bioconductor: ArrayExpress | Projects

10.1371/journal.pone.0253340

Placental DNA methylation changes and the early prediction of autism in full-term newborns
Cited by: 11
Author(s): Ray O. Bahado‐Singh, Sangeetha Vishweswaraiah, Buket Aydas, Uppala Radhakrishna
Software Mentions: 3
Published: almost 5 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

10.7717/peerj.175

Data reuse and the open data citation advantage
Cited by: 358
Author(s): Heather Piwowar
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0243684

Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)
Cited by: 19
Author(s): Roger Brown, Lindsey Moore, Amir Mani, Sonal Patel, Irene Salinas
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0222921

Computational identification of key genes that may regulate gene expression reprogramming in Alzheimer’s patients
Cited by: 20
Author(s): Judith A. Potashkin, Virginie Bottero, José A. Santiago, James P. Quinn
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0226905

Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells
Cited by: 9
Author(s): Xiangqin Ji, Penglei Jiang, Juntao Luo, Mengjia Li, Yajing Bai, Junfang Zhang, Bingshe Han
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0239938

Severity of bovine tuberculosis is associated with innate immune-biased transcriptional signatures of whole blood in early weeks after experimental Mycobacterium bovis infection
Cited by: 6
Author(s): Jayne E Wiarda, Paola M. Boggiatto, Darrell O. Bayles, W. Ray Waters, Tyler C. Thacker, Mitchell V. Palmer
Software Mentions: 3
Published: over 5 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: about 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: over 6 years ago

10.1371/journal.pone.0179065

Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis
Cited by: 64
Author(s): Thomas Mohr, Verena Haudek-Prinz, Astrid Slany, Johannes Grillari, M. Micksche, Christopher Gerner
Software Mentions: 3
Published: almost 9 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: about 7 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

10.1093/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: about 7 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: over 14 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

10.1371/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: over 5 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.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

10.3389/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

10.1371/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

10.3389/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

10.1186/1471-2164-14-514

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: over 13 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: almost 7 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

10.1186/1471-2164-10-420

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: over 17 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: almost 5 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: about 8 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

10.3389/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: over 5 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: almost 5 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: over 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: over 17 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

10.1186/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: about 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: about 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: over 9 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: over 6 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

10.7150/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: over 5 years ago

10.3389/fbioe.2020.584614

Revisiting the Growth Modulon of Corynebacterium glutamicum Under Glucose Limited Chemostat Conditions
Cited by: 5
Author(s): Michaela Graf, Thorsten Haas, Attila Teleki, André Feith, Martin Cerff, Wolfgang Wiechert, Katharina Nöh, Tobias Busche, Jörn Kalinowski, Ralf Takors
Software Mentions: 3
Published: over 5 years ago

10.1186/1476-4598-9-189

The dietary isothiocyanate sulforaphane modulates gene expression and alternative gene splicing in a PTEN null preclinical murine model of prostate cancer
Cited by: 50
Author(s): Μαρία Τράκα, Caroline A Spinks, Joanne F. Doleman, Antonietta Melchini, Richard Y. Ball, Robert Mills, Richard Mithen
Software Mentions: 3
Published: almost 16 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: over 11 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: over 11 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

10.12688/f1000research.10960.2

A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification
Cited by: 11
Author(s): Jessica Roelands, Julie Decock, Sabri Boughorbel, Darawan Rinchai, Cristina Maccalli, Michele Ceccarelli, Michael A. Black, Chris Print, Jeff Chou, Scott Presnell, Charlie Quinn, Puthen V. Jithesh, Najeeb Syed, Salha B.J. Al Bader, Shahinaz Bedri, Ena Wang, Francesco M. Marincola, Damien Chaussabel, Peter J.K. Kuppen, Lance D. Miller, Davide Bedognetti, Wouter Hendrickx
Software Mentions: 3
Published: about 8 years ago

10.12688/f1000research.9611.3

Revisiting inconsistency in large pharmacogenomic studies
Cited by: 42
Author(s): Zhaleh Safikhani, Петр Смирнов, Mark Freeman, Nehmé El-Hachem, Adrian She, Rene Quevedo, Anna Goldenberg, Nicolai J. Birkbak, Christos Hatzis, Leming Shi, Andrew H. Beck, Hugo J.W.L. Aerts, John Quackenbush, Benjamin Haibe‐Kains
Software Mentions: 3
Published: over 8 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: almost 6 years ago

10.1186/2047-783X-18-44

RETRACTED ARTICLE: Gene expression profiling analysis of hepatocellular carcinoma
Cited by: 4
Author(s): Deyong Kong, Heming Chen, Weiqun Chen, Shuiyi Liu, Hui Wang, Tangwei Wu, Hongda Lu, Qing Kong, Xiaodong Huang, Zhongxin Lu
Software Mentions: 3
Published: over 12 years ago

10.1111/j.1525-142X.2010.00400.x

Molecular signaling in zebrafish development and the vertebrate phylotypic period
Cited by: 37
Author(s): Aurélie Comte, Julien Roux, Marc Robinson‐Rechavi
Software Mentions: 3
Published: about 16 years ago

10.3390/microarrays5030023

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories
Cited by: 9
Author(s): Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
Software Mentions: 3
Published: over 9 years ago

10.15252/emmm.201606711

Gene signature driving invasive mucinous adenocarcinoma of the lung
Cited by: 72
Author(s): Minzhe Guo, Koichi Tomoshige, Michael Meister, Thomas Muley, Takuya Fukazawa, Tomoshi Tsuchiya, Rebekah Karns, Arne Warth, Iris M. Fink-Baldauf, Takeshi Nagayasu, Yoshio Naomoto, Yan Xu, Marcus Mall, Yutaka Maeda
Software Mentions: 3
Published: about 9 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: about 5 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: almost 9 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

10.1093/database/bay003

TISSUES 2.0: an integrative web resource on mammalian tissue expression
Cited by: 110
Author(s): Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
Software Mentions: 3
Published: over 8 years ago

10.18632/aging.103073

MicroRNA-375 exacerbates knee osteoarthritis through repressing chondrocyte autophagy by targeting ATG2B
Cited by: 30
Author(s): Hongxing Li, Zhiling Li, Yigang Pi, Yang Chen, Lin Mei, Yiliao Luo, Jingping Xie, Xinzhan Mao
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-8-428

Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison
Cited by: 226
Author(s): S. Pilati, Michele Perazzolli, A. Malossini, Alessandro Cestaro, L. Dematté, Paolo Fontana, A. Dal Rì, Roberto Viola, Riccardo Velasco, C. Moser
Software Mentions: 3
Published: over 18 years ago

10.1093/database/baab006

Curation of over 10 000 transcriptomic studies to enable data reuse
Cited by: 18
Author(s): Nathaniel Lim, Stepan Tesar, Manuel Belmadani, Guillaume Poirier-Morency, B. Ogan Mancarci, Jordan Sicherman, Matthew P. Jacobson, Justin Leong, Pei‐Hua Tan, Paul Pavlidis
Software Mentions: 3
Published: over 5 years ago

10.1016/j.devcel.2019.05.020

Drosophila Ovarian Germline Stem Cell Cytocensor Projections Dynamically Receive and Attenuate BMP Signaling
Cited by: 25
Author(s): Scott G. Wilcockson, Hilary L. Ashe
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-5176-x

funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data
Cited by: 5
Author(s): Liis Kolberg, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-494

Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast
Cited by: 2
Author(s): Lucas D. Ward, Junbai Wang, Harmen J. Bussemaker
Software Mentions: 3
Published: almost 12 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: over 13 years ago

10.1002/cam4.1633

Molecular heterogeneity in human papillomavirus‐dependent and ‐independent vulvar carcinogenesis
Cited by: 16
Author(s): Dorian R.A. Swarts, Quirinus J.M. Voorham, Annina P. van Splunter, Saskia M. Wilting, Daoud Sie, Divera T.M. Pronk, Marc van Beurden, Daniëlle A.M. Heideman, Peter J.F. Snijders, Chris J.L.M. Meijer, Renske D.M. Steenbergen, Maaike Bleeker
Software Mentions: 3
Published: over 7 years ago

10.1007/s00262-020-02718-1

Immune checkpoint-related serum proteins and genetic variants predict outcomes of localized prostate cancer, a cohort study
Cited by: 35
Author(s): Qinchuan Wang, Yuanqing Ye, Hao Yu, Shu-Hong Lin, Huakang Tu, Dong Liang, David W. Chang, Maosheng Huang, Xifeng Wu
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-13-S14-S5

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
Cited by: 12
Author(s): Ivan Merelli, Federica Viti, Luciano Milanesi
Software Mentions: 3
Published: over 13 years ago

10.1093/database/bay011

BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology
Cited by: 23
Author(s): Kleanthi Lakiotaki, Nikolaos Vorniotakis, Michail Tsagris, Γεώργιος Γεωργακόπουλος, Ioannis Tsamardinos
Software Mentions: 3
Published: over 8 years ago

10.1093/database/baz106

Enabling semantic queries across federated bioinformatics databases
Cited by: 22
Author(s): Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson‐Rechavi, Christophe Dessimoz
Software Mentions: 3
Published: over 7 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: almost 14 years ago

10.1186/s12935-021-01932-w

SNRPD1 confers diagnostic and therapeutic values on breast cancers through cell cycle regulation
Cited by: 7
Author(s): Xiaofeng Dai, Lihui Yu, Xiao Chen, Jianying Zhang
Software Mentions: 3
Published: almost 5 years ago

10.1155/2012/650842

ArraySearch: A Web-Based Genomic Search Engine
Cited by: 1
Author(s): Tyler J. Wilson, Xijin Ge
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pgen.0040014

Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules
Cited by: 481
Author(s): Todd P. Michael, Todd C. Mockler, Ghislaı̀n Breton, Connor McEntee, Amanda Byer, Jonathan D. Trout, Samuel P. Hazen, Rongkun Shen, Henry D. Priest, Christopher Sullivan, Scott A. Givan, Marcelo J. Yanovsky, Fangxin Hong, Steve A. Kay, Joanne Chory
Software Mentions: 3
Published: about 18 years ago

10.1186/s12859-020-3364-6

Detection of suspicious interactions of spiking covariates in methylation data
Cited by: 0
Author(s): Miriam Sieg, Gregor Richter, Arne S. Schäefer, Jochen Kruppa
Software Mentions: 3
Published: about 6 years ago

10.1016/j.dib.2020.106604

RNA-Seq transcriptome data of human cells infected with influenza A/Puerto Rico/8/1934 (H1N1) virus
Cited by: 6
Author(s): Evgenii Zhuravlev, Mariia Sergeeva, Sergey Malanin, Р. Н. Амирханов, Dmitriy V. Semenov, Tatiana V. Grigoryeva, Andrey Komissarov, Г. А. Степанов
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-11-27

Genomics Portals: integrative web-platform for mining genomics data
Cited by: 13
Author(s): Kaustubh Shinde, Mukta Phatak, Johannes M. Freudenberg, Jing Chen, Qian Li, Joshi K Vineet, Zhen Hu, Krishnendu Ghosh, Jarosław Meller, Mario Medvedovic
Software Mentions: 3
Published: about 16 years ago

10.1093/bib/bby051

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
Cited by: 103
Author(s): Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura E. Taggart, Huiru Zheng, Eileen E. Parkes, Jaine K. Blayney
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0142443

Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma
Cited by: 9
Author(s): Abhinav Kaushik, Yashuma Bhatia, Shakir Ali, Dinesh Gupta
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-019-5748-4

Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets
Cited by: 1
Author(s): Dirkjan Schokker, Ina Hulsegge, H. Woelders, Johanna M.J. Rebel
Software Mentions: 3
Published: almost 7 years ago

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: over 14 years ago

10.1186/bcr2926

Identification of germline alterations of the mad homology 2 domain of SMAD3 and SMAD4 from the Ontario site of the breast cancer family registry (CFR)
Cited by: 17
Author(s): Eric Tram, Irada Ibrahim‐Zada, Laurent Briollais, Julia A. Knight, Irene L. Andrulis, Hilmi Özçelik
Software Mentions: 3
Published: over 14 years ago

10.1186/s12859-019-2912-4

TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Cited by: 2
Author(s): Salvatore Alaimo, Annalisa Di Maria, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti
Software Mentions: 3
Published: over 6 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: almost 11 years ago

10.1371/journal.pone.0228314

Influence of heat stress on reference genes stability in heart and liver of two chickens genotypes
Cited by: 5
Author(s): Juliana Gracielle Gonzaga Gromboni, Hellenn Cardoso Oliveira, Daniele Botelho Diniz Marques, Adriana García, Ronaldo Vasconcelos Farias Filho, Caio Fernando Gromboni, Teillor Machado Souza, Amauri Arias Wenceslau
Software Mentions: 3
Published: about 6 years ago

10.1186/bcr2256

Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression
Cited by: 46
Author(s): Cecilia Williams, Luísa A. Helguero, Karin Edvardsson, Lars Arne Haldosén, Jan‐Åke Gustafsson
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2105-6-264

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination
Cited by: 33
Author(s): David G. Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, Andrew J. Wood, Karim Nashar, Douglas B. Kell, Andy Brass
Software Mentions: 2
Published: over 20 years ago

10.1186/bcr2109

PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes
Cited by: 25
Author(s): Anna Git, Inmaculada Spiteri, Cherie Blenkiron, Mark J. Dunning, Jessica C. Pole, Suet-Feung Chin, Yanzhong Wang, James Smith, Frederick J. Livesey, Carlos Caldas
Software Mentions: 2
Published: almost 18 years ago

10.1186/bcr2192

A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer
Cited by: 117
Author(s): Fabien Reyal, Martin H. van Vliet, Nicola J. Armstrong, Hugo M. Horlings, Karin E. de Visser, M Kok, Andrew E. Teschendorff, Stella Mook, Laura van ’t Veer, Carlos Caldas, Rémy Salmon, Marc J. van de Vijver, Lodewyk F.A. Wessels
Software Mentions: 2
Published: over 17 years ago

10.1186/bcr2334

Genomic profiling of breast tumours in relation to BRCAabnormalities and phenotypes
Cited by: 131
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Óskar Þór Jóhannsson, Katrín Ólafsdóttir, Margrét Steinarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2164-9-232

Genomic analysis of post-mating changes in the honey bee queen (Apis mellifera)
Cited by: 122
Author(s): Sarah D. Kocher, Freddie-Jeanne Richard, David R. Tarpy, Christina M. Grozinger
Software Mentions: 2
Published: almost 18 years ago

10.1186/bcr3403

Embryonic mammary signature subsets are activated in Brca1 -/- and basal-like breast cancers
Cited by: 47
Author(s): Marketa Zvelebil, Erik Oliemuller, Qiong Gao, Olivia Wansbury, Alan Mackay, Howard Kendrick, Matthew J. Smalley, Jorge S. Reis‐Filho, Beatrice A. Howard
Software Mentions: 2
Published: about 13 years ago

10.1186/s13058-015-0539-6

Mouse mammary stem cells express prognostic markers for triple-negative breast cancer
Cited by: 32
Author(s): Kelly Soady, Howard Kendrick, Qiong Gao, Andrew Tutt, Marketa Zvelebil, Liliana Ordonez, Jelmar Quist, David Wei-Min Tan, Clare M. Isacke, Anita Grigoriadis, Matthew J. Smalley
Software Mentions: 2
Published: about 11 years ago

10.3390/cancers12102823

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling
Cited by: 5
Author(s): Ian M. Overton, Andrew H. Sims, Jeremy A. Owen, Bret S.E. Heale, Matthew J. Ford, Alexander L R Lubbock, Erola Pairo-Castineira, Abdelkader Essafi
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-6-101

MARS: Microarray analysis, retrieval, and storage system
Cited by: 59
Author(s): Michael Maurer, Robert Molidor, Alexander Sturn, Jürgen Hartler, Hubert Hackl, Gernot Stocker, Andreas Prokesch, Marcel Scheideler, Zlatko Trajanoski
Software Mentions: 2
Published: almost 21 years ago

10.1590/1414-431X2020e10388

Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification
Cited by: 0
Author(s): Lucas Delmonico, John C. Obenauer, Thomas P. Stockfisch, Marcia V. Fournier
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12030549

Sphere-Forming Culture for Expanding Genetically Distinct Patient-Derived Glioma Stem Cells by Cellular Growth Rate Screening
Cited by: 2
Author(s): Ki Soon Shin, Hong-Jae Shin, Hee Jin Cho, Hyunju Kang, Jin Ku Lee, Yun Jee Seo, Yong Jae Shin, Donggeon Kim, Harim Koo, Doo‐Sik Kong, Ho Jun Seol, Jung-Il Lee, Hye Won Lee, Do‐Hyun Nam
Software Mentions: 2
Published: about 6 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962