bioconductor: ArrayExpress | Projects

10.1093/jxb/ert337

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
Cited by: 109
Author(s): Selahattin Danisman, Aalt D. J. van Dijk, Andrea Bimbó, Froukje van der Wal, Lars Hennig, Stefan de Folter, Gerco C. Angenent, Richard G. H. Immink
Software Mentions: 1
Published: over 12 years ago

10.1093/jxb/ert397

Overexpression of<i>PYL5</i>in rice enhances drought tolerance, inhibits growth, and modulates gene expression
Cited by: 178
Author(s): Hyun-Mi Kim, Kyeyoon Lee, Hyunsik Hwang, Nikita Bhatnagar, Dool Yi Kim, In Sun Yoon, Myung-Ok Byun, Sun Tae Kim, Ki‐Hong Jung, Beom-Gi Kim
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-13-33

Transcriptional ontogeny of the developing liver
Cited by: 41
Author(s): Janice S. Lee, William O. Ward, Geremy W. Knapp, Hongzu Ren, Beena Vallanat, Barbara D. Abbott, Karen J. Ho, Seth J. Karp, J. Christopher Corton
Software Mentions: 1
Published: over 14 years ago

10.1016/j.kint.2018.11.040

Lrig2 and Hpse2, mutated in urofacial syndrome, pattern nerves in the urinary bladder
Cited by: 25
Author(s): Neil Roberts, Emma Hilton, Filipa Lopes, Subir Singh, Michael J. Randles, Natalie J. Gardiner, Karl Chopra, Riccardo Coletta, Zunera Bajwa, Robert J. Hall, Wyatt W. Yue, Franz Schaefer, Stefanie Weber, Roger Henriksson, Helen M. Stuart, Håkan Hedman, William G. Newman, Adrian S. Woolf
Software Mentions: 1
Published: about 7 years ago

10.1155/2021/7079359

Association of the PINX1 Variant rs6984094, Which Lengthens Telomeres, with Systemic Lupus Erythematosus Susceptibility in Chinese Populations
Cited by: 2
Author(s): Yuanyuan Qi, Xin-Ran Liu, HE Ying-xin, Min Zhou, Xianghui Ning, Yunkai Zhai, Xiaoxue Zhang, Xiaoyang Wang, Ya-Fei Zhao, Caixia Yan, Zhigang Zhao
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.ppat.1000066

The Uptake of Apoptotic Cells Drives Coxiella burnetii Replication and Macrophage Polarization: A Model for Q Fever Endocarditis
Cited by: 49
Author(s): Marie Benoit, Éric Ghigo, Christian Capo, Didier Raoult, Jean‐Louis Mège
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2105-9-183

Data capture in bioinformatics: requirements and experiences with Pedro
Cited by: 16
Author(s): Daniel Jameson, Kevin Garwood, Christopher Garwood, Tim Booth, Pinar Alper, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.ppat.1000529

Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Cited by: 74
Author(s): Roy R. Chaudhuri, Sarah Peters, Stephen J. Pleasance, Helen Northen, Chrissie Willers, Gavin K. Paterson, Danielle B. Cone, Andrew G. Allen, Paul Owen, Gil Shalom, Dov J. Stekel, Ian G. Charles, Duncan J. Maskell
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.ppat.1000813

Innate Killing of Leishmania donovani by Macrophages of the Splenic Marginal Zone Requires IRF-7
Cited by: 60
Author(s): Rebecca A. Phillips, Mattias Svensson, Naveed Aziz, Asher Maroof, Najmeeyah Brown, Lynette Beattie, Nathalie Signoret, Paul M. Kaye
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-10-S12-S10

Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data
Cited by: 4
Author(s): Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano, Ulrich Pfeffer
Software Mentions: 1
Published: over 16 years ago

10.1089/omi.2016.0041

Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-Wide DNA Methylation Profiles and RNA Expression
Cited by: 48
Author(s): Emil Nilsson, Adrian Boström, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-11-418

Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar)
Cited by: 124
Author(s): Samuel Martín, Alex Douglas, D.F. Houlihan, Christopher J. Secombes
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.ppat.1003083

A Strong Immune Response in Young Adult Honeybees Masks Their Increased Susceptibility to Infection Compared to Older Bees
Cited by: 70
Author(s): James C. Bull, Eugene V. Ryabov, Gill Prince, Andrew Mead, Cunjin Zhang, Laura Baxter, J. K. Pell, Juliet L. Osborne, Dave Chandler
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-14-8

XperimentR: painless annotation of a biological experiment for the laboratory scientist
Cited by: 7
Author(s): Christopher Tomlinson, Geraint Barton, Mark Woodbridge, Sarah Butcher
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.ppat.1005469

In Vivo Molecular Dissection of the Effects of HIV-1 in Active Tuberculosis
Cited by: 44
Author(s): Lucy Bell, Gabriele Pollara, Pascoe Mellissa, Gillian S. Tomlinson, Rannakoe Lehloenya, Jennifer Roe, Richard Meldau, R F Miller, Alan D. Ramsay, Benjamin M. Chain, Keertan Dheda, Mahdad Noursadeghi
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.ppat.1007315

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing
Cited by: 47
Author(s): Daniela Begolo, Isabel M. Vincent, Federica Giordani, Ina Pöhner, Michael Witty, T.G. Rowan, Zakaria Bengaly, Kirsten Gillingwater, Yvonne R. Freund, Rebecca C. Wade, Michael P. Barrett, Christine Clayton
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms21061941

Fighting Against Promoter DNA Hyper-Methylation: Protective Histone Modification Profiles of Stress-Resistant Intestinal Stem Cells
Cited by: 1
Author(s): Torsten Thalheim, Lydia Hopp, Maria Herberg, Susann Siebert, Christiane Kerner, Marianne Quaas, Michal R. Schweiger, Gabriela Aust, Joerg Galle
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-5464-0

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes
Cited by: 3
Author(s): Marzena Mura, Roman Jaksik, Anna Lalik, Krzysztof Biernacki, Marek Kimmel, Joanna Rzeszowska-Wolny, Krzysztof Fujarewicz
Software Mentions: 1
Published: over 7 years ago

10.1073/pnas.1912109117

The circadian clock protein REVERBα inhibits pulmonary fibrosis development
Cited by: 50
Author(s): Peter Cunningham, P. J. J. De Meijer, Alicja Nazgiewicz, Simon Anderson, Lee A. Borthwick, James Bagnall, Gareth Kitchen, Monika Lodyga, Nicola Begley, Rajamiyer Venkateswaran, Rajesh Shah, Paul F. Mercer, Hannah J. Durrington, Neil C. Henderson, Karen Piper Hanley, Andrew J. Fisher, Rachel C. Chambers, David A. Bechtold, Julie Gibbs, A. S. I. Loudon, Martin K. Rutter, Boris Hinz, David Ray, John Blaikley
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-7-319

Systematic interpretation of microarray data using experiment annotations
Cited by: 17
Author(s): Kurt Fellenberg, Christian Busold, Olaf Witt, Andrea S. Bauer, Boris Beckmann, Nicole Hauser, Marcus Frohme, Stefan Winter, Jürgen Dippon, Jörg D. Hoheisel
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pone.0008018

Sulfur Metabolism Actively Promotes Initiation of Cell Division in Yeast
Cited by: 17
Author(s): Heidi M. Blank, Shefali Rajendra Gajjar, Andrey Belyanin, Michael Polymenis
Software Mentions: 1
Published: over 16 years ago

10.4161/rna.29196

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress
Cited by: 23
Author(s): Samuel Marguerat, Katherine Lawler, Alvis Brāzma, Jürg Bähler
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0161993

PKC-ALDH2 Pathway Plays a Novel Role in Adipocyte Differentiation
Cited by: 20
Author(s): Yu-Hsiang Yu, Pei Ru Liao, Chien Jung Guo, Che Hong Chen, Daria Mochly‐Rosen, Lee‐Ming Chuang
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0079627

Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts
Cited by: 1
Author(s): Thong Tien Nguyen, Cathal Seoighe
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms20215274

The CCR4–NOT Deadenylase Complex Maintains Adipocyte Identity
Cited by: 11
Author(s): Akinori Takahashi, Shohei Takaoka, Shungo Kobori, Tomokazu Yamaguchi, Sara Ferwati, Keiji Kuba, Tadashi Yamamoto, Toru Suzuki
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0001546

Systematic Validation and Atomic Force Microscopy of Non-Covalent Short Oligonucleotide Barcode Microarrays
Cited by: 13
Author(s): Michael A. Cook, Chi Kin Chan, Paul Jorgensen, Troy Ketela, Daniel K. C. So, Mike Tyers, Chi Yip Ho
Software Mentions: 1
Published: over 18 years ago

10.1186/1748-717X-5-25

MicroRNA expression after ionizing radiation in human endothelial cells
Cited by: 135
Author(s): Mechthild Wagner-Ecker, Christian Schwager, Ute Wirkner, Amir Abdollahi, Peter E. Huber
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0002798

Diurnal and Circadian Rhythms in the Tomato Transcriptome and Their Modulation by Cryptochrome Photoreceptors
Cited by: 63
Author(s): Paolo Facella, Loredana Lopez, Fabrizio Carbone, David W. Galbraith, Giovanni Giuliano, Gaetano Perrotta
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2105-8-360

Linking microarray reporters with protein functions
Cited by: 12
Author(s): Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. Evelo
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0048363

Functional Similarities between Pigeon ‘Milk’ and Mammalian Milk: Induction of Immune Gene Expression and Modification of the Microbiota
Cited by: 28
Author(s): Meagan J Gillespie, Dragana Stanley, Honglei Chen, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0131336

MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing
Cited by: 29
Author(s): Li Zhang, Pengfei Wei, Xudong Shen, Yuanwei Zhang, Bo Xu, Jun Zhou, Song Fan, Zongyao Hao, Hao Shi, Xiansheng Zhang, Rui Kong, Lingfan Xu, Duohong Zou, Chaozhao Liang
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0080747

PaGenBase: A Pattern Gene Database for the Global and Dynamic Understanding of Gene Function
Cited by: 100
Author(s): Jianbo Pan, Shichang Hu, Dan Shi, Mei-Chun Cai, Yin-Bo Li, Quan Zou, Zhi-Liang Ji
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0070294

Prediction Errors in Learning Drug Response from Gene Expression Data – Influence of Labeling, Sample Size, and Machine Learning Algorithm
Cited by: 15
Author(s): Immanuel Bayer, Philip Groth, Sebastian Schneckener
Software Mentions: 1
Published: almost 13 years ago

10.1186/ar1903

Cited by: 51
Author(s): Johan Lindberg, Erik af Klint, Ann‐Kristin Ulfgren, André Stark, T. Andersson, Peter Nilsson, Lars Klareskog, Joakim Lundeberg
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pone.0026023

Hormone Receptor and ERBB2 Status in Gene Expression Profiles of Human Breast Tumor Samples
Cited by: 6
Author(s): Anna Dvorkin‐Gheva, John A. Hassell
Software Mentions: 1
Published: over 14 years ago

10.1186/1477-7827-7-133

Fhl5/Act, a CREM-binding transcriptional activator required for normal sperm maturation and morphology, is not essential for testicular gene expression
Cited by: 13
Author(s): Aurélie Lardenois, Frédéric Chalmel, Philippe Demougin, Noora Kotaja, Paolo Sassone‐Corsi, Michael Primig
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0250747

Glycans unique to the relapse-prone subset within triple-negative breast cancer as revealed by lectin array-based analysis of surgical specimens
Cited by: 3
Author(s): Madoka Sakata-Matsuzawa, Kaori Denda-Nagai, Haruhiko Fujihira, Miki Noji, Katrin Ishii-Schrade, Atsushi Matsuda, Atsushi Kuno, Misato Okazaki, Keiichi Nakai, Yoshiya Horimoto, Mitsue Saito, Tatsuro Irimura
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0048896

Survival of Staphylococcus aureus ST398 in the Human Nose after Artificial Inoculation
Cited by: 23
Author(s): Bibi C. G. C. Slingerland, Mehri Tavakol, Alex J. McCarthy, Jodi A. Lindsay, Susan V. Snijders, Jaap A. Wagenaar, Alex van Belkum, Margreet C. Vos, Henri A. Verbrugh, Willem J. B. van Wamel
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0152786

Adipocytes as a Link Between Gut Microbiota-Derived Flagellin and Hepatocyte Fat Accumulation
Cited by: 13
Author(s): Eveliina Munukka, Petri Wiklund, Tiina Partanen, Sakari Välimäki, Eija K. Laakkonen, Maarit Lehti, Pamela Fischer-Posovzsky, Martin Wabitsch, Sulin Cheng, Pentti Huovinen, Satu Pekkala
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0113053

Toward Computational Cumulative Biology by Combining Models of Biological Datasets
Cited by: 8
Author(s): Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, Samuel Kaski
Software Mentions: 1
Published: over 11 years ago

10.1186/1477-7827-8-154

Profiling spermatogenic failure in adult testes bearing Sox9-deficient Sertoli cells identifies genes involved in feminization, inflammation and stress
Cited by: 11
Author(s): Aurélie Lardenois, Frédéric Chalmel, Francisco Barrionuevo, Philippe Demougin, Gerd Scherer, Michael Primig
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0080047

A Small RNA Encoded in the Rv2660c Locus of Mycobacterium tuberculosis Is Induced during Starvation and Infection
Cited by: 32
Author(s): Joanna Houghton, Teresa Cortes, Olga T. Schubert, Graham Rose, Angela Rodgers, Megan De Ste Croix, Rudolf Aebersold, Douglas B. Young, Kristine B. Arnvig
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0139446

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions
Cited by: 32
Author(s): Francesco Iorio, Roshan L. Shrestha, Nicolas Levin, Viviane Boilot, Mathew J. Garnett, Julio Sáez-Rodríguez, Viji M. Draviam
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0001403

Probing Host Pathogen Cross-Talk by Transcriptional Profiling of Both Mycobacterium tuberculosis and Infected Human Dendritic Cells and Macrophages
Cited by: 185
Author(s): Ludovic Tailleux, Simon J. Waddell, Mattia Pelizzola, Alessandra Mortellaro, Michael Withers, Antoine Tanne, Paola Ricciardi Castagnoli, Brigitte Gicquel, Neil G. Stoker, Philip D. Butcher, Maria Foti, Olivier Neyrolles
Software Mentions: 1
Published: over 18 years ago

10.1016/j.jmb.2012.10.014

Gene Function Hypotheses for the Campylobacter jejuni Glycome Generated by a Logic-Based Approach
Cited by: 18
Author(s): Michael J.E. Sternberg, Alireza Tamaddoni‐Nezhad, Victor I. Lesk, Emily Kay, Paul G. Hitchen, Adrian P. Cootes, Lieke B. van Alphen, Marc P. Lamoureux, Harold C. Jarrell, Christopher J. Rawlings, Evelyn C. Soo, Christine M. Szymanski, Anne Dell, Brendan W. Wren, Stephen Muggleton
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0082684

Genetic Interaction between Mutations in c-Myb and the KIX Domains of CBP and p300 Affects Multiple Blood Cell Lineages and Influences Both Gene Activation and Repression
Cited by: 27
Author(s): Lawryn H. Kasper, Tsutomu Fükuyama, Stephanie Lerach, Yunchao Chang, Wu Xu, Song Wu, Kelli L. Boyd, Paul K. Brindle
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0106278

SDF-1 Chemokine Signalling Modulates the Apoptotic Responses to Iron Deprivation of Clathrin-Depleted DT40 Cells
Cited by: 2
Author(s): Alena Pance, Frank Ralf Morrissey-Wettey, Helen Craig, Alison Downing, Richard Talbot, Antony P. Jackson
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-9-3

Switch-like genes populate cell communication pathways and are enriched for extracellular proteins
Cited by: 36
Author(s): Adam Ertel, Aydın Tözeren
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0030781

Circadian Rhythms of Fetal Liver Transcription Persist in the Absence of Canonical Circadian Clock Gene Expression Rhythms In Vivo
Cited by: 8
Author(s): Chengwei Li, Shuang Yu, Xiaoling Zhong, Jianguo Wu, Xiaodong Li
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0007158

miR-155 Inhibition Sensitizes CD4+ Th Cells for TREG Mediated Suppression
Cited by: 81
Author(s): Heiko Stahl, Tanja Fauti, Nina D. Ullrich, Tobias Bopp, Jan Kubach, Werner Rust, Paul Labhart, Vassili Alexiadis, Christian Becker, Mathias Hafner, Andreas Weith, Martin Lenter, Helmut Jonuleit, Edgar Schmitt, Detlev Mennerich
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0004955

A Cross-Study Transcriptional Analysis of Parkinson's Disease
Cited by: 79
Author(s): Greg T. Sutherland, Nicholas Matigian, Alistair M. Chalk, Matthew Anderson, Peter A. Silburn, Alan Mackay‐Sim, Christine A. Wells, George D. Mellick
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0073072

Transmembrane Prostatic Acid Phosphatase (TMPAP) Interacts with Snapin and Deficient Mice Develop Prostate Adenocarcinoma
Cited by: 27
Author(s): Ileana B. Quintero, Annakaisa Herrala, César L. Araujo, Anitta E. Pulkka, Sampsa Hautaniemi, Kristian Ovaska, Evgeny Pryazhnikov, Evgeny Kulesskiy, Maija Ruuth, Ylermi Soini, Raija Sormunen, Leonard Khirug, Pirkko Vihko
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0032150

Identification of Candidate Susceptibility and Resistance Genes of Mice Infected with Streptococcus suis Type 2
Cited by: 12
Author(s): Jie Rong, Wei Zhang, Xiaohui Wang, Hongjie Fan, Lu Chen, Huochun Yao
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0112655

Identification of Modulators of the Nuclear Receptor Peroxisome Proliferator-Activated Receptor α (PPARα) in a Mouse Liver Gene Expression Compendium
Cited by: 58
Author(s): Keiyu Oshida, Naresh Vasani, Russell S. Thomas, Dawn Applegate, Mitchell B. Rosen, Barbara D. Abbott, Christopher Lau, Grace L. Guo, Lauren M. Aleksunes, Curtis D. Klaassen, J. Christopher Corton
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0181812

Reprogramming human gallbladder cells into insulin-producing β-like cells
Cited by: 33
Author(s): Feorillo Galivo, Eric Benedetti, Yuhan Wang, Carl Pelz, Jonathan Schug, Klaus H. Kaestner, Markus Grompe
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0045200

Transcriptomic Assay of CD8+ T Cells in Treatment-Naïve HIV, HCV-Mono-Infected and HIV/HCV-Co-Infected Chinese
Cited by: 7
Author(s): Jin Zhao, Yi Liu, Jing Lu, Zheng Yang, Ying Chen, Chenli Zheng, Dan Huang, Yufeng Li, Lin Chen, Jinquan Cheng, Hsiang‐Fu Kung, Ming‐Liang He
Software Mentions: 1
Published: almost 14 years ago

10.1186/1742-4690-11-59

Microarray analysis reveals global modulation of endogenous retroelement transcription by microbes
Cited by: 45
Author(s): George R. Young, Bettina Mavrommatis, George Kassiotis
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0123342

Differential Transcriptional Profiling of Damaged and Intact Adjacent Dorsal Root Ganglia Neurons in Neuropathic Pain
Cited by: 39
Author(s): Ann-Kristin Reinhold, Laura Batti, Daniel Bilbao, Andreas Buneß, Heike L. Rittner, Paul A. Heppenstall
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0176353

Intracellular signaling entropy can be a biomarker for predicting the development of cervical intraepithelial neoplasia
Cited by: 4
Author(s): Masakazu Sato, Kei Kawana, Katsuyuki Adachi, Asaha Fujimoto, Midori Yoshida, Hitomi Nakamura, Hidetoshi Nishida, Tatsuo Inoue, Ayumi Taguchi, Juri Ogishima, Shuichiro Eguchi, Aki Yamashita, Kensuke Tomio, Osamu Wada-Hiraike, Katsutoshi Oda, Takeshi Nagamatsu, Yutaka Osuga, Tomoyuki Fujii
Software Mentions: 1
Published: about 9 years ago

10.3390/ijms151019037

ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates
Cited by: 7
Author(s): Michael Roemer, Linus Backert, Johannes Eichner, Andreas Zell
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0001973

Genomic Diversity among Beijing and non-Beijing Mycobacterium tuberculosis Isolates from Myanmar
Cited by: 20
Author(s): Ruth Stavrum, Håvard Valvatne, Trond Hellem Bø, Inge Jonassen, Jason Hinds, Philip D. Butcher, Harleen M. S. Grewal
Software Mentions: 1
Published: about 18 years ago

10.1186/s12284-015-0059-0

Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice
Cited by: 26
Author(s): Hinako Takehisa, Yutaka Satō, Baltazar A. Antonio, Yoshiaki Nagamura
Software Mentions: 1
Published: almost 11 years ago

10.1016/j.yjmcc.2019.02.006

The cardiomyocyte “redox rheostat”: Redox signalling via the AMPK-mTOR axis and regulation of gene and protein expression balancing survival and death
Cited by: 25
Author(s): Daniel N. Meijles, Georgia Zoumpoulidou, Thomais Markou, Kerry A Rostron, Rishi Patel, Kenneth Lay, Balvinder S. Handa, Bethany Wong, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0116973

A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network
Cited by: 39
Author(s): Felipe Leal Valentim, S. van Mourik, David Posé, Min C. Kim, Markus Schmid, Roeland C. H. J. van Ham, Marco Busscher, Gabino F. Sánchez-Pérez, Jaap Molenaar, Gerco C. Angenent, Richard G. H. Immink, Aalt D. J. van Dijk
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0064880

The Elongation Complex Components BRD4 and MLLT3/AF9 Are Transcriptional Coactivators of Nuclear Retinoid Receptors
Cited by: 14
Author(s): Sébastien Flajollet, Christophe Rachez, Maheul Ploton, Céline Schulz, Rozenn Gallais, Raphaël Métivier, Michał Pawlak, Aymeric Leray, Al Amine Issulahi, Laurent Héliot, Bart Staels, Gilles Salbert, Philippe Lefèbvre
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0198555

The immunosuppressive face of sepsis early on intensive care unit—A large-scale microarray meta-analysis
Cited by: 29
Author(s): Dominik Schaack, Benedikt Hermann Siegler, Sandra Tamulyte, Markus Weigand, Florian Uhle
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0045744

Transcriptome Analysis of Responses to Rhodomyrtone in Methicillin-Resistant Staphylococcus aureus
Cited by: 29
Author(s): Wipawadee Sianglum, Potjanee Srimanote, Peter W. Taylor, Helena Rosado, Supayang Piyawan Voravuthikunchai
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0004285

Rapid Changes in Transcription Profiles of the Plasmodium yoelii yir Multigene Family in Clonal Populations: Lack of Epigenetic Memory?
Cited by: 25
Author(s): Deirdre Cunningham, Jannik Fonager, William Jarra, Céline Carret, Peter R. Preiser, Jean Langhorne
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0022859

Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis
Cited by: 121
Author(s): Cheng-Wei Chang, Wei‐Chung Cheng, Chaang-Ray Chen, Wun‐Yi Shu, Min-Lung Tsai, Ching-Lung Huang, Ian C. Hsu
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0199991

PASI: A novel pathway method to identify delicate group effects
Cited by: 4
Author(s): Maria K. Jaakkola, Aidan McGlinchey, Рику Клен, Laura L. Elo
Software Mentions: 1
Published: almost 8 years ago

10.1186/ar2294

Expression and regulation of CCL18 in synovial fluid neutrophils of patients with rheumatoid arthritis
Cited by: 49
Author(s): Judith Auer, Bläss Markus, Hendrik Schulze‐Koops, Stefan Rußwurm, Thomas Nagel, Joachim R. Kalden, Martin Röllinghoff, H U Beuscher
Software Mentions: 1
Published: over 19 years ago

10.1038/sdata.2015.77

Comprehensive systems biology analysis of a 7-month cigarette smoke inhalation study in C57BL/6 mice
Cited by: 25
Author(s): Sam Ansari, Karine Baumer, Stéphanie Boué, Sophie Dijon, Rémi Dulize, Kim Ekroos, Ashraf Elamin, Foong Clement, Emmanuel Guedj, Julia Hoeng, Nikolai V. Ivanov, Krishnan Subash, Patrice Leroy, Florian Martin, Céline Merg, Michael J. Peck, Manuel C. Peitsch, Blaine Phillips, Walter K. Schlage, Thomas Schneider, Marja Talikka, Bjoern Titz, Patrick Vanscheeuwijck, Emilija Veljkovic, Terhi Vihervaara, Grégory Vuillaume, Ching Qing Woon
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0055506

Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?
Cited by: 34
Author(s): David Cohen, Marie‐Béatrice Bogeat‐Triboulot, Silvère Vialet-Chabrand, Rémy Merret, Pierre‐Emmanuel Courty, Sébastien Moretti, François Bizet, Agnès Guilliot, Irène Hummel
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0118511

MicroRNA-572 Improves Early Post-Operative Cognitive Dysfunction by Down-Regulating Neural Cell Adhesion Molecule 1
Cited by: 31
Author(s): Xiuchong Yu, Shupeng Liu, Jinbao Li, Xiaoping Fan, Yuanjie Chen, Xiaoying Bi, Shanrong Liu, Xiaoming Deng
Software Mentions: 1
Published: over 11 years ago

10.1038/sdata.2017.125

Precision annotation of digital samples in NCBI’s gene expression omnibus
Cited by: 34
Author(s): Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D. Azad, Mohamad Omar Hadied, S. Mahmood Raza, Benjamin Abhishek Rayikanti, Bin Chen, Harikrishna Paik, Dvir Aran, Jordan Spatz, Daniel S. Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A. Musen, Atul J. Butte
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0190533

Elucidation of the mechanism behind the potentiating activity of baicalin against Burkholderia cenocepacia biofilms
Cited by: 17
Author(s): Lisa Slachmuylders, Heleen Van Acker, Gilles Brackman, Andrea Saß, Filip Van Nieuwerburgh, Tom Coenye
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0042228

Loss of Abdominal Muscle in Pitx2 Mutants Associated with Altered Axial Specification of Lateral Plate Mesoderm
Cited by: 14
Author(s): Diana G. Eng, Hsiao-Yen Ma, Jun Xu, Hung-Ping Shih, Michael Groß, Chrissa Kiouss
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0051129

Identification of Putative Rhamnogalacturonan-II Specific Glycosyltransferases in Arabidopsis Using a Combination of Bioinformatics Approaches
Cited by: 16
Author(s): Aline Voxeur, Aurélie André, C. Breton, Patrice Lerouge
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0080625

MicroRNA-99 Family Members Suppress Homeobox A1 Expression in Epithelial Cells
Cited by: 33
Author(s): Dan Chen, Zujian Chen, Y. Jin, Dragan Dragas, Leitao Zhang, Barima S. Adjei, Anxun Wang, Yang Dai, Xiaofeng Zhou
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0049077

Gadd45α: A Novel Diabetes-Associated Gene Potentially Linking Diabetic Cardiomyopathy and Baroreflex Dysfunction
Cited by: 13
Author(s): Ning Wang, Chao Yang, Fang Xie, Lichao Sun, Xiaolin Su, Ying Wang, Ran Wei, Rong Zhang, Xia Li, Baofeng Yang, Jing Ai
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0019844

Extracellular Matrix Formation Enhances the Ability of Streptococcus pneumoniae to Cause Invasive Disease
Cited by: 60
Author(s): Claudia Trappetti, Abiodun D. Ogunniyi, Marco R. Oggioni, James C. Paton
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0228408

GLIPR1 expression is reduced in multiple myeloma but is not a tumour suppressor in mice
Cited by: 2
Author(s): Natasha Friend, Jacqueline E. Noll, Khatora S. Opperman, Kimberley C. Clark, Krzysztof M. Mrozik, Kate Vandyke, Duncan R. Hewett, Andrew C.W. Zannettino
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0230313

A 3-gene biomarker signature to predict response to taxane-based neoadjuvant chemotherapy in breast cancer
Cited by: 5
Author(s): Jim Kallarackal, Florian Bürger, S. Del Bianco, Alessandro Romualdi, Martina Schad
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0001791

Transcriptomic Analyses Reveal Novel Genes with Sexually Dimorphic Expression in the Zebrafish Gonad and Brain
Cited by: 109
Author(s): Rajini Sreenivasan, Minnie Cai, Richárd Bártfai, Xingang Wang, Alan Christoffels, László Orbán
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0087665

Genome-Wide Screening Identified That miR-134 Acts as a Metastasis Suppressor by Targeting Integrin β1 in Hepatocellular Carcinoma
Cited by: 69
Author(s): Rujing Zha, Weijie Guo, Zhenfeng Zhang, Zhaoping Qiu, Qifeng Wang, Jie Ding, Shenglin Huang, Taoyang Chen, Jianren Gu, Ming Yao, Xianghuo He
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-8-202

Species differences in brain gene expression profiles associated with adult behavioral maturation in honey bees
Cited by: 48
Author(s): Moushumi Sen Sarma, Charles W. Whitfield, Gene E. Robinson
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pone.0013079

QKI-7 Regulates Expression of Interferon-Related Genes in Human Astrocyte Glioma Cells
Cited by: 8
Author(s): Lin Jiang, Peter Saetre, Katarzyna J. Radomska, Elena Jazin, Eva Carlström
Software Mentions: 1
Published: over 15 years ago

10.3390/ijms20225783

Genome-Wide Identification and Characterization of ABC Transporters in Nine Rosaceae Species Identifying MdABCG28 as a Possible Cytokinin Transporter linked to Dwarfing
Cited by: 19
Author(s): Yi Feng, Qiran Sun, Guifen Zhang, Ting Wu, Xinzhong Zhang, Xuefeng Xu, Zhenhai Han, Yi Wang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0055764

Simultaneous Quantification of Multiple Bacteria by the BactoChip Microarray Designed to Target Species-Specific Marker Genes
Cited by: 17
Author(s): Annalisa Ballarini, Nicola Segata, Curtis Huttenhower, Olivier Jousson
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0177701

SiGNet: A signaling network data simulator to enable signaling network inference
Cited by: 7
Author(s): Elizabeth A. Coker, Costas Mitsopoulos, Paul Workman, Bissan Al‐Lazikani
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0013658

Whole Blood Transcriptomics in Cardiac Surgery Identifies a Gene Regulatory Network Connecting Ischemia Reperfusion with Systemic Inflammation
Cited by: 34
Author(s): Orfeas Liangos, Sophie Domhan, Christian Schwager, Martin Zeier, Peter E. Huber, Francesco Addabbo, Michael S. Goligorsky, Lynn Hlatky, Bertrand L. Jaber, Amir Abdollahi
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0114627

Altered MicroRNA Expression Profile in Exosomes during Osteogenic Differentiation of Human Bone Marrow-Derived Mesenchymal Stem Cells
Cited by: 184
Author(s): Jiajie Xu, Guangxiao Yang, Xiaohong Pan, Shuijun Zhang, Chen Zhao, Bin-Song Qiu, Haifeng Gu, Jian-fei Hong, Li Cao, Yu Chen, Bing Xia, Qinsheng Bi, Yaping Wang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0171508

A distal intergenic region controls pancreatic endocrine differentiation by acting as a transcriptional enhancer and as a polycomb response element
Cited by: 12
Author(s): Joris van Arensbergen, Sébastien Dussaud, Corinne Pardanaud-Glavieux, Javier García-Hurtado, Claire Sauty, Aline Guerci, Jorge Ferrer, Philippe Ravassard
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0063296

Efferocytosis Promotes Suppressive Effects on Dendritic Cells through Prostaglandin E2 Production in the Context of Autoimmunity
Cited by: 23
Author(s): Irma Pujol‐Autonell, Rosa-Maria Ampudia, Raquel Planas, Sílvia Marín-Gallén, Jorge Carrascal, Álex Sánchez, Ana V. Marín, Manel Puig-Domingo, Ricardo Pujol-Borrell, Joan Verdaguer, Marta Vives-Pi
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0017359

The PI3K p110δ Regulates Expression of CD38 on Regulatory T Cells
Cited by: 71
Author(s): Daniel T. Patton, Marcus D. Wilson, Wendy C. Rowan, Dalya R. Soond, Klaus Okkenhaug
Software Mentions: 1
Published: over 15 years ago

10.1038/sdata.2018.29

Uniform resolution of compact identifiers for biomedical data
Cited by: 49
Author(s): Sarala M. Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A. McMurry, Niall Beard, Rafael C. Jiménez, Jeffrey S. Grethe, Henning Hermjakob, Maryann E. Martone, Tim W. Clark
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0183410

snoRNA and piRNA expression levels modified by tobacco use in women with lung adenocarcinoma
Cited by: 25
Author(s): Natasha Andressa Nogueira Jorge, Gabriel Wajnberg, Carlos Gil Ferreira, Benilton Carvalho, Fábio Passetti
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-14-169

Transcriptome analysis of pigeon milk production – role of cornification and triglyceride synthesis genes
Cited by: 38
Author(s): Meagan J Gillespie, Tamsyn M. Crowley, Volker Häring, Susanne Wilson, Jennifer Harper, Jean Payne, Diane Green, Paul Monaghan, John A. Donald, Kevin R. Nicholas, Robert J. Moore
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0011066

Contrasting Transcriptional Responses of a Virulent and an Attenuated Strain of Mycobacterium tuberculosis Infecting Macrophages
Cited by: 43
Author(s): Alice H. Li, Simon J. Waddell, Jason Hinds, Chad A. Malloff, Manjeet Bains, Robert E. W. Hancock, Wan L. Lam, Philip D. Butcher, Richard W. Stokes
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0030960

Role of Position 627 of PB2 and the Multibasic Cleavage Site of the Hemagglutinin in the Virulence of H5N1 Avian Influenza Virus in Chickens and Ducks
Cited by: 61
Author(s): K. A. Schat, John Bingham, Jeff Butler, Li Mei Chen, Sue Lowther, Tamsyn M. Crowley, Robert J. Moore, Ruben O. Donis, John W. Lowenthal
Software Mentions: 1
Published: over 14 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962