bioconductor: ArrayExpress | Projects

10.3389/fonc.2019.01515

CXCL1 as an Unfavorable Prognosis Factor Negatively Regulated by DACH1 in Non-small Cell Lung Cancer
Cited by: 24
Author(s): Shengnan Yu, Ming Yi, Lei Xu, Shuang Qin, An‐Ping Li, Kongming Wu
Software Mentions: 1
Published: about 6 years ago

10.3389/fonc.2017.00332

Human Epididymis Protein 4 Promotes Events Associated with Metastatic Ovarian Cancer via Regulation of the Extracelluar Matrix
Cited by: 19
Author(s): Jennifer Ribeiro, Hilary Gaudet, Mehreen Ali Khan, Christoph Schorl, Nicole James, M. Oliver, Paul DiSilvestro, Richard G. Moore, Naohiro Yano
Software Mentions: 1
Published: about 8 years ago

10.3389/fonc.2019.00026

EYA2 Correlates With Clinico-Pathological Features of Breast Cancer, Promotes Tumor Proliferation, and Predicts Poor Survival
Cited by: 16
Author(s): Hanxiao Xu, Yanmei Jiao, Ming Yi, Wei Zhao, Zeyu Wu
Software Mentions: 1
Published: about 7 years ago

10.3389/fonc.2021.605884

Exosomal LncRNA LBX1-AS1 Derived From RBPJ Overexpressed-Macrophages Inhibits Oral Squamous Cell Carcinoma Progress via miR-182-5p/FOXO3
Cited by: 17
Author(s): Yilong Ai, Haigang Wei, Si-Pei Wu, Zhe Tang, Xia Li, Chen Zou
Software Mentions: 1
Published: almost 5 years ago

10.3389/fonc.2020.00044

Clinical Significance of Circulating miR-1273g-3p and miR-122-5p in Pancreatic Cancer
Cited by: 19
Author(s): Tommaso Mazza, Domenica Gioffreda, Andrea Fontana, Tommaso Biagini, Massimo Carella, Orazio Palumbo, Evaristo Maiello, Francesca Bazzocchi, Angelo Andriulli, Francesca Tavano
Software Mentions: 1
Published: about 6 years ago

10.3389/fonc.2020.00068

Comprehensive Review of Web Servers and Bioinformatics Tools for Cancer Prognosis Analysis
Cited by: 70
Author(s): Hong Zheng, Guosen Zhang, Lu Zhang, Qiang Wang, Huimin Li, Yali Han, Longxiang Xie, Zhongyi Yan, Yongqiang Li, Yang An, H. Dong, Wan Zhu, Xiangqian Guo
Software Mentions: 1
Published: about 6 years ago

10.3389/fonc.2019.00145

Spheroid-Induced Epithelial-Mesenchymal Transition Provokes Global Alterations of Breast Cancer Lipidome: A Multi-Layered Omics Analysis
Cited by: 29
Author(s): Yun Pyo Kang, Jung-ho Yoon, Nguyen Phuoc Long, Gi‐Bang Koo, Hyunjin Noh, Seung-Jae Oh, Sae Bom Lee, Hyung Min Kim, Ji Yeon Hong, Wonjun Lee, Seul Ji Lee, Soon‐Sun Hong, Sung Won Kwon, You‐Sun Kim
Software Mentions: 1
Published: almost 7 years ago

10.3389/fphar.2018.00847

UBE2C Is a Potential Biomarker of Intestinal-Type Gastric Cancer With Chromosomal Instability
Cited by: 43
Author(s): Jun Zhang, Xinyu Liu, Guanzhen Yu, Lei Liu, Jiejun Wang, Xiaoyu Chen, Yuhai Bian, Yuan Ji, Xiaoyan Zhou, Yinan Chen, Jun Ji, Zhen Xiang, Li Guo, Jing‐Yuan Fang, Yihong Sun, Hui Cao, Zhenggang Zhu, Yingyan Yu
Software Mentions: 1
Published: over 7 years ago

10.3389/fphar.2017.00563

Transcriptome Profiling in Systems Vascular Medicine
Cited by: 22
Author(s): Suowen Xu
Software Mentions: 1
Published: over 8 years ago

10.3389/fphar.2020.00533

Cyclooxygenase 2-Regulated Genes an Alternative Avenue to the Development of New Therapeutic Drugs for Colorectal Cancer
Cited by: 17
Author(s): Alicia M. Hidalgo-Estévez, Konstantinos Stamatakis, Marta Jiménez-Martínez, Ricardo López‐Pérez, Manuel Fresno
Software Mentions: 1
Published: almost 6 years ago

10.3389/fphys.2018.00937

Blood Gene Expression and Vascular Function Biomarkers in Professional Saturation Diving
Cited by: 15
Author(s): Fatima Zohra Kiboub, Andreas Møllerløkken, Astrid Hjelde, Arnar Flatberg, Øyvind Loennechen, Ingrid Eftedal
Software Mentions: 1
Published: over 7 years ago

10.3389/fphys.2019.00474

Mitochondrial Adaptations in Elderly and Young Men Skeletal Muscle Following 2 Weeks of Bed Rest and Rehabilitation
Cited by: 30
Author(s): Alessia Buso, Marina Comelli, Raffaella Picco, Miriam Isola, Benedetta Magnesa, Rado Pišot, Jörn Rittweger, Desy Salvadego, Boštjan Šimunič, Bruno Grassi, Irene Mavelli
Software Mentions: 1
Published: almost 7 years ago

10.3389/fpls.2021.640324

Identification and Characterization of Perennial Ryegrass (Lolium perenne) Vernalization Genes
Cited by: 2
Author(s): Rowan P. Herridge, * Samarth, Lynette Brownfield, Richard C. Macknight
Software Mentions: 1
Published: almost 5 years ago

10.3389/fpls.2020.00753

Light Regulation of Chlorophyll and Glycoalkaloid Biosynthesis During Tuber Greening of Potato S. tuberosum
Cited by: 12
Author(s): Haruko Okamoto, Laurence J. M. Ducreux, J. William Allwood, Pete E. Hedley, Alison J. Wright, Vidyanath Gururajan, Matthew J. Terry, Mark A. Taylor
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2016.01836

An LRR/Malectin Receptor-Like Kinase Mediates Resistance to Non-adapted and Adapted Powdery Mildew Fungi in Barley and Wheat
Cited by: 39
Author(s): Jeyaraman Rajaraman, Dimitar Douchkov, Goetz Hensel, Francesca L. Stefanato, Anna Gordon, Nelzo C. Ereful, Octav Caldararu, Andrei-José Petrescu, Jochen Kumlehn, Lesley A. Boyd, Patrick Schweizer
Software Mentions: 1
Published: about 9 years ago

10.3389/fpls.2017.00445

Altered Expression of Genes Implicated in Xylan Biosynthesis Affects Penetration Resistance against Powdery Mildew
Cited by: 22
Author(s): Jamil Chowdhury, Stefanie Lück, Jeyaraman Rajaraman, Dimitar Douchkov, Neil J. Shirley, Julian G. Schwerdt, Patrick Schweizer, Geoffrey B. Fincher, Rachel A. Burton, Alan Little
Software Mentions: 1
Published: almost 9 years ago

10.3389/fpls.2017.02158

Biology in the Dry Seed: Transcriptome Changes Associated with Dry Seed Dormancy and Dormancy Loss in the Arabidopsis GA-Insensitive sleepy1-2 Mutant
Cited by: 25
Author(s): Sven K. Nelson, Tohru Ariizumi, Camille M. Steber
Software Mentions: 1
Published: about 8 years ago

10.3389/fpls.2020.00098

BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L.
Cited by: 15
Author(s): Sungho Lee, Tak H. Lee, Sunmo Yang, Insuk Lee
Software Mentions: 1
Published: almost 6 years ago

10.3389/fpls.2016.00903

Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach
Cited by: 11
Author(s): Jun Li, Patrick Xuechun Zhao
Software Mentions: 1
Published: over 9 years ago

10.3389/fpls.2012.00294

Reverse Engineering: A Key Component of Systems Biology to Unravel Global Abiotic Stress Cross-Talk
Cited by: 34
Author(s): Swetlana Friedel, Björn Usadel, Nicolaus von Wirén, Nese Sreenivasulu
Software Mentions: 1
Published: about 14 years ago

10.3389/fpls.2019.00315

ABA-Induced Vegetative Diaspore Formation in Physcomitrella patens
Cited by: 27
Author(s): Muhammad Arif, Manuel Hiß, Marta Tomek, Hauke Busch, Rabea Meyberg, Stefanie Tintelnot, Ralf Reski, Stefan A. Rensing, Wolfgang Frank
Software Mentions: 1
Published: almost 7 years ago

10.1534/g3.117.300225

A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes
Cited by: 30
Author(s): Jean-Clément Mars, Marianne Sabourin-Felix, Michel G. Tremblay, Tom Moss
Software Mentions: 1
Published: about 8 years ago

10.3390/genes5030726

Enterococcus faecalis Infection and Reactive Oxygen Species Down-Regulates the miR-17-92 Cluster in Gastric Adenocarcinoma Cell Culture
Cited by: 22
Author(s): Jesper A.B. Strickertsson, Lene Juel Rasmussen, Lennart Friis‐Hansen
Software Mentions: 1
Published: over 11 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: over 7 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: almost 7 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: about 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: over 5 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: over 8 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: over 6 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: about 11 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: about 21 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: about 21 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: about 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: about 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: about 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: about 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: about 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: about 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: about 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: about 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: about 19 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/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/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/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/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/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

10.1186/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/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/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/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

10.1186/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/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/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

10.1016/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

10.1172/jci.insight.143643

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

10.1128/JB.00473-13

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

10.1186/jbiol54

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

10.1074/jbc.M114.598300

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

10.1186/2041-1480-1-S1-S1

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

10.1186/2041-1480-5-25

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

10.1186/2041-1480-5-37

CLO: The cell line ontology
Cited by: 84
Author(s): Sirarat Sarntivijai, Yuling Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew Brush, Melissa Haendel, Jie Zheng, Christian J. Stoeckert, Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He
Software Mentions: 1
Published: about 12 years ago

10.7150/jca.29293

Clinical Significance of microRNA-196b-5p in Hepatocellular Carcinoma and its Potential Molecular Mechanism
Cited by: 11
Author(s): Lu Zhang, Bin Luo, Yi‐Wu Dang, Rong‐Quan He, Zhigang Peng, Gang Chen, Zhaoyong Feng
Software Mentions: 1
Published: about 7 years ago

10.7150/jca.34693

Distinct Roles of VEGFA and ANGPT2 in Lung Adenocarcinoma and Squamous Cell Carcinoma
Cited by: 20
Author(s): Shuang Qin, Ming Yi, Dechao Jiao, An‐Ping Li, Zeyu Wu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-021-87599-9

Chemotherapy confers a conserved secondary tolerance to EGFR inhibition via AXL-mediated signaling bypass
Cited by: 4
Author(s): Mark Borris D. Aldonza, Roben Delos Reyes, Young Seo Kim, Jayoung Ku, Ana Melisa Barsallo, Ji Young Hong, Sang Kook Lee, Han Suk Ryu, Yong Keun Park, Je Yoel Cho, Yoosik Kim
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-021-88504-0

Disentangling age-dependent DNA methylation: deterministic, stochastic, and nonlinear
Cited by: 14
Author(s): O. S. Vershinina, Maria Giulia Bacalini, Alexey Zaikin, Claudio Franceschi, Mikhail Ivanchenko
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-021-88803-6

Transcriptomic phases of periodontitis lesions using the nonhuman primate model
Cited by: 12
Author(s): Jeffrey L. Ebersole, Radhakrishnan Nagarajan, Sreenatha Kirakodu, Octavio A. González
Software Mentions: 1
Published: almost 5 years ago

10.3390/s140100532

Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays
Cited by: 11
Author(s): Roman Jaksik, Michał Marczyk, Joanna Polańska, Joanna Rzeszowska-Wolny
Software Mentions: 1
Published: about 12 years ago

10.1186/2193-1801-2-386

HER-2 gene amplification in human breast cancer without concurrent HER-2 over-expression
Cited by: 21
Author(s): Shiuh Wen Luoh, Betsy Ramsey, Amy Hanlon Newell, Megan L. Troxell, Zhi Hu, Koei Chin, Paul T. Spellman, Susan B. Olson, Edward J. Keenan
Software Mentions: 1
Published: over 12 years ago

10.4056/sigs.4851102

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records
Cited by: 35
Author(s): Scott Federhen, Karen Clark, Tanya Barrett, Helen Parkinson, James Ostell, Yuichi Kodama, Jun Mashima, Yasukazu Nakamura, Guy Cochrane, Ilene Karsch-Mizrachi
Software Mentions: 1
Published: about 12 years ago

10.1186/scrt192

Profiling of transcriptional and epigenetic changes during directed endothelial differentiation of human embryonic stem cells identifies FOXA2 as a marker of early mesoderm commitment
Cited by: 13
Author(s): Lynsey Howard, Ruth M. Mackenzie, Nikolay A. Pchelintsev, Tony McBryan, John McClure, Martin W. McBride, Nicole M. Kane, Peter D. Adams, Graeme Milligan, Andrew H. Baker
Software Mentions: 1
Published: almost 13 years ago

10.1186/scrt60

Gene expression changes with differentiation of cord blood stem cells to respiratory epithelial cells: a preliminary observation
Cited by: 5
Author(s): Michael Berger, Sharon R. Minnerath, Sheryl Adams, Barbara M. Tigges, Stacey Sprague, David H. McKenna
Software Mentions: 1
Published: about 15 years ago

10.1186/scrt127

A comparison of the efficacy of transplantation of bone marrow-derived mesenchymal stem cells and unrestricted somatic stem cells on outcome after acute myocardial infarction
Cited by: 21
Author(s): Aidan Flynn, Xizhe Chen, Enda O’Connell, Timothy O’Brien
Software Mentions: 1
Published: over 13 years ago

10.1002/stem.2652

Common and Distinctive Functions of the Hippo Effectors Taz and Yap in Skeletal Muscle Stem Cell Function
Cited by: 82
Author(s): Congshan Sun, Vanessa D. de Mello, Abdalla D. Mohamed, Huascar Pedro Ortuste Quiroga, Amaya García-Muñoz, Abdullah Al Bloshi, Annie Tremblay, Alex von Kriegsheim, Elaina Susan Renata Collie-Duguid, Neil Vargesson, David Matallanas, Henning Wackerhage, Peter S. Zammit
Software Mentions: 1
Published: over 8 years ago

10.1155/2017/1478606

From Blood to Lesioned Brain: An In Vitro Study on Migration Mechanisms of Human Nasal Olfactory Stem Cells
Cited by: 16
Author(s): Stéphane Girard, Isabelle Virard, Emmanuelle Lacassagne, Jean-Michel Paumier, Hanae Lahlou, Françoise Jabès, Yves Molino, Delphine Stephan, Kévin Baranger, Maya Belghazi, Arnaud Devèze, Michel Khrestchatisky, Emmanuel Nivet, François S. Roman, François Féron
Software Mentions: 1
Published: about 9 years ago

10.7150/thno.42480

Esophageal, gastric and colorectal cancers: Looking beyond classical serological biomarkers towards glycoproteomics-assisted precision oncology
Cited by: 34
Author(s): Elisabete Fernandes, Janine Sores, Sofia Cotton, Andreia Peixoto, Dylan Ferreira, Rui Freitas, Celso A. Reis, Lúcio Lara Santos, José Alexandre Ferreira
Software Mentions: 1
Published: about 6 years ago

10.1136/thoraxjnl-2019-213200

Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1
Cited by: 14
Author(s): C. A. Brandsma, Victor Guryev, Wim Timens, Ana Ciconelle, Dirkje S. Postma, Rainer Bischoff, Martin Johansson, Ekaterina S. Ovchinnikova, Johan Malm, György Markó-Varga, Thomas E. Fehniger, Maarten van den Berge, Péter Horvatovich
Software Mentions: 1
Published: about 6 years ago

10.1016/j.tranon.2021.101132

ViBiBa: Virtual BioBanking for the DETECT multicenter trial program - decentralized storage and processing
Cited by: 0
Author(s): Hannah Asperger, Jan-Philipp Cieslik, Barbara Alberter, Cäcilia Köstler, Bernhard Polzer, Volkmar Müller, Klaus Pantel, Sabine Riethdorf, André Koch, Andreas D. Hartkopf, Lisa Wiesmüller, Wolfgang Janni, Fabienne Schochter, A Franken, Dieter Niederacher, Tanja Fehm, Hans Neubauer
Software Mentions: 1
Published: over 4 years ago

10.1016/j.trecan.2020.10.011

Expanding and Remixing the Metadata Landscape
Cited by: 5
Author(s): Ariel A. Hippen, Casey S. Greene
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.tube.2012.12.003

Adenylylation of mycobacterial Glnk (PII) protein is induced by nitrogen limitation
Cited by: 11
Author(s): Katrina Williams, Mark H. Bennett, Geraint Barton, Victoria A Jenkins, Brian D. Robertson
Software Mentions: 1
Published: almost 13 years ago

10.1016/j.tube.2013.05.004

Overexpression of the Rv0805 phosphodiesterase elicits a cAMP-independent transcriptional response
Cited by: 12
Author(s): Nishad Matange, Debbie M. Hunt, Roger S. Buxton, Sandhya S. Visweswariah
Software Mentions: 1
Published: over 12 years ago

10.1016/j.tube.2013.05.005

Characterisation of the Mycobacterium tuberculosis alternative sigma factor SigG: Its operon and regulon
Cited by: 14
Author(s): Alison Gaudion, Lisa F. Dawson, E. A. Davis, Katherine Smollett
Software Mentions: 1
Published: over 12 years ago

10.4274/tjh.2015.0145

Expression Profiles of the Individual Genes Corresponding to the Genes Generated by Cytotoxicity Experiments with Bortezomib in Multiple Myeloma
Cited by: 3
Author(s): Mehdi Ghasemi, Semih Alpsoy, Seyhan Türk, Ümi̇t Yavuz Malkan, Şükrü Atakan, İbrahim C. Haznedaroğlu, Gülsen Güneş, Mehmet Gündüz, Burak Yılmaz, Sezgin Etgül, Seda Aydın, Tuncay Aslan, Nilgün Sayınalp, Salih Aksu, Halûk Demiroğlu, Osman Özcebe, Yahya Büyükaşık, Hakan Göker
Software Mentions: 1
Published: about 9 years ago

10.1128/mBio.01334-14

Mechanisms Underlying the Exquisite Sensitivity of Candida albicans to Combinatorial Cationic and Oxidative Stress That Enhances the Potent Fungicidal Activity of Phagocytes
Cited by: 63
Author(s): Despoina Kaloriti, Martin Jacobsen, Zhikang Yin, Miranda Patterson, Anna Tillmann, Deborah A. Smith, Emily A. Cook, Tao You, Melissa Grimm, Iryna Bohovych, Celso Grebogi, Brahm H. Segal, Neil A. R. Gow, Ken Haynes, Janet Quinn, Alistair J. P. Brown
Software Mentions: 1
Published: over 11 years ago

10.1128/mBio.00430-16

The Acinetobacter baumannii Two-Component System AdeRS Regulates Genes Required for Multidrug Efflux, Biofilm Formation, and Virulence in a Strain-Specific Manner
Cited by: 95
Author(s): Grace E. Richmond, Laura P. Evans, Michael Anderson, Matthew E. Wand, Laura C. Bonney, Alasdair Ivens, Kim Lee Chua, Mark A. Webber, J. Mark Sutton, Marnie L. Peterson, Laura J. V. Piddock
Software Mentions: 1
Published: almost 10 years ago

10.1128/mBio.00642-16

DamX Controls Reversible Cell Morphology Switching in Uropathogenic Escherichia coli
Cited by: 43
Author(s): Surabhi Khandige, Cecilie Antoinette Asferg, Karina Juhl Rasmussen, Martin Jakob Larsen, Martin Overgaard, Thomas Emil Andersen, Jakob Møller‐Jensen
Software Mentions: 1
Published: over 9 years ago

10.1128/mBio.00968-17

Lack of AcrB Efflux Function Confers Loss of Virulence on Salmonella enterica Serovar Typhimurium
Cited by: 92
Author(s): Xuan Wang-Kan, Jessica M A Blair, Barbara Chirullo, Jonathan W. Betts, Roberto M. La Ragione, Alasdair Ivens, Vito Ricci, Timothy J. Opperman, Laura J. V. Piddock
Software Mentions: 1
Published: over 8 years ago

10.1128/mBio.00109-21

Metabolomics Reveal Potential Natural Substrates of AcrB in Escherichia coli and Salmonella enterica Serovar Typhimurium
Cited by: 14
Author(s): Xuan Wang-Kan, Giovanny Rodrı́guez-Blanco, Andrew D. Southam, Catherine Winder, Warwick B. Dunn, Alasdair Ivens, Laura J. V. Piddock
Software Mentions: 1
Published: almost 5 years ago

10.1186/s40246-020-00269-1

Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals
Cited by: 4
Author(s): Andreanna Burman, Rolando García-Milián, Shannon Whirledge
Software Mentions: 1
Published: over 5 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962