bioconductor: ArrayExpress | Projects

10.1186/1471-2180-8-20

Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e σB regulon
Cited by: 135
Author(s): Torsten Hain, Hamid Hossain, Som Subhra Chatterjee, Silke Machata, Ute Volk, Sandra Wagner, Benedikt Brors, Stefan A. Haas, Carsten Kuenne, André Billion, Sonja Otten, Jan Pané‐Farré, Susanne Engelmann, Trinad Chakraborty
Software Mentions: 3
Published: about 18 years ago

10.1038/srep32417

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 20
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-17730-2

Constitutively elevated levels of SOCS1 suppress innate responses in DF-1 immortalised chicken fibroblast cells
Cited by: 28
Author(s): Efstathios S. Giotis, CS Ross, RC Robey, Axel Nohturfft, Stephen Goodbourn, Michael A. Skinner
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0242880

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows
Cited by: 7
Author(s): Lisa Ekman, Elisabeth Bagge, Ann-Kristin Nyman, Karin Persson Waller, Märit Pringle, Bo Segerman
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-7-51

Comparison of the latest commercial short and long oligonucleotide microarray technologies
Cited by: 49
Author(s): Aurélien de Reyniès, Daniela Géromin, Jean‐Michel Cayuela, Fabien Petel, Philippe Dessen, François Sigaux, David S. Rickman
Software Mentions: 3
Published: almost 20 years ago

10.1186/s12911-016-0325-0

Legal assessment tool (LAT): an interactive tool to address privacy and data protection issues for data sharing
Cited by: 7
Author(s): Wolfgang Kuchinke, Christian Krauth, René Bergmann, Töresin Karakoyun, Astrid Woollard, Irene Schluender, Benjamin Braasch, Martin Eckert, Christian Ohmann
Software Mentions: 3
Published: over 9 years ago

10.1038/s41597-019-0046-1

Navigating in vitro bioactivity data by investigating available resources using model compounds
Cited by: 1
Author(s): Sten Ilmjärv, Fiona Augsburger, Jerven Bolleman, Robin Liechti, Alan Bridge, Jenny Sandström, Vincent Jaquet, Ioannis Xenarios, Karl-Heinz Krause
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12870-020-2305-x

Linking crop traits to transcriptome differences in a progeny population of tetraploid potato
Cited by: 7
Author(s): Erik Alexandersson, Sandeep Kushwaha, Aastha Subedi, Deborah Weighill, Sharlee Climer, Daniel Jacobson, Erik Andréasson
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2105-7-286

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology
Cited by: 53
Author(s): Bruz Marzolf, Eric W. Deutsch, Patrick Moss, D. S. Campbell, Michael H. Johnson, Timothy Galitski
Software Mentions: 3
Published: over 19 years ago

10.1186/s12859-014-0386-y

Finding gene regulatory network candidates using the gene expression knowledge base
Cited by: 8
Author(s): Aravind Venkatesan, Sushil Tripathi, Alejandro Sanz de Galdeano, Ward Blondé, Astrid Lægreid, Vladimir Mironov, Martin Kuiper
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2105-10-133

SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes
Cited by: 4
Author(s): Hideya Kawaji, Yoshihide Hayashizaki, Carsten O. Daub
Software Mentions: 3
Published: almost 17 years ago

10.1186/s12859-019-2705-9

Network meta-analysis correlates with analysis of merged independent transcriptome expression data
Cited by: 11
Author(s): Christine Winter, Robin Kosch, Martin Ludlow, Albert D. M. E. Osterhaus, Klaus Jung
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2229-13-147

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

10.1371/journal.pone.0039205

Effect of Chemical Mutagens and Carcinogens on Gene Expression Profiles in Human TK6 Cells
Cited by: 15
Author(s): Lode Godderis, Reuben Thomas, Alan Hubbard, Ali Mustafa Tabish, Peter Hoet, Luoping Zhang, Martyn T. Smith, Hendrik Veulemans, Cliona M. McHale
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-018-22284-y

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis
Cited by: 19
Author(s): Li Jin, Peng Yu
Software Mentions: 3
Published: almost 8 years ago

10.1186/1755-8794-1-42

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis
Cited by: 127
Author(s): Andrew H. Sims, Graeme J. Smethurst, Yvonne Hey, Michał Okoniewski, Stuart D Pepper, Anthony Howell, Crispin Miller, Robert B. Clarke
Software Mentions: 3
Published: over 17 years ago

10.1186/1755-8794-7-28

Integrative analysis of the transcriptome profiles observed in type 1, type 2 and gestational diabetes mellitus reveals the role of inflammation
Cited by: 27
Author(s): Adriane Feijó Evangelista, Cristhianna V. A. Collares, Deise Ferreira Xavier, Cristiana Santos de Macedo, Fernanda S. Manoel-Caetano, Diane Meyre Rassi, Maria Cristina Foss‐Freitas, Milton César Foss, Elza T. Sakamoto-Hojo, Catherine Nguyen, Denis Puthier, Geraldo A. S. Passos, Eduardo Antônio Donadi
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0238809

MicroRNA expression profiles in molecular subtypes of clear-cell renal cell carcinoma are associated with clinical outcome and repression of specific mRNA targets
Cited by: 3
Author(s): Annelies Verbiest, Vincent van Hoef, Cristina Rodríguez‐Antona, Jesús García-Donás, Osvaldo Graña‐Castro, Maarten Albersen, Marcella Baldewijns, Annouschka Laenen, Eduard Roussel, Patrick Schöffski, Agnieszka Woźniak, Stefano Caruso, Gabrielle Couchy, Jessica Zucman–Rossi, Benoît Beuselinck
Software Mentions: 3
Published: over 5 years ago

10.1038/sdata.2018.198

RNA-seq of macrophages of amoeboid or mesenchymal migratory phenotype due to specific structure of environment
Cited by: 13
Author(s): Vladimı́r Čermák, Aneta Gandalovičová, Ladislav Merta, Jitka Fučíková, Radek Špíšek, Daniel Rösel, Jan Brábek
Software Mentions: 3
Published: over 7 years ago

10.7150/jca.38741

Construction and validation of an eight-gene signature with great prognostic value in bladder cancer
Cited by: 13
Author(s): Xin Yan, Xun Fu, Zixin Guo, Xiaoping Li, Tong-Zu Liu, Sheng Li
Software Mentions: 3
Published: about 6 years ago

10.7150/jca.60647

FOXD3-induced miR-133a blocks progression and metastasis of colorectal cancer through regulating UBA2
Cited by: 4
Author(s): Yuanfang Cheng, Yajuan Wang, Yuanzun Cheng, Qingmei Yang, Lejing Zhang, Zhaoxi Li, Jiancheng Cheng
Software Mentions: 3
Published: about 5 years ago

10.1186/s12920-020-0712-3

MyoMiner: explore gene co-expression in normal and pathological muscle
Cited by: 7
Author(s): Apostolos Malatras, Ioannis Michalopoulos, Stéphanie Duguez, Gillian Butler‐Browne, Simone Spuler, William Duddy
Software Mentions: 3
Published: almost 6 years ago

10.1186/1755-8794-5-66

Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines
Cited by: 199
Author(s): Andreas Schlicker, Garry Beran, Christine Chresta, Gael McWalter, Alison Pritchard, Susie Weston, Sarah Runswick, Sara Davenport, Kerry Heathcote, D Castro, George M. Orphanides, Tim French, Lodewyk Wessels
Software Mentions: 3
Published: about 13 years ago

10.1186/s12864-015-1785-9

MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data
Cited by: 11
Author(s): Khadija El Amrani, Harald Stachelscheid, Fritz Lekschas, Armin Kurtz, Miguel A. Andrade‐Navarro
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0037287

Chemical PARP Inhibition Enhances Growth of Arabidopsis and Reduces Anthocyanin Accumulation and the Activation of Stress Protective Mechanisms
Cited by: 45
Author(s): Philipp Schulz, Jenny Neukermans, Katrien Van Der Kelen, Per Mühlenbock, Frank Van Breusegem, Graham Noctor, Markus Teige, Michael Metzlaff, Matthew A. Hannah
Software Mentions: 3
Published: over 13 years ago

10.1534/g3.119.401031

Loss of N-Glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines
Cited by: 13
Author(s): William F. Mueller, Petra Jakob, Han Sun, Sandra Clauder‐Münster, Sonja Ghidelli-Disse, Diana Paola Serralde Ordóñez, Markus Böesche, Marcus Bantscheff, Paul Collier, Bettina Haase, Vladimı́r Beneš, Malte Paulsen, Peter Sehr, Joe Lewis, Gerard Drewes, Lars M. Steinmetz
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0239450

Integrative analysis of long non-coding RNA and mRNA in broilers with valgus-varus deformity
Cited by: 10
Author(s): Hehe Tang, Yaping Guo, Zhenzhen Zhang, Zhuanjian Li, Yanhua Zhang, Yuanfang Li, Xiangtao Kang, Ruili Han
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0240269

Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases
Cited by: 6
Author(s): Rosana Veroneze, Sâmia Cruz Tfaile Corbi, Bárbara Roque da Silva, Cristiane S. Rocha, Cláudia Vianna Maurer-Morelli, Silvana Regina Perez Orrico, Joni Augusto Cirelli, Fernando J. Von Zuben, Raquel Mantuaneli Scarel‐Caminaga
Software Mentions: 3
Published: over 5 years ago

10.1186/2043-9113-2-22

mCOPA: analysis of heterogeneous features in cancer expression data
Cited by: 18
Author(s): Chenwei Wang, Alperen Taciroglu, Stefan Maetschke, Colleen C. Nelson, Mark A. Ragan, Melissa J. Davis
Software Mentions: 3
Published: about 14 years ago

10.1038/s41597-019-0011-z

Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley
Cited by: 21
Author(s): Camilla Beate Hill, Debbie Wong, Josquin Tibbits, Kerrie Forrest, Matthew Hayden, Xiaoqi Zhang, Sharon Westcott, Tefera Tolera Angessa, Chengdao Li
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-25085-5

RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells
Cited by: 67
Author(s): Anda R. Gliga, Sebastiano Di Bucchianico, Jessica M. Lindvall, Bengt Fadeel, Hanna Karlsson
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2407-12-426

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

10.1186/s12920-016-0185-6

Breast cancer subtype predictors revisited: from consensus to concordance?
Cited by: 5
Author(s): Herman M. J. Sontrop, Marcel J. T. Reinders, Perry D. Moerland
Software Mentions: 3
Published: over 9 years ago

10.3389/fphar.2019.00198

A Meta-Analysis of the Performance of a Blood-Based Exposure Response Gene Signature Across Clinical Studies on the Tobacco Heating System 2.2 (THS 2.2)
Cited by: 2
Author(s): Florian Martin, Marja Talikka, Nikolai V. Ivanov, Christelle Haziza, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2350-13-25

Systems analysis of inflammatory bowel disease based on comprehensive gene information
Cited by: 7
Author(s): Satoru Suzuki, Takako Toda, Yutaka Fukuoka, Dennis P. Wall, Hiroshi Tanaka, Peter J. Tonellato
Software Mentions: 3
Published: almost 14 years ago

10.3389/fphys.2019.00433

Increasing Upstream Chromatin Long–Range Interactions May Favor Induction of Circular RNAs in LysoPC-Activated Human Aortic Endothelial Cells
Cited by: 16
Author(s): Angus Li, Yu Sun, Charles Drummer, Yifan Lu, Daohai Yu, Yan Zhou, Xinyuan Li, Simone J. Pearson, Candice Johnson, Catherine C. Yu, William Y. Yang, Kevin Mastascusa, Xiaohua Jiang, Jianxin Sun, Thomas J. Rogers, Wenhui Hu, Hong Wang, Xiaofeng Yang
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0253864

The KrasG12D;Trp53fl/fl murine model of undifferentiated pleomorphic sarcoma is macrophage dense, lymphocyte poor, and resistant to immune checkpoint blockade
Cited by: 3
Author(s): Karys Hildebrand, Arvind K. Singla, Reid McNeil, Kayla L. Marritt, Kurt Hildebrand, Franz J. Zemp, Jahanara Rajwani, Doha Itani, Pinaki Bose, Douglas J. Mahoney, Frank R. Jirik, Michael J. Monument
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0226707

High expression of olfactomedin-4 is correlated with chemoresistance and poor prognosis in pancreatic cancer
Cited by: 15
Author(s): Ryotaro Ohkuma, Erica Yada, Shumpei Ishikawa, Daisuke Komura, Hidenobu Ishizaki, Koji Tamada, Yutaro Kubota, Kazuyuki Hamada, Hiroo Ishida, Yuya Hirasawa, Hirotsugu Ariizumi, Etsuko Satoh, Midori Shida, Makoto Watanabe, Rie Onoue, Kiyohiro Ando, Junji Tsurutani, Kiyoshi Yoshimura, Takehiko Yokobori, Tetsuro Sasada, Takeshi Aoki, Masahiko Murakami, Tomoko Norose, Nobuyuki Ohike, Masafumi Takimoto, Masahiko Izumizaki, Shinichi Kobayashi, Takuya Tsunoda, Satoshi Wada
Software Mentions: 3
Published: about 6 years ago

10.3389/fphys.2018.00618

Coactivation of TLR2 and TLR8 in Primary Human Monocytes Triggers a Distinct Inflammatory Signaling Response
Cited by: 14
Author(s): Korbinian Bösl, Miriam S. Giambelluca, Markus Haug, Marit Bugge, Terje Espevik, Richard K. Kandasamy, Bjarte Bergstrøm
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2019.00190

OSlms: A Web Server to Evaluate the Prognostic Value of Genes in Leiomyosarcoma
Cited by: 24
Author(s): Qiang Wang, Longxiang Xie, Yifang Dang, Xiaoxiao Sun, Tiantian Xie, JJ Guo, Yali Han, Zhongyi Yan, Wan Zhu, Yunlong Wang, Wei Li, Xiangqian Guo
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-13-412

Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data
Cited by: 34
Author(s): Peter D. Tonner, Vinodh Srinivasasainagendra, Shaojie Zhang, Degui Zhi
Software Mentions: 3
Published: over 13 years ago

10.3389/fnins.2012.00156

A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs
Cited by: 13
Author(s): Sergei A. Manakov, Andrew Morton, Anton J. Enright, Seth G. N. Grant
Software Mentions: 3
Published: about 14 years ago

10.3389/fonc.2020.570281

A Three-Metabolic-Genes Risk Score Model Predicts Overall Survival in Clear Cell Renal Cell Carcinoma Patients
Cited by: 8
Author(s): Yiqiao Zhao, Zijia Tao, Xiaonan Chen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0115911

The Transcriptomic and Proteomic Landscapes of Bone Marrow and Secondary Lymphoid Tissues
Cited by: 14
Author(s): Sandra Andersson, Kenneth Nilsson, Linn Fagerberg, Björn M. Hallström, Christer Sundström, Anna Danielsson, Karolina Edlund, Mathias Uhlén, Anna Asplund
Software Mentions: 3
Published: about 11 years ago

10.1155/2008/789026

NCR-PCOPGene: An Exploratory Tool for Analysis of Sample-Classes Effect on Gene-Expression Relationships
Cited by: 2
Author(s): Juan Cedano, Mario Huerta, Enrique Querol
Software Mentions: 3
Published: about 17 years ago

10.1371/journal.pone.0078868

Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets
Cited by: 4
Author(s): Wensheng Zhang, Andrea Edwards, Erik K. Flemington, Kun Zhang
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2407-11-450

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

10.1371/journal.pone.0234299

Yellow sea mediated segregation between North East Asian Dryophytes species
Cited by: 18
Author(s): Amaël Borzée, Kevin R. Messenger, Shinhyeok Chae, Desiree Andersen, Jordy Groffen, Ye Inn Kim, Junghwa An, Siti N. Othman, Kyongsin Ri, Tu Yong Nam, Yoonhyuk Bae, Jin Ren, Jia Tang Li, Ming‐Feng Chuang, Yoonjung Yi, Yucheol Shin, Taejoon Kwon, Yikweon Jang, Mi Sook Min
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-015-0510-7

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

10.1186/1471-2164-10-26

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

10.1371/journal.pone.0251565

The protein and volatile components of trail mucus in the Common Garden Snail, Cornu aspersum
Cited by: 7
Author(s): Kaylene R. Ballard, Anne Klein, R. Andrew Hayes, Tianfang Wang, Scott F. Cummins
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-11-104

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

10.1186/1471-2105-10-138

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

10.1186/s12885-016-2453-4

Context dependent regulatory patterns of the androgen receptor and androgen receptor target genes
Cited by: 26
Author(s): Jan Roger Olsen, Waqas Azeem, Margrete R. Hellem, Kristo Marvyin, Yaping Hua, Yi Qu, Lisha Li, Biaoyang Lin, Xiaoting Ke, Anne Margrete Øyan, Karl H. Kalland
Software Mentions: 3
Published: over 9 years ago

10.3389/fnmol.2017.00250

Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder
Cited by: 25
Author(s): Matilde Cirnigliaro, Cristina Barbagallo, Mariangela Gulisano, Carla Noemi Domini, Rita Barone, Davide Barbagallo, Marco Ragusa, Cinzia Di Pietro, Renata Rizzo, Michele Purrello
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-10-147

Effects of sample size on robustness and prediction accuracy of a prognostic gene signature
Cited by: 79
Author(s): Seon‐Young Kim
Software Mentions: 3
Published: over 16 years ago

10.3389/fimmu.2019.02136

Identification and Characterization of Post-activated B Cells in Systemic Autoimmune Diseases
Cited by: 37
Author(s): Sarah Y. Weißenberg, Franziska Szelinski, Eva Schrezenmeier, Ana‐Luisa Stefanski, Annika Wiedemann, Héctor Rincón‐Arévalo, Anna Welle, Annemarie Jungmann, Karl Nordström, Jörn Walter, Juliana Imgenberg‐Kreuz, Gunnel Nordmark, Lars Rönnblom, Prathyusha Bachali, Michelle D. Catalina, Amrie C. Grammer, Peter E. Lipsky, Andreia C. Lino, Thomas Dörner
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2018.00083

Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned
Cited by: 57
Author(s): Emily Price, Wendy P. Robinson
Software Mentions: 3
Published: almost 8 years ago

10.1093/ajcn/nqz012

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

10.3389/fendo.2021.628907

Identification of Key Pathways and Genes in Obesity Using Bioinformatics Analysis and Molecular Docking Studies
Cited by: 7
Author(s): Harish Joshi, Basavaraj Vastrad, Nidhi Joshi, Chanabasayya Vastrad, Anandkumar Tengli, Iranna Kotturshetti
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-10-419

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation
Cited by: 32
Author(s): Sergei A. Manakov, Seth G. N. Grant, Anton J. Enright
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-7-228

Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts
Cited by: 26
Author(s): Claudia Mabel Terenti Romero, David DeShazer, Tamara Feldblyum, Jacques Ravel, Donald E. Woods, Heenam Stanley Kim, Yan Yu, Catherine M. Ronning, William C. Nierman
Software Mentions: 3
Published: over 19 years ago

10.1371/journal.pntd.0005559

MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni
Cited by: 32
Author(s): Anna V. Protasio, Stijn van Dongen, Julie Collins, Leonor Quintais, Diogo M Ribeiro, Florian Sessler, Martin Hunt, Gabriel Rinaldi, James J. Collins, Anton J. Enright, Matthew Berriman
Software Mentions: 3
Published: over 8 years ago

10.3389/fcell.2021.642697

Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord
Cited by: 3
Author(s): Filipe Almeida Monteiro, Rafael Mendes Miranda, Marta C Samina, Ana Cristina Dias, Alexandre A.S.F. Raposo, Patrícia Oliveira, Carlos Reguenga, Diogo S. Castro, Deolinda Lima
Software Mentions: 3
Published: almost 5 years ago

10.3389/fcell.2021.703489

Reconstruction of the Cytokine Signaling in Lysosomal Storage Diseases by Literature Mining and Network Analysis
Cited by: 3
Author(s): Silvia Parolo, Danilo Tomasoni, Pranami Bora, Alan Ramponi, Chanchala Kaddi, Karim Azer, Enrico Domenici, Susana Neves-Zaph, Rosario Lombardo
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pntd.0008059

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

10.1002/1878-0261.12522

PARP1 expression in soft tissue sarcomas is a poor‐prognosis factor and a new potential therapeutic target
Cited by: 15
Author(s): François Bertucci, Pascal Finetti, Audrey Monneur, Delphine Perrot, Christine Chevreau, Axel Le Cesne, Jean‐Yves Blay, Olivier Mir, Daniel Birnbaum
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-514

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

10.1186/1471-2164-10-420

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

10.1371/journal.pgen.1003067

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

10.1016/j.molmet.2020.101015

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

10.1038/s41419-019-1397-4

EMT is associated with an epigenetic signature of ECM remodeling genes
Cited by: 83
Author(s): Paul Peixoto, Amandine Etcheverry, Marc Aubry, Anaïs Missey, Camille Lachat, Jérôme Perrard, Elodie Hendrick, Régis Delage-Mourroux, Jean Mosser, Christophe Borg, Jean-Paul Feugeas, Michaël Herfs, Michaël Boyer-Guittaut, Éric Hervouet
Software Mentions: 3
Published: almost 7 years ago

10.1111/mec.13362

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

10.1016/j.mce.2020.111007

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

10.1186/1471-2105-11-73

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

10.1186/1471-2105-13-85

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

10.1186/1471-2164-10-98

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

10.1186/s12943-020-01155-z

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

10.1186/1471-2164-14-127

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

10.1186/s12943-016-0554-y

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

10.3389/fncel.2020.599152

Intrinsically Self-renewing Neuroprogenitors From the A/J Mouse Spiral Ganglion as Virtually Unlimited Source of Mature Auditory Neurons
Cited by: 7
Author(s): Francis Rousset, Vivianne Beatrix Christina Kokje, Rebecca Sipione, Dominik Schmidbauer, German Nacher-Soler, Sten Ilmjärv, Marta Coelho, Stefan Fink, François Voruz, Antoun El Chemaly, Antoine Marteyn, Hubert Löwenheim, Karl‐Heinz Krause, Marcus Müller, Rudolf Glückert, Pascal Senn
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0246983

Who infects whom?—Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data
Cited by: 9
Author(s): Annette Nigsch, Suelee Robbe‐Austerman, Tod Stuber, Paulina D. Pavinski Bitar, Yrjö T. Gröhn, Y.H. Schukken
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-15-S14-S4

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

10.1371/journal.pgen.1005250

Genetic Regulation of Bone Metabolism in the Chicken: Similarities and Differences to Mammalian Systems
Cited by: 41
Author(s): Martin Johnsson, Kenneth B. Jonsson, Leif C. Andersson, Per Jensen, I. A. Wright
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0241754

Emergence of a novel chikungunya virus strain bearing the E1:V80A substitution, out of the Mombasa, Kenya 2017-2018 outbreak
Cited by: 9
Author(s): Fredrick Eyase, Solomon Langat, Irina Maljkovic Berry, Francis Mulwa, Albert Nyunja, James Mu, Samuel Owaka, Samson Limbaso, Victor Ofula, Hellen Koka, Edith Koskei, Joel Lutomiah, Richard G. Jarman, Rosemary Sang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0130262

How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq
Cited by: 31
Author(s): Luis Fernando García-Ortega, Octavio Martínez
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0224900

UM171 induces a homeostatic inflammatory-detoxification response supporting human HSC self-renewal
Cited by: 28
Author(s): Jalila Chagraoui, Bernhard Lehnertz, Simon Girard, Jean François Spinella, Iman Fares, Elisa Tomellini, Nadine Mayotte, Sophie Corneau, Tara MacRae, Laura Simon, Guy Sauvageau
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1006179

Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes
Cited by: 83
Author(s): Kyuha Choi, Carsten Reinhard, Heïdi Serra, Piotr A Ziolkowski, Charles J Underwood, Xiaohui Zhao, Thomas J. Hardcastle, Nataliya E. Yelina, Catherine Griffin, Matthew A. Jackson, Christine Mézard, Gil McVean, Gregory P. Copenhaver, Ian Henderson
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0128845

Comparison of High-Level Microarray Analysis Methods in the Context of Result Consistency
Cited by: 37
Author(s): Kornel Chromiński, Magdalena Tkacz
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1005969

Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators
Cited by: 49
Author(s): So Yeon Kwon, Valentina Grisan, Boyun Jang, John Herbert, Paul Badenhorst
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pgen.1000574

Alternative Splicing of NURF301 Generates Distinct NURF Chromatin Remodeling Complexes with Altered Modified Histone Binding Specificities
Cited by: 53
Author(s): So Yeon Kwon, Hua Xiao, Carl Wu, Paul Badenhorst
Software Mentions: 3
Published: over 16 years ago

10.1042/BSR20210617

Integrated bioinformatics analysis reveals novel key biomarkers and potential candidate small molecule drugs in gestational diabetes mellitus
Cited by: 5
Author(s): Varun Alur, Varshita Raju, Basavaraj Vastrad, Anandkumar Tengli, Chanabasayya Vastrad, Shivakumar Kotturshetti
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1003868

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

10.1371/journal.pgen.0030145

Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells
Cited by: 80
Author(s): Marica Grs̆ković, Christina Chaivorapol, Alexandre Gaspar-Maia, Hao Li, Miguel Ramalho-Santos
Software Mentions: 3
Published: over 18 years ago

10.1371/journal.pone.0029917

Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe
Cited by: 29
Author(s): Huei-Mei Chen, Adam P. Rosebrock, Sohail Khan, Bruce Futcher, Janet Leatherwood
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pcbi.1005703

Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
Cited by: 32
Author(s): Lingfei Wang, Tom Michoel
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1005157

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

10.1371/journal.pgen.1000311

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

10.1371/journal.pone.0228964

Genetic characteristics of Jiaji Duck by whole genome re-sequencing
Cited by: 7
Author(s): Lihong Gu, Wang Feng, Zhemin Lin, Tieshan Xu, Dajie Lin, Manping Xing, Shuo Yang, Zhe Chao, Baoguo Ye, Licong Peng, Chunhui Hui, Lizhi Liu, Shuisheng Hou
Software Mentions: 3
Published: almost 6 years ago

10.3390/metabo11040221

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

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962