bioconductor: ArrayExpress | Projects

10.1186/1471-2199-8-112

Checkpoint independence of most DNA replication origins in fission yeast
Cited by: 36
Author(s): Katie L Mickle, Sunita Ramanathan, Adam P. Rosebrock, Anna Maria Oliva, Amna Chaudari, Chulee Yompakdee, David Scott, Janet Leatherwood, Joel A. Huberman
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pone.0091334

Transcript Analysis Reveals a Specific HOX Signature Associated with Positional Identity of Human Endothelial Cells
Cited by: 52
Author(s): Mark Toshner, Benjamin J. Dunmore, Eoín McKinney, Mark Southwood, Paola Caruso, Paul D. Upton, John P Waters, Mark L. Ormiston, Jeremy N. Skepper, Gerard B. Nash, Radgonde Amer, Nicholas W. Morrell
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2199-8-119

Checkpoint effects and telomere amplification during DNA re-replication in fission yeast
Cited by: 10
Author(s): Katie L Mickle, Anna Maria Oliva, Joel A. Huberman, Janet Leatherwood
Software Mentions: 1
Published: over 18 years ago

10.1038/srep25975

A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure
Cited by: 24
Author(s): Sayak Mukhopadhyay, Ratan K. Saha, Anbarasi Palanisamy, Madhurima Ghosh, A. Biswas, Saheli Roy, Arijit Pal, Kathakali Sarkar, Sangram Bagh
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0039148

Leukemia Gene Atlas – A Public Platform for Integrative Exploration of Genome-Wide Molecular Data
Cited by: 48
Author(s): Katja Hebestreit, Sören Gröttrup, Daniel Emden, Jannis Veerkamp, Christian Rückert, Hans-Ulrich Klein, Carsten Müller‐Tidow, Martin Dugas
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2199-11-95

Overexpression of miR-128 specifically inhibits the truncated isoform of NTRK3 and upregulates BCL2 in SH-SY5Y neuroblastoma cells
Cited by: 78
Author(s): Monia Guidi, Margarita Muiños‐Gimeno, Birgit Kagerbauer, Eulàlia Martı́, Xavier Estivill, Yolanda Espinosa‐Parrilla
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0010027

ERK1/2 Signaling Dominates Over RhoA Signaling in Regulating Early Changes in RNA Expression Induced by Endothelin-1 in Neonatal Rat Cardiomyocytes
Cited by: 35
Author(s): Andrew Keith Marshall, Oliver Barrett, Timothy E. Cullingford, Achchuthan Shanmugasundram, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2180-7-88

Comparative gene expression profiling in two congenic mouse strains following Bordetella pertussis infection
Cited by: 7
Author(s): Sander Banus, Rob J. Vandebriel, Jeroen L. A. Pennings, Eric R. Gremmer, Piet W. Wester, Henk J. van Kranen, Timo M. Breit, Peter Démant, Frits R. Mooi, Barbara Hoebee, Tjeerd G. Kimman
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pone.0126837

A Ranking-Based Meta-Analysis Reveals Let-7 Family as a Meta-Signature for Grade Classification in Breast Cancer
Cited by: 14
Author(s): Yasemin Öztemur, Tufan Bekmez, Alp Aydos, Işık G. Yuluğ, Birkan Bozkurt, Bala Gür Dedeoğlu
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2180-12-104

The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated
Cited by: 120
Author(s): Alex J. McCarthy, Jodi A. Lindsay
Software Mentions: 1
Published: over 14 years ago

10.1038/srep26747

Intestinal APCs of the endogenous nanomineral pathway fail to express PD-L1 in Crohn’s disease
Cited by: 26
Author(s): Jack Robertson, Carolin Haas, Laetitia Pele, Tom P. Monie, Charles Charalambos, Miles Parkes, Rachel E. Hewitt, Jonathan J. Powell
Software Mentions: 1
Published: about 10 years ago

10.1038/srep27152

Hypoxia induced CCL28 promotes angiogenesis in lung adenocarcinoma by targeting CCR3 on endothelial cells
Cited by: 37
Author(s): Guichun Huang, Leilei Tao, Shihao Shen, Longbang Chen
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0134595

Distinct Responses of Mycobacterium smegmatis to Exposure to Low and High Levels of Hydrogen Peroxide
Cited by: 22
Author(s): Xiaojing Li, Wu Jun, Jiao Han, Yongfei Hu, Kaixia Mi
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2180-13-224

Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions
Cited by: 8
Author(s): Yared H. Kidane, Christopher B. Lawrence, T. M. Murali
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2180-9-246

Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus
Cited by: 7
Author(s): J. F. Yuan, Zhang Sj, Osman Jafer, RA Furlong, OE Chausiaux, Carole A. Sargent, Zhang Gh, Nabeel A. Affara
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0023466

Transcriptome Analysis of Potato Leaves Expressing the Trehalose-6-Phosphate Synthase 1 Gene of Yeast
Cited by: 31
Author(s): Mihály Kondrák, Ferenc Marincs, Balázs Kalapos, Zsófia Juhász, Zsófia Bánfalvi
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0064011

Transcriptional Analysis of Temporal Gene Expression in Germinating Clostridium difficile 630 Endospores
Cited by: 61
Author(s): Marcin Dembek, Richard A. Stabler, Adam A. Witney, Brendan W. Wren, Neil F. Fairweather
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0016192

Global Transcriptional Analysis of Spontaneous Sakacin P-Resistant Mutant Strains of Listeria monocytogenes during Growth on Different Sugars
Cited by: 20
Author(s): Girum Tadesse Tessema, Trond Møretrø, Lars Snipen, Lars Axelsson, Kristine Naterstad
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2180-8-73

Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni
Cited by: 20
Author(s): Sandra Rodin, Anders F. Andersson, Valtteri Wirta, Lena Eriksson, Marianne Ljungström, Britta Björkholm, Hans Lindmark, Lars Engstrand
Software Mentions: 1
Published: over 18 years ago

10.1038/srep28006

Circulating Plasma microRNAs can differentiate Human Sepsis and Systemic Inflammatory Response Syndrome (SIRS)
Cited by: 92
Author(s): Stefano Caserta, Florian Kern, Jonathan Cohen, Stephen Drage, Sarah F. Newbury, Martin J. Llewelyn
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2180-12-212

Insight into the bacterial gut microbiome of the North American moose (Alces alces)
Cited by: 45
Author(s): Suzanne L. Ishaq, André‐Denis G. Wright
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0003563

HFR1 Is Crucial for Transcriptome Regulation in the Cryptochrome 1-Mediated Early Response to Blue Light in Arabidopsis thaliana
Cited by: 20
Author(s): Xiaoning Zhang, Yingjie Wu, John W. Tobias, Brian P. Brunk, Gerald F. Deitzer, Dongmei Li
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0026905

Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis
Cited by: 25
Author(s): Qinghua Xu, Shujuan Ni, Fei Wu, Fang Liu, Xun Ye, Bruno Mougin, Meng Xia, Xiang Du
Software Mentions: 1
Published: almost 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: about 5 years ago

10.1038/srep29201

Antibody-Dependent Enhancement of Dengue Virus Infection in Primary Human Macrophages; Balancing Higher Fusion against Antiviral Responses
Cited by: 95
Author(s): Jacky Flipse, Mayra Diosa-Toro, Tabitha E. Hoornweg, Denise P. I. van de Pol, Silvio Urcuqui-Inchima, Jolanda M. Smit
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0053341

Identification of Gene Clusters Associated with Host Adaptation and Antibiotic Resistance in Chinese Staphylococcus aureus Isolates by Microarray-Based Comparative Genomics
Cited by: 12
Author(s): Henan Li, Chunjiang Zhao, Hongbin Chen, Feifei Zhang, Wenqiang He, Xiaojuan Wang, Qi Wang, Ruifu Yang, Dongsheng Zhou, Hui Wang
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2180-10-106

The HP0256 gene product is involved in motility and cell envelope architecture of Helicobacter pylori
Cited by: 3
Author(s): François P. Douillard, Kevin Ryan, Michael Lane, Delphine L. Caly, Stanley A. Moore, Charles W. Penn, Jason Hinds, Paul W. O’Toole
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0215452

Array expression meta-analysis of cancer stem cell genes identifies upregulation of PODXL especially in DCC low expression meningiomas
Cited by: 4
Author(s): Hans-Juergen Schulten, Deema Hussein
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0039718

Transcriptional Profiling of Serogroup B Neisseria meningitidis Growing in Human Blood: An Approach to Vaccine Antigen Discovery
Cited by: 25
Author(s): Åsa K. Hedman, Mingshi Li, Paul R. Langford, J. Simon Kroll
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0065058

Retinoic Acid-Activated Ndrg1a Represses Wnt/β-catenin Signaling to Allow Xenopus Pancreas, Oesophagus, Stomach, and Duodenum Specification
Cited by: 20
Author(s): Tiejun Zhang, Xiaogang Guo, Yonglong Chen
Software Mentions: 1
Published: about 13 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: over 15 years ago

10.1371/journal.pone.0061262

The Expression of Glyceraldehyde-3-Phosphate Dehydrogenase Associated Cell Cycle (GACC) Genes Correlates with Cancer Stage and Poor Survival in Patients with Solid Tumors
Cited by: 41
Author(s): Dunrui Wang, Daniel R. Moothart, Douglas R. Lowy, Xiaolan Qian
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0006408

Transcriptomic Profiling of Central Nervous System Regions in Three Species of Honey Bee during Dance Communication Behavior
Cited by: 40
Author(s): Moushumi Sen Sarma, Sandra L. Rodriguez-Zas, Feng Hong, Sheng Zhong, Gene E. Robinson
Software Mentions: 1
Published: about 17 years ago

10.1038/srep30778

A novel human-specific splice isoform alters the critical C-terminus of Survival Motor Neuron protein
Cited by: 37
Author(s): Joonbae Seo, Natalia N. Singh, Eric W. Ottesen, Brian M. Lee, Ravindra Singh
Software Mentions: 1
Published: about 10 years ago

10.1186/s12911-021-01634-3

A framework for validating AI in precision medicine: considerations from the European ITFoC consortium
Cited by: 18
Author(s): Rosy Tsopra, Xose M Fernandez-Suarez, Claudio Luchinat, Lilia Alberghina, Hans Lehrach, Marco Vanoni, Felix Dreher, Osman Uğur Sezerman, Marc Cuggia, Marie de Tayrac, Edvīns Miklaševičs, Lucian Mihai Itu, Marius Geantă, Lesley A. Ogilvie, Florence Godey, C. Boldisor, Boris Campillo‐Gimenez, Cosmina Cioroboiu, Costin Florian Ciușdel, Simona M. Coman, Oliver Hijano Cubelos, Alexandru Itu, Bodo Lange, Matthieu Le Gallo, Alexandra Lespagnol, Giancarlo Mauri, H Okan Soykam, Bastien Rance, Paola Turano, Leonardo Tenori, Alessia Vignoli, Christoph Wierling, Nora Benhabilès, Anita Burgun
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12920-017-0293-y

Differential gene expression in disease: a comparison between high-throughput studies and the literature
Cited by: 52
Author(s): Raul Rodriguez‐Esteban, Xiaoyu Jiang
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0063184

Database Citation in Full Text Biomedical Articles
Cited by: 30
Author(s): Şenay Kafkas, Jee-Hyub Kim, Johanna McEntyre
Software Mentions: 1
Published: about 13 years ago

10.1186/s12920-014-0063-z

Integrated differential transcriptome maps of Acute Megakaryoblastic Leukemia (AMKL) in children with or without Down Syndrome (DS)
Cited by: 22
Author(s): Maria Chiara Pelleri, Allison Piovesan, Maria Caracausi, Anna C. Berardi, Lorenza Vitale, Pierluigi Strippoli
Software Mentions: 1
Published: over 11 years ago

10.1186/1755-8794-6-35

Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers
Cited by: 34
Author(s): Adam L. Cohen, Stephen R. Piccolo, Luis Cheng, Rafaella Soldi, Bing Han, W. Evan Johnson, Andrea Bild
Software Mentions: 1
Published: almost 13 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

10.3390/ani10101924

Ovarian Transcriptomic Analysis Reveals Differential Expression Genes Associated with Cell Death Process after Selection for Ovulation Rate in Rabbits
Cited by: 0
Author(s): Marta Serna-García, Rosa Peiró, Eva Serna, M. A. Santacreu
Software Mentions: 1
Published: almost 6 years ago

10.1186/1755-8794-2-18

PrognoScan: a new database for meta-analysis of the prognostic value of genes
Cited by: 698
Author(s): Hideaki Mizuno, Koji Kitada, Katsunori Nakai, Akinori Sarai
Software Mentions: 1
Published: over 17 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

10.1186/1755-8794-2-41

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus
Cited by: 12
Author(s): Yaomin Hu, Pamela J. Kaisaki, Karène Argoud, Steven P. Wilder, Karin J. Wallace, Peng Yeong Woon, Christine Blancher, Lise Tarnow, Per‐Henrik Groop, Samy Hadjadj, Michel Marre, Hans‐Henrik Parving, Martin Farrall, Roger D. Cox, Mark Lathrop, Nathalie Vionnet, Marie-Thérèse Bihoreau, Dominique Guyader
Software Mentions: 1
Published: about 17 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: about 15 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: about 20 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

10.1186/1755-8794-3-5

Insight in modulation of inflammation in response to diclofenac intervention: a human intervention study
Cited by: 34
Author(s): Marjan J. van Erk, Suzan Wopereis, Carina M. Rubingh, T. van Vliet, Elwin Verheij, N.H.P. Cnubben, Theresa L. Pedersen, John W. Newman, Age K. Smilde, J. van der Greef, H. Hendriks, Ben van Ommen
Software Mentions: 1
Published: over 16 years ago

10.1186/1755-8794-2-12

Impaired immune function in Gulf War Illness
Cited by: 71
Author(s): Toni Whistler, Mary A Fletcher, William Lonergan, Xiao Rong Zeng, Jin Mann S. Lin, A. LaPerriere, Suzanne D. Vernon, Nancy G. Klimas
Software Mentions: 1
Published: over 17 years ago

10.1186/1755-8794-1-33

An approach to analyse the specific impact of rapamycin on mRNA-ribosome association
Cited by: 16
Author(s): Raphaël Genolet, Tanguy Araud, Laetitia Maillard, Pascale Jaquier-Gubler, Joseph Curran
Software Mentions: 1
Published: about 18 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: almost 13 years ago

10.1186/1755-8794-2-11

Promoter methylation correlates with reduced NDRG2expression in advanced colon tumour
Cited by: 36
Author(s): Ada Piepoli, Rosa Cotugno, Giuseppe Merla, Annamaria Gentile, Bartolomeo Augello, M. Quitadamo, Antonio Merla, Anna Panza, Massimo Carella, Rosalia Maglietta, A. D’Addabbo, Nicola Ancona, Saverio Fusilli, Francesco Perri, Angelo Andriulli
Software Mentions: 1
Published: over 17 years ago

10.1038/srep33924

Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin
Cited by: 17
Author(s): Magdalena B. Rother, Kristin Jensen, Mirjam van der Burg, Fleur S. van de Bovenkamp, Roel Kroek, Wilfred F. J. van IJcken, Vincent H.J. van der Velden, Tom Cupedo, Ole Kristoffer Olstad, Jacques J. M. van Dongen, Menno C. van Zelm
Software Mentions: 1
Published: almost 10 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: about 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: almost 11 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: over 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: about 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: almost 13 years ago

10.1186/s12920-016-0227-0

A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without
Cited by: 10
Author(s): Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner, Nicki Tiffin
Software Mentions: 1
Published: over 9 years ago

10.1038/srep34730

Novel population of small tumour-initiating stem cells in the ovaries of women with borderline ovarian cancer
Cited by: 40
Author(s): Irma Virant‐Klun, Martin Štimpfel
Software Mentions: 1
Published: almost 10 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: about 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

10.1186/1471-2350-8-36

Cerebellar gene expression profiles of mouse models for Rett syndrome reveal novel MeCP2 targets
Cited by: 110
Author(s): ChaRandle Jordan, Hong Hua Li, Helen H. Kwan, Uta Francke
Software Mentions: 1
Published: about 19 years ago

10.1038/srep34719

Hepatic Deletion of Janus Kinase 2 Counteracts Oxidative Stress in Mice
Cited by: 23
Author(s): Madeleine Themanns, Kristina M. Mueller, Sonja M. Kessler, Nicole Golob-Schwarzl, Thomas Mohr, Doris Kaltenecker, Jérôme Bourgeais, Jamile Paier-Pourani, Katrin Friedbichler, Doris Schneller, Michaela Schlederer, Eva Zebedin-Brandl, Luigi Terracciano, Xiaonan Han, Lukas Kenner, Kay Uwe Wagner, Wolfgang Mikulits, Andrey V. Kozlov, Markus H. Heim, Fabrice Gouilleux, Johannes Haybaeck, Richard Moriggl
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12916-017-0929-y

A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes
Cited by: 40
Author(s): Jean‐Philippe Foy, Louis Bazire, Sandra Ortiz-Cuàran, Sophie Deneuve, Janice Kielbassa, Emilie Thomas, Alain Viari, Alain Puisieux, P. Goudot, Chloé Bertolus, Nicolas Foray, Youlia Kirova, Pierre Verrelle, Pierre Saintigny
Software Mentions: 1
Published: almost 9 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: over 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

10.1155/2018/1270483

Kynurenic Acid Protects against Thioacetamide-Induced Liver Injury in Rats
Cited by: 24
Author(s): Sebastian Marciniak, Artur Wnorowski, Katarzyna Smolińska, Beata Walczyna, Waldemar A. Turski, Tomasz Kocki, Piotr Paluszkiewicz, Jolanta Parada-Turska
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12916-016-0609-3

Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy
Cited by: 45
Author(s): Isobella Honeyborne, Timothy D. McHugh, Iitu Kuittinen, Anna Cichońska, Dimitrios Evangelopoulos, Katharina Ronacher, Paul D. van Helden, Stephen H. Gillespie, Delmiro Fernández-Reyes, Gerhard Walzl, Juho Rousu, Philip D. Butcher, Simon J. Waddell
Software Mentions: 1
Published: over 10 years ago

10.1186/s12879-016-1533-z

The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
Cited by: 13
Author(s): Steven T. Pullan, Jon C. Allnutt, Rebecca Devine, Kim A. Hatch, Rose E. Jeeves, Charlotte L. Hendon-Dunn, Philip Marsh, Joanna Bacon
Software Mentions: 1
Published: about 10 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

10.1038/srep39262

Genome-wide Analysis of WD40 Protein Family in Human
Cited by: 37
Author(s): Xudong Zou, Xue-Jia Hu, Jing Ma, Tuan Li, Zhiqiang Ye, Yun Na Wu
Software Mentions: 1
Published: over 9 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/s12865-017-0238-4

Cattle infection response network and its functional modules
Cited by: 5
Author(s): Hamid Beiki, A. Pakdel, A Nejati Javaremi, Ali Masoudi‐Nejad, James M. Reecy
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-13-49

Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice
Cited by: 29
Author(s): Rumdeep K Grewal, S. K. Gupta, Sampa Das
Software Mentions: 1
Published: over 14 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

10.1186/1471-2105-10-330

BASE - 2nd generation software for microarray data management and analysis
Cited by: 50
Author(s): Johan Vallon‐Christersson, Nicklas Nordborg, Martin Svensson, Jari Häkkinen
Software Mentions: 1
Published: almost 17 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

10.1186/1471-2164-15-438

RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Cited by: 26
Author(s): Marta Vergara-Irigaray, María Fookes, Nicholas R. Thomson, Christoph M. Tang
Software Mentions: 1
Published: about 12 years ago

10.1038/srep45828

A 3q gene signature associated with triple negative breast cancer organ specific metastasis and response to neoadjuvant chemotherapy
Cited by: 19
Author(s): Jun Qian, Heidi Chen, Xiangming Ji, Rosana Eisenberg, A. Bapsi Chakravarthy, Ingrid A. Mayer, Pierre P. Massion
Software Mentions: 1
Published: over 9 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

10.1186/2051-5960-2-23

The prognostic role of intragenic copy number breakpoints and identification of novel fusion genes in paediatric high grade glioma
Cited by: 20
Author(s): Diana Carvalho, Alan Mackay, Lynn Bjerke, Richard G. Grundy, Célia Lopes, Rui Manuel Reis, Chris Jones
Software Mentions: 1
Published: over 12 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: almost 12 years ago

10.1038/s41598-017-01156-x

The centrosomal OFD1 protein interacts with the translation machinery and regulates the synthesis of specific targets
Cited by: 35
Author(s): Daniela Iaconis, Maria Monti, Mario Renda, Arianne van Koppen, Roberta Tammaro, Marco Chiaravalli, Flora Cozzolino, Paola Pignata, Claudia Crina, Piero Pucci, Alessandra Boletta, Vincenzo Belcastro, Rachel Giles, Enrico Maria Surace, Simone Gallo, Mario Pende, Brunella Franco
Software Mentions: 1
Published: over 9 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/s13195-014-0070-5

PLD3 is accumulated on neuritic plaques in Alzheimer’s disease brains
Cited by: 35
Author(s): Jun‐ichi Satoh, Yoshihiro Kino, Yoji Yamamoto, Natsuki Kawana, Tsuyoshi Ishida, Yuko Saito, Kunimasa Arima
Software Mentions: 1
Published: almost 12 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/s12864-016-2771-6

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

10.1186/1471-2164-10-215

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

10.1371/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: over 15 years ago

10.1038/s41598-017-04709-2

DACH1 suppresses breast cancer as a negative regulator of CD44
Cited by: 29
Author(s): Hanxiao Xu, Shengnan Yu, Xun Yuan, Jing Xiong, Dong Kuang, Richard G. Pestell, Kongming Wu
Software Mentions: 1
Published: about 9 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: over 10 years ago

10.1186/1471-2164-11-682

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

10.1038/s41598-017-05872-2

Functional and Transcriptomic Characterization of Peritoneal Immune-Modulation by Addition of Alanyl-Glutamine to Dialysis Fluid
Cited by: 12
Author(s): Rebecca Herzog, Lilian Kuster, Julia Powers Becker, Tobias Gluexam, Dietmar Pils, Andreas Spittler, Manoj Bhasin, Seth L. Alper, Andreas Vychytil, Christoph Aufricht, Klaus Kratochwill
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0056681

SGLT5 Reabsorbs Fructose in the Kidney but Its Deficiency Paradoxically Exacerbates Hepatic Steatosis Induced by Fructose
Cited by: 30
Author(s): Taku Fukuzawa, Motoharu Fukazawa, Otoya Ueda, Hideaki Shimada, Kito Aki, Mami Kakefuda, Yoshiaki Kawase, Naoko Wada, Chisato Goto, Naoshi Fukushima, Kou-ichi Jishage, Kazuo Honda, George L. King, Yojiro Kawabe
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-017-06810-y

Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1
Cited by: 13
Author(s): James McCaffrey, Nicholas J.A. Webb, Toryn Poolman, Maryline Fresquet, Cressida Moxey, Leo Zeef, Ian J. Donaldson, David Ray, Rachel Lennon
Software Mentions: 1
Published: about 9 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

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962