkpoint-related serum proteins and genetic variants predict outcomes of localized prostate cancer, a cohort study
Cited by: 35
Author(s): Qinchuan Wang, Yuanqing Ye, Hao Yu, Shu-Hong Lin, Huakang Tu, Dong Liang, David W. Chang, Maosheng Huang, Xifeng Wu
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2105-13-S14-S5

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
Cited by: 12
Author(s): Ivan Merelli, Federica Viti, Luciano Milanesi
Software Mentions: 3
Published: almost 14 years ago

10.12688/f1000research.10960.2

A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification
Cited by: 11
Author(s): Jessica Roelands, Julie Decock, Sabri Boughorbel, Darawan Rinchai, Cristina Maccalli, Michele Ceccarelli, Michael A. Black, Chris Print, Jeff Chou, Scott Presnell, Charlie Quinn, Puthen V. Jithesh, Najeeb Syed, Salha B.J. Al Bader, Shahinaz Bedri, Ena Wang, Francesco M. Marincola, Damien Chaussabel, Peter J.K. Kuppen, Lance D. Miller, Davide Bedognetti, Wouter Hendrickx
Software Mentions: 3
Published: over 8 years ago

10.1186/s12935-021-01932-w

SNRPD1 confers diagnostic and therapeutic values on breast cancers through cell cycle regulation
Cited by: 7
Author(s): Xiaofeng Dai, Lihui Yu, Xiao Chen, Jianying Zhang
Software Mentions: 3
Published: about 5 years ago

10.1111/j.1525-142X.2010.00400.x

Molecular signaling in zebrafish development and the vertebrate phylotypic period
Cited by: 37
Author(s): Aurélie Comte, Julien Roux, Marc Robinson‐Rechavi
Software Mentions: 3
Published: over 16 years ago

10.1186/s12859-020-3364-6

Detection of suspicious interactions of spiking covariates in methylation data
Cited by: 0
Author(s): Miriam Sieg, Gregor Richter, Arne S. Schäefer, Jochen Kruppa
Software Mentions: 3
Published: over 6 years ago

10.1186/2047-783X-18-44

RETRACTED ARTICLE: Gene expression profiling analysis of hepatocellular carcinoma
Cited by: 4
Author(s): Deyong Kong, Heming Chen, Weiqun Chen, Shuiyi Liu, Hui Wang, Tangwei Wu, Hongda Lu, Qing Kong, Xiaodong Huang, Zhongxin Lu
Software Mentions: 3
Published: over 12 years ago

10.12688/f1000research.9611.3

Revisiting inconsistency in large pharmacogenomic studies
Cited by: 42
Author(s): Zhaleh Safikhani, Петр Смирнов, Mark Freeman, Nehmé El-Hachem, Adrian She, Rene Quevedo, Anna Goldenberg, Nicolai J. Birkbak, Christos Hatzis, Leming Shi, Andrew H. Beck, Hugo J.W.L. Aerts, John Quackenbush, Benjamin Haibe‐Kains
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2164-11-27

Genomics Portals: integrative web-platform for mining genomics data
Cited by: 13
Author(s): Kaustubh Shinde, Mukta Phatak, Johannes M. Freudenberg, Jing Chen, Qian Li, Joshi K Vineet, Zhen Hu, Krishnendu Ghosh, Jarosław Meller, Mario Medvedovic
Software Mentions: 3
Published: over 16 years ago

10.1093/bib/bby051

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
Cited by: 103
Author(s): Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura E. Taggart, Huiru Zheng, Eileen E. Parkes, Jaine K. Blayney
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-019-5748-4

Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets
Cited by: 1
Author(s): Dirkjan Schokker, Ina Hulsegge, H. Woelders, Johanna M.J. Rebel
Software Mentions: 3
Published: about 7 years ago

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: over 14 years ago

10.1186/bcr2926

Identification of germline alterations of the mad homology 2 domain of SMAD3 and SMAD4 from the Ontario site of the breast cancer family registry (CFR)
Cited by: 17
Author(s): Eric Tram, Irada Ibrahim‐Zada, Laurent Briollais, Julia A. Knight, Irene L. Andrulis, Hilmi Özçelik
Software Mentions: 3
Published: almost 15 years ago

10.1186/s12859-019-2912-4

TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Cited by: 2
Author(s): Salvatore Alaimo, Annalisa Di Maria, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.0040014

Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules
Cited by: 481
Author(s): Todd P. Michael, Todd C. Mockler, Ghislaı̀n Breton, Connor McEntee, Amanda Byer, Jonathan D. Trout, Samuel P. Hazen, Rongkun Shen, Henry D. Priest, Christopher Sullivan, Scott A. Givan, Marcelo J. Yanovsky, Fangxin Hong, Steve A. Kay, Joanne Chory
Software Mentions: 3
Published: over 18 years ago

10.18632/oncotarget.5876

KIAA0101 is associated with human renal cell carcinoma proliferation and migration induced by erythropoietin
Cited by: 27
Author(s): Shengjun Fan, Xin Li, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 3
Published: over 10 years ago

10.1111/jipb.13026

Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores
Cited by: 14
Author(s): M. Estrella Santamaría, Alejandro Dorado García, Ana Arnáiz, Irene Rosa‐Diaz, Gara Romero‐Hernandez, Isabel Dı́az, Manuel Martínez
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-23514-z

Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level
Cited by: 22
Author(s): Vicky L. Hunt, Akinori Hino, Akemi Yoshida, Taisei Kikuchi
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0251233

Mapping Rora expression in resting and activated CD4+ T cells
Cited by: 23
Author(s): Liora Haim-Vilmovsky, Johan Henriksson, Jennifer Walker, Zhichao Miao, Eviatar Natan, Gozde Kar, Simon Clare, Jillian L. Barlow, Evelina Charidemou, Lira Mamanova, Xi Chen, Valentina Proserpio, Jhuma Pramanik, Steven Woodhouse, Anna V. Protasio, Mirjana Efremova, Julian L. Griffin, Matt Berriman, Gordon Dougan, Jasmin Fisher, John C. Marioni, Andrew N. J. McKenzie, Sarah A. Teichmann
Software Mentions: 3
Published: about 5 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962