bioconductor: ArrayExpress | Projects

10.1186/1752-0509-2-58

Short time-series microarray analysis: Methods and challenges
Cited by: 43
Author(s): Xuewei Wang, Ming Tsang Wu, Lirong Zheng, Christina Chan
Software Mentions: 1
Published: almost 18 years ago

ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work
Cited by: 69
Author(s): Gregor Warsow, Boris Greber, Steffi Falk, Clemens Harder, Marcin Siatkowski, Sandra Schordan, Anup Som, Nicole Endlich, Hans R. Schöler, Dirk Repsilber, Karlhans Endlich, Georg Fuellen
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0008939

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

10.1371/journal.pone.0020063

Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
Cited by: 72
Author(s): Masayuki Murata, Hiroko Fujimoto, Kaori Nishimura, Kannikar Charoensuk, Hiroshi Nagamitsu, Satish Raina, Tomoyuki Kosaka, Taku Oshima, Nagahisa Ogasawara, Mamoru Yamada
Software Mentions: 1
Published: about 15 years ago

10.1186/1752-0509-4-62

Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis
Cited by: 51
Author(s): Elizabeth Allen, Annick Moing, Timothy M. D. Ebbels, Mickaël Maucourt, A. D. Tomos, Dominique Rolin, Mark A. Hooks
Software Mentions: 1
Published: about 16 years ago

10.1186/1752-0509-5-125

A Systems Biology Strategy for Predicting Similarities and Differences of Drug Effects: Evidence for Drug-specific Modulation of Inflammation in Atherosclerosis
Cited by: 15
Author(s): Robert Kleemann, Svetlana Bureeva, Ally Perlina, Jim Kaput, Lars Verschuren, Peter Y. Wielinga, Eva Hurt-Camejo, Yuri Nikolsky, Ben van Ommen, Teake Kooistra
Software Mentions: 1
Published: over 15 years ago

10.1186/1752-0509-4-86

Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems
Cited by: 7
Author(s): Michał Dąbrowski, Norbert Dojer, Małgorzata Zawadzka, Jakub Mieczkowski, Bożena Kamińska
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0109978

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

10.1186/1752-0509-3-86

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network
Cited by: 39
Author(s): Osnat Atias, Benny Chor, Daniel Chamovitz
Software Mentions: 1
Published: almost 17 years ago

10.1186/1752-0509-9-S2-S3

KPP: KEGG Pathway Painter
Cited by: 18
Author(s): Ganiraju C. Manyam, Aybike Birerdinc, Ancha Baranova
Software Mentions: 1
Published: about 11 years ago

10.1186/1752-0509-5-68

Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus
Cited by: 37
Author(s): Ian M. Overton, Shirley A. Graham, Katherine A. Gould, Jason Hinds, Catherine H. Botting, Sally L. Shirran, Geoffrey J. Barton, Peter J. Coote
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2105-15-53

Eureka-DMA: an easy-to-operate graphical user interface for fast comprehensive investigation and analysis of DNA microarray data
Cited by: 1
Author(s): Sagi Abelson
Software Mentions: 1
Published: over 12 years ago

10.1186/s12918-018-0579-5

New perspectives: systems medicine in cardiovascular disease
Cited by: 13
Author(s): Frank Krämer, Steffen Just, Tanja Zeller
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2105-8-400

CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
Cited by: 45
Author(s): Gert Sclep, Joke Allemeersch, Robin Liechti, Björn De Meyer, Jim Beynon, Rishikesh P. Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin Kuiper, Pierre Hilson
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0053478

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

10.1371/journal.pone.0109745

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

10.1038/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: about 5 years ago

10.1186/1756-0500-4-78

Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2)
Cited by: 22
Author(s): Richard A. Lewis, Sanjay Shahi, Emma Laing, Giselda Bucca, Georgios Efthimiou, Michael E. Bushell, Colin P. Smith
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0181231

CSmiRTar: Condition-Specific microRNA targets database
Cited by: 20
Author(s): Wei Wu, Bor Wen Tu, Tsung Te Chen, Shang Wei Hou, Joseph T. Tseng
Software Mentions: 1
Published: almost 9 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: about 5 years ago

10.1186/1756-0500-7-148

Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays
Cited by: 0
Author(s): Liliana Sofia Mendonça Cardoso, Cláudia Elvas Suissas, Mário Ramirez, Marília Antunes, Francisco Pinto
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0054717

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

10.1371/journal.pone.0089318

Global Meta-Analysis of Transcriptomics Studies
Cited by: 11
Author(s): José Caldas, Susana Vinga
Software Mentions: 1
Published: over 12 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: about 5 years ago

10.1371/journal.pone.0037646

Stromal Genes Add Prognostic Information to Proliferation and Histoclinical Markers: A Basis for the Next Generation of Breast Cancer Gene Signatures
Cited by: 17
Author(s): Dwain Mefford, Joel Mefford
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0084428

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

10.1371/journal.pone.0067802

Insulin Receptor-Overexpressing β-Cells Ameliorate Hyperglycemia in Diabetic Rats through Wnt Signaling Activation
Cited by: 14
Author(s): Mi‐Hyun Kim, Seung-Hyun Hong, Moon‐Kyu Lee
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0006576

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

10.1186/1471-2105-11-389

GeneBrowser 2: an application to explore and identify common biological traits in a set of genes
Cited by: 6
Author(s): Joel P. Arrais, João Fernandes, João E. Pereira, José Luís Oliveira
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0006554

Genome-Wide Profile of Pleural Mesothelioma versus Parietal and Visceral Pleura: The Emerging Gene Portrait of the Mesothelioma Phenotype
Cited by: 63
Author(s): Oluf Dimitri Røe, Endre Anderssen, E. Helge, Caroline Hild Pettersen, Anja Olsen, Helmut Sandeck, Rune Haaverstad, Steinar Lundgren, Erik G. Larsson
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12859-015-0870-z

Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment
Cited by: 30
Author(s): Roman Hornung, Anne‐Laure Boulesteix, David Causeur
Software Mentions: 1
Published: over 10 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: over 12 years ago

10.1186/1471-2105-9-379

MiMiR – an integrated platform for microarray data sharing, mining and analysis
Cited by: 18
Author(s): Christopher Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L. Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Timothy J. Aitman, Laurence Gamé
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-8-233

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data
Cited by: 46
Author(s): Miika J. Ahdesmäki, Harri Lähdesmäki, Andrew Y. Gracey, llya Shmulevich, Olli Yli‐Harja
Software Mentions: 1
Published: almost 19 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: almost 13 years ago

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

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

10.1371/journal.pone.0218934

Ticagrelor induces paraoxonase-1 (PON1) and better protects hypercholesterolemic mice against atherosclerosis compared to clopidogrel
Cited by: 10
Author(s): Hasseri Halim, Decha Pinkaew, Preedakorn Chunhacha, Patuma Sinthujaroen, Perumal Thiagarajan, Kenichi Fujise
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0065034

Cholecalciferol (Vitamin D3) Improves Myelination and Recovery after Nerve Injury
Cited by: 102
Author(s): Jean-François Chabas, Delphine Stephan, Tanguy Marqueste, Stéphane García, Marie‐Noëlle Lavaut, Catherine Nguyen, R. Legré, Michel Khrestchatisky, Patrick Decherchi, François Féron
Software Mentions: 1
Published: about 13 years ago

10.1186/1756-0500-5-401

Critical COPD respiratory illness is linked to increased transcriptomic activity of neutrophil proteases genes
Cited by: 33
Author(s): Raquel Almansa, Lorenzo Socías, Monica Sanchez-Garcia, Ignacio Martín‐Loeches, Milagros Del Olmo, David Andaluz‐Ojeda, Felipe Bobillo, Lucía Rico, Agueda Herrero, Vicente Roig, C Alicia San-Jose, Sara Rosich, Julia Barbado, Carlos Disdier, Raúl Ortíz de Lejarazu, Maria C Gallegos, Victoria Fernández, Jesús F. Bermejo-Martín
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12859-020-03868-w

DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization
Cited by: 12
Author(s): Jin-Xing Liu, Mingming Gao, Zhen Cui, Ying-Lian Gao, Feng Li
Software Mentions: 1
Published: about 5 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: over 12 years ago

10.1371/journal.pone.0030269

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

10.1186/1756-0500-3-16

Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
Cited by: 2
Author(s): Michael Gruenberger, Rudi Alberts, Damian Smedley, Morris A. Swertz, Paul N. Schofield, Klaus Schughart
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2466-13-63

Altered microRNA expression profile during epithelial wound repair in bronchial epithelial cells
Cited by: 15
Author(s): Aleksandra Szczepankiewicz, Peter M. Lackie, John W. Holloway
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0016419

Genetic Variation in Spatio-Temporal Confined USA300 Community-Associated MRSA Isolates: A Shift from Clonal Dispersion to Genetic Evolution?
Cited by: 15
Author(s): Neeltje Carpaij, Rob J. L. Willems, Thomas W. Rice, Robert A. Weinstein, Jason Hinds, Adam A. Witney, Jodi A. Lindsay, Marc J. M. Bonten, Ad C. Fluit
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-021-04213-5

Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria
Cited by: 5
Author(s): Ian Leifer, Mishael Sánchez-Pérez, Cecilia Ishida, Hernán A. Makse
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-244X-7-46

Inflammation-related genes up-regulated in schizophrenia brains
Cited by: 245
Author(s): Peter Saetre, Lina Emilsson, Elin Axelsson, Johan Kreuger, Eva Lindholm, Elena Jazin
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pone.0184317

Differential expression of tetraspanin superfamily members in dendritic cell subsets
Cited by: 19
Author(s): Malou Zuidscherwoude, Kuntal Worah, Alie van der Schaaf, Sonja I. Buschow, Annemiek B. van Spriel
Software Mentions: 1
Published: almost 9 years ago

10.1186/1753-6561-5-S4-S4

Jejunal gene expression patterns correlate with severity of systemic infection in chicken
Cited by: 4
Author(s): Dirkjan Schokker, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0021463

E-Cadherin Acts as a Regulator of Transcripts Associated with a Wide Range of Cellular Processes in Mouse Embryonic Stem Cells
Cited by: 29
Author(s): Francesca Soncin, Lisa Mohamet, Sarah Ritson, Kate Hawkins, Nicoletta Bobola, Leo Zeef, Catherine L.R. Merry, Christopher M. Ward
Software Mentions: 1
Published: almost 15 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: about 13 years ago

10.1371/journal.pone.0023944

A Stratified Transcriptomics Analysis of Polygenic Fat and Lean Mouse Adipose Tissues Identifies Novel Candidate Obesity Genes
Cited by: 45
Author(s): Nicholas M. Morton, Yvonne B. Nelson, Zoi Michailidou, Emma M. Di Rollo, Lynne Ramage, Patrick W. F. Hadoke, Jonathan R. Seckl, L. Bünger, Simon Horvat, Christopher J. Kenyon, Donald R. Dunbar
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2229-10-77

Large impact of the apoplast on somatic embryogenesis in Cyclamen persicum offers possibilities for improved developmental control in vitro
Cited by: 30
Author(s): Claudia Hoenemann, Sandra Richardt, Katja Krüger, Andreas Zimmer, Annette Hohe, Stefan A. Rensing
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2229-8-76

Articulation of three core metabolic processes in Arabidopsis: Fatty acid biosynthesis, leucine catabolism and starch metabolism
Cited by: 70
Author(s): Wieslawa I. Mentzen, Peng Jisheng, Nick Ransom, Basil J. Nikolau, Eve Syrkin Wurtele
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2229-12-74

Effects of yeast trehalose-6-phosphate synthase 1 on gene expression and carbohydrate contents of potato leaves under drought stress conditions
Cited by: 57
Author(s): Mihály Kondrák, Ferenc Marincs, Ferenc Antal, Zsófia Juhász, Zsófia Bánfalvi
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0075290

Coordinated and Interactive Expression of Genes of Lipid Metabolism and Inflammation in Adipose Tissue and Liver during Metabolic Overload
Cited by: 22
Author(s): Wen Miin Liang, Giulia Tonini, Petra Mulder, Thomas Kelder, Marjan van Erk, Anita M. van den Hoek, Rob Mariman, Peter Y. Wielinga, Michela Baccini, Teake Kooistra, Annibale Biggeri, Robert Kleemann
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2229-7-56

Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis
Cited by: 151
Author(s): Xiaoping Tan, Blake C. Meyers, Alexander Kozik, Marilyn A. L. West, Michèle Morgante, Dina A. St. Clair, Andrew F. Bent, Richard W. Michelmore
Software Mentions: 1
Published: over 18 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: over 15 years ago

10.1371/journal.pone.0041683

Identification of Novel Markers of Mouse Fetal Ovary Development
Cited by: 43
Author(s): Huijun Chen, Jodie Palmer, Rathi D Thiagarajan, Marcel E. Dinger, Emmanuelle Lesieur, Hansheng Sheng Chiu, Alexandra Schulz, Cassy M. Spiller, Sean M. Grimmond, Melissa H. Little, Peter Koopman, Dagmar Wilhelm
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0138889

Adipose Tissue Dysfunction and Altered Systemic Amino Acid Metabolism Are Associated with Non-Alcoholic Fatty Liver Disease
Cited by: 63
Author(s): Sulin Cheng, Reija Autio, Ronald Borra, Xiaowei Ojanen, Leiting Xu, Timo Törmäkangas, Markku Alén
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0009894

Functional Clustering of Periodic Transcriptional Profiles through ARMA(p,q)
Cited by: 32
Author(s): Ning Li, Timothy L. McMurry, Arthur Berg, Zhong Wang, Scott A. Berceli, Rongling Wu
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0020938

COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia
Cited by: 24
Author(s): Kristof Engelen, Qiang Fu, Pieter Meysman, Aminael Sánchez-Rodríguez, Riet De Smet, Kim Lemmens, Ana Carolina Fierro, Kathleen Marchal
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0006759

Butyrate-Induced Transcriptional Changes in Human Colonic Mucosa
Cited by: 143
Author(s): Steven Vanhoutvin, Freddy J. Troost, Henrike M. Hamer, Patrick Lindsey, Ger H. Koek, Daisy Jonkers, Andrea Kodde, Koen Venema, Robert Jan Brummer
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0075882

microRNA-22 Promotes Heart Failure through Coordinate Suppression of PPAR/ERR-Nuclear Hormone Receptor Transcription
Cited by: 72
Author(s): Priyatansh Gurha, Tiannan Wang, Ashley H. Larimore, Yassine Sassi, Cei Abreu‐Goodger, Maricela Ramirez, Anilkumar K. Reddy, Stefan Engelhardt, George E. Taffet, Xander H.T. Wehrens, Mark L. Entman, Antony Rodríguez
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2229-9-19

TRUNCATULIX - a data warehouse for the legume community
Cited by: 11
Author(s): Kolja Henckel, Kai J. Runte, Thomas Bekel, Michael Dondrup, Tobias Jakobi, H. Küster, Alexander Goesmann
Software Mentions: 1
Published: over 17 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: almost 14 years ago

10.1371/journal.pone.0006880

Nuclear Receptor SHP Activates miR-206 Expression via a Cascade Dual Inhibitory Mechanism
Cited by: 44
Author(s): Guisheng Song, Lili Wang
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0040900

Distinct Genes Related to Drug Response Identified in ER Positive and ER Negative Breast Cancer Cell Lines
Cited by: 18
Author(s): Kui Shen, Shara D. Rice, David A. Gingrich, Dakun Wang, Mi Zhang, Chunqiao Tian, Zhenyu Ding, Stacey L. Brower, Paul R. Ervin, Michael J. Gabrin, George C. Tseng, Nan Song
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0028552

The Discovery of Putative Urine Markers for the Specific Detection of Prostate Tumor by Integrative Mining of Public Genomic Profiles
Cited by: 15
Author(s): Min Chen, Kai Wang, Liang Zhang, Cheng Li, Yongliang Yang
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2229-9-15

Validation of candidate genes putatively associated with resistance to SCMV and MDMV in maize (Zea mays L.) by expression profiling
Cited by: 53
Author(s): Anna Użarowska, Giuseppe Dionisio, Barbara Sarholz, Hans‐Peter Piepho, Ming Xu, Christina Ingvardsen, G. Wenzel, Thomas Lübberstedt
Software Mentions: 1
Published: over 17 years ago

10.7554/eLife.66865

Metabolic flexibility via mitochondrial BCAA carrier SLC25A44 is required for optimal fever
Cited by: 10
Author(s): Takeshi Yoneshiro, Nobuhiko Kataoka, Jacquelyn M. Walejko, Kenji Ikeda, Zachary D. Brown, Momoko Yoneshiro, Scott B. Crown, Tsuyoshi Osawa, Juro Sakai, Robert W. McGarrah, Phillip J. White, Kazuhiro Nakamura, Shingo Kajimura
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2229-10-202

Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.)
Cited by: 59
Author(s): Pete E. Hedley, Joanne Russell, Linzi Jorgensen, Sandra Gordon, Jenny Morris, Christine A. Hackett, Linda Cardle, Rex Brennan
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0018796

Stroma Regulates Increased Epithelial Lateral Cell Adhesion in 3D Culture: A Role for Actin/Cadherin Dynamics
Cited by: 31
Author(s): Karen Chambers, Joanna Pearson, Naveed Aziz, Peter O’Toole, David R. Garrod, Shona Lang
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0084187

High Expression of CD109 Antigen Regulates the Phenotype of Cancer Stem-Like Cells/Cancer-Initiating Cells in the Novel Epithelioid Sarcoma Cell Line ESX and Is Related to Poor Prognosis of Soft Tissue Sarcoma
Cited by: 53
Author(s): Makoto Emori, Tomohide Tsukahara, Masaki Murase, Masanobu Kano, Kenji Murata, Akiko Takahashi, Terufumi Kubo, Hiroko Asanuma, Kazuyo Yasuda, Vitaly Kochin, Mitsunori Kaya, Satoshi Nagoya, Jun Nishio, Hiroshi Iwasaki, Tomoko Sonoda, Tadashi Hasegawa, Toshihiko Torigoe, Takuro Wada, Toshihiko Yamashita, Noriyuki Sato
Software Mentions: 1
Published: over 12 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: almost 9 years ago

10.1186/1471-2229-12-204

Expression of geminiviral AC2 RNA silencing suppressor changes sugar and jasmonate responsive gene expression in transgenic tobacco plants
Cited by: 39
Author(s): Arto Soitamo, Balaji Jada, Kirsi Lehto
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2229-12-17

Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source-sink tissues in a segregating potato population
Cited by: 16
Author(s): Bjorn Kloosterman, A. M. Anithakumari, Pierre-Yves Chibon, Marian Oortwijn, Gerard C van der Linden, R.G.F. Visser, Christian W.B. Bachem
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0010692

Skeletal Site-Related Variation in Human Trabecular Bone Transcriptome and Signaling
Cited by: 33
Author(s): Satya S. Varanasi, Ole Kristoffer Olstad, Daniel Swan, P. L. Sanderson, Vigdis T. Gautvik, Sjur Reppe, Roger M. Francis, Kaare M. Gautvik, Harish K. Datta
Software Mentions: 1
Published: about 16 years ago

10.1007/s00401-012-0957-9

Identification of novel pathways involved in the pathogenesis of human adamantinomatous craniopharyngioma
Cited by: 151
Author(s): Cynthia L. Andoniadou, Carles Gaston‐Massuet, Rukmini Reddy, Ralph P. Schneider, María A. Blasco, Paul Le Tissier, Thomas S. Jacques, Larysa Pevny, Mehul Dattani, Juan Pedro Martinez-Barbera
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0100178

Chondroitin Sulfate Proteoglycan CSPG4 as a Novel Hypoxia-Sensitive Marker in Pancreatic Tumors
Cited by: 21
Author(s): Shereen Keleg, Titov Alexandr, Anette Heller, Thomas Giese, Christine Tjaden, Sufian S. Ahmad, Matthias M. Gaida, Andrea S. Bauer, Jens Werner, Nathalia A. Giese
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2229-11-39

Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
Cited by: 45
Author(s): Yoshiharu Y. Yamamoto, Yohei Yoshioka, Mitsuro Hyakumachi, Kyonoshin Maruyama, Kazuko Yamaguchi-Shinozaki, Mutsutomo Tokizawa, Hiroyuki Koyama
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2229-14-155

Salicylic acid signaling inhibits apoplastic reactive oxygen species signaling
Cited by: 61
Author(s): Enjun Xu, Mikael Brosché
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0004344

The Staphylococcus aureus Response to Unsaturated Long Chain Free Fatty Acids: Survival Mechanisms and Virulence Implications
Cited by: 157
Author(s): John Kenny, Deborah Ward, Elisabet Josefsson, Ing-Marie Jonsson, Jason Hinds, Huw H. Rees, Jodi A. Lindsay, Andrej Tarkowski, Malcolm J. Horsburgh
Software Mentions: 1
Published: over 17 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: over 9 years ago

10.1371/journal.pone.0089297

Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets
Cited by: 43
Author(s): Alexander Kaever, Manuel Landesfeind, Kirstin Feussner, Burkhard Morgenstern, Ivo Feußner, Peter Meinicke
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2229-10-108

Expression profiling of Crambe abyssinicaunder arsenate stress identifies genes and gene networks involved in arsenic metabolism and detoxification
Cited by: 66
Author(s): Bibin Paulose, Suganthi Kandasamy, Om Parkash Dhankher
Software Mentions: 1
Published: about 16 years ago

10.1186/1748-7188-4-5

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data
Cited by: 5
Author(s): Sahely Bhadra, Chiranjib Bhattacharyya, Nagasuma Chandra, I. Saira Mian
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0009426

The Genome of Streptococcus mitis B6 - What Is a Commensal?
Cited by: 105
Author(s): Dalia Denapaite, Reinhold Brückner, Michael Nuhn, Peter Reichmann, Bernhard Henrich, Patrick Maurer, Yvonne Schähle, Peter Selbmann, Wolfgang Zimmermann, R. Wambutt, Regine Hakenbeck
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-12-97

Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms
Cited by: 1
Author(s): Andrew Timothy Milnthorpe, Mikhail Soloviev
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0110288

Integrated Analysis of Microarray Data of Atherosclerotic Plaques: Modulation of the Ubiquitin-Proteasome System
Cited by: 11
Author(s): Zhe Wang, Dong Guo, Bin Yang, Jian Wang, Rong Wang, Xiaowei Wang, Qunye Zhang
Software Mentions: 1
Published: over 11 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: over 6 years ago

10.1371/journal.pone.0031867

Human Cryptochrome-1 Confers Light Independent Biological Activity in Transgenic Drosophila Correlated with Flavin Radical Stability
Cited by: 26
Author(s): Jacqueline Vieira, Alex R. Jones, Antoine Danon, Michiyo Sakuma, Nathalie Hoang, David Robles, Shirley Tait, Derren J. Heyes, Marie Christine Picot, Taishi Yoshii, Charlotte Helfrich‐Förster, Guillaume Soubigou, Jean Yves Coppée, André Klarsfeld, François Rouyer, Nigel S. Scrutton, Margaret Ahmad
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-7-311

Web-based analysis of the mouse transcriptome using Genevestigator
Cited by: 25
Author(s): Oliver Laule, Matthias Hirsch‐Hoffmann, Tomás Hrúz, Wilhelm Gruissem, Philip Zimmermann
Software Mentions: 1
Published: almost 20 years ago

10.1371/journal.pone.0014207

Transcriptional Analysis Implicates Endoplasmic Reticulum Stress in Bovine Spongiform Encephalopathy
Cited by: 24
Author(s): Yue Tang, Wei Xiang, Linda A. Terry, Hans A. Kretzschmar, Otto Windl
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2229-9-28

Differential patterns of reactive oxygen species and antioxidative mechanisms during atrazine injury and sucrose-induced tolerance in Arabidopsis thaliana plantlets
Cited by: 264
Author(s): Fanny Ramel, Cécile Sulmon, Matthieu Bogard, Ivan Couée, Gwenola Gouesbet
Software Mentions: 1
Published: over 17 years ago

10.1186/2050-6511-15-5

Skin sensitizers differentially regulate signaling pathways in MUTZ-3 cells in relation to their individual potency
Cited by: 34
Author(s): Ann-Sofie Albrekt, Henrik Johansson, Anna Börje, Carl Borrebaeck, Malin Lindstedt
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0088089

Phenotypic Modulation of Primary Vascular Smooth Muscle Cells by Short-Term Culture on Micropatterned Substrate
Cited by: 66
Author(s): Sea‐Jin Chang, Sang Yun Song, Jungsul Lee, Jonghee Yoon, Junseong Park, Sungyoung Choi, Je‐Kyun Park, Kyunghee Choi, Chulhee Choi
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0018088

Identification of a Gene Regulatory Network Necessary for the Initiation of Oligodendrocyte Differentiation
Cited by: 90
Author(s): Victoria A. Swiss, Tung Nguyen, Jason C. Dugas, Adiljan Ibrahim, Ben A. Barres, Ioannis P. Androulakis, Patrizia Casaccia
Software Mentions: 1
Published: about 15 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: over 6 years ago

10.1371/journal.pone.0153562

Competence Classification of Cumulus and Granulosa Cell Transcriptome in Embryos Matched by Morphology and Female Age
Cited by: 26
Author(s): Rehannah Borup, Lea Langhoff Thuesen, Claus Yding Andersen, Anders Nyboe-Andersen, Sören Ziebe, Ole Winther, Marie Louise Grøndahl
Software Mentions: 1
Published: about 10 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962