bioconductor: ArrayExpress | Projects

10.1186/s12920-017-0293-y

Differential gene expression in disease: a comparison between high-throughput studies and the literature
Cited by: 52
Author(s): Raul Rodriguez‐Esteban, Xiaoyu Jiang
Software Mentions: 1
Published: over 8 years ago

10.1186/s12920-014-0063-z

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

10.1186/1755-8794-6-35

Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers
Cited by: 34
Author(s): Adam L. Cohen, Stephen R. Piccolo, Luis Cheng, Rafaella Soldi, Bing Han, W. Evan Johnson, Andrea Bild
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-7-311

Web-based analysis of the mouse transcriptome using Genevestigator
Cited by: 25
Author(s): Oliver Laule, Matthias Hirsch‐Hoffmann, Tomás Hrúz, Wilhelm Gruissem, Philip Zimmermann
Software Mentions: 1
Published: over 19 years ago

10.1038/srep33924

Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin
Cited by: 17
Author(s): Magdalena B. Rother, Kristin Jensen, Mirjam van der Burg, Fleur S. van de Bovenkamp, Roel Kroek, Wilfred F. J. van IJcken, Vincent H.J. van der Velden, Tom Cupedo, Ole Kristoffer Olstad, Jacques J. M. van Dongen, Menno C. van Zelm
Software Mentions: 1
Published: over 9 years ago

10.1038/srep34730

Novel population of small tumour-initiating stem cells in the ovaries of women with borderline ovarian cancer
Cited by: 40
Author(s): Irma Virant‐Klun, Martin Štimpfel
Software Mentions: 1
Published: over 9 years ago

10.1186/1755-8794-2-18

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

10.1186/s13148-018-0542-8

Epigenetic regulation of ID4 in breast cancer: tumor suppressor or oncogene?
Cited by: 20
Author(s): Daniela Nasif, Emanuel Campoy, Sergio Laurito, Richard L. Branham, Guillermo Urrutia, María Roqué, Marı́a Teresita Branham
Software Mentions: 1
Published: over 7 years ago

10.1186/1755-8794-2-41

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus
Cited by: 12
Author(s): Yaomin Hu, Pamela J. Kaisaki, Karène Argoud, Steven P. Wilder, Karin J. Wallace, Peng Yeong Woon, Christine Blancher, Lise Tarnow, Per‐Henrik Groop, Samy Hadjadj, Michel Marre, Hans‐Henrik Parving, Martin Farrall, Roger D. Cox, Mark Lathrop, Nathalie Vionnet, Marie-Thérèse Bihoreau, Dominique Guyader
Software Mentions: 1
Published: over 16 years ago

10.1186/s13148-020-00851-3

Genome-wide DNA methylation profiles of low- and high-grade adenoma reveals potential biomarkers for early detection of colorectal carcinoma
Cited by: 32
Author(s): Fan Jian, Jun Li, Shicheng Guo, Chengcheng Tao, Haikun Zhang, Wenjing Wang, Ying Zhang, Dake Zhang, Shigang Ding, Changqing Zeng
Software Mentions: 1
Published: almost 6 years ago

10.1186/1755-8794-3-5

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

10.1007/s10585-016-9810-1

Prognostic value of 5-microRNA based signature in T2-T3N0 colon cancer
Cited by: 49
Author(s): Maciej Bobowicz, Marcin Skrzypski, Piotr Czapiewski, Michał Marczyk, Agnieszka Maciejewska, Michał Jankowski, Anna Szulgo-Paczkowska, Wojciech Zegarski, Ryszard Pawłowski, Joanna Polańska, Wojciech Biernat, Janusz Jaśkiewicz, Jacek Jassem
Software Mentions: 1
Published: over 9 years ago

10.1093/cid/ciaa503

The Current Status of Enteric Fever Diagnostics and Implications for Disease Control
Cited by: 2
Author(s): Stephen Baker, Christoph J. Blohmke, Mailis Maes, Peter I Johnston, Thomas C. Darton
Software Mentions: 1
Published: over 5 years ago

10.1038/srep34719

Hepatic Deletion of Janus Kinase 2 Counteracts Oxidative Stress in Mice
Cited by: 23
Author(s): Madeleine Themanns, Kristina M. Mueller, Sonja M. Kessler, Nicole Golob-Schwarzl, Thomas Mohr, Doris Kaltenecker, Jérôme Bourgeais, Jamile Paier-Pourani, Katrin Friedbichler, Doris Schneller, Michaela Schlederer, Eva Zebedin-Brandl, Luigi Terracciano, Xiaonan Han, Lukas Kenner, Kay Uwe Wagner, Wolfgang Mikulits, Andrey V. Kozlov, Markus H. Heim, Fabrice Gouilleux, Johannes Haybaeck, Richard Moriggl
Software Mentions: 1
Published: over 9 years ago

10.1038/cti.2015.17

Expression profiling pre‐diabetic mice to uncover drugs with clinical application to type 1 diabetes
Cited by: 2
Author(s): Dimeng Pang, Katharine M. Irvine, Ahmed M. Mehdi, Helen E. Thomas, Mark Harris, Emma E. Hamilton‐Williams, Ranjeny Thomas
Software Mentions: 1
Published: over 10 years ago

10.1186/2001-1326-3-7

Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development
Cited by: 108
Author(s): Maria Frantzi, Akshay Bhat, Agnieszka Latosinska
Software Mentions: 1
Published: almost 12 years ago

10.1186/1755-8794-2-12

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

10.1155/2018/1270483

Kynurenic Acid Protects against Thioacetamide-Induced Liver Injury in Rats
Cited by: 24
Author(s): Sebastian Marciniak, Artur Wnorowski, Katarzyna Smolińska, Beata Walczyna, Waldemar A. Turski, Tomasz Kocki, Piotr Paluszkiewicz, Jolanta Parada-Turska
Software Mentions: 1
Published: over 7 years ago

10.1038/s42003-019-0281-1

SnRK2 protein kinases represent an ancient system in plants for adaptation to a terrestrial environment
Cited by: 69
Author(s): Akihisa Shinozawa, Ryoko Otake, Daisuke Takezawa, Taishi Umezawa, Kenji Kono, Keisuke Tanaka, Anna Amagai, Shin-nosuke Ishikawa, Yusuke Hara, Yasuko Kamisugi, Andrew C. Cuming, Koichi Hori, Hiroyuki Ohta, Fumiyuki Takahashi, Kazuo Shinozaki, Takahisa Hayashi, Teruaki Taji, Yoichi Sakata
Software Mentions: 1
Published: about 7 years ago

10.1038/srep39262

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

10.1186/1755-8794-1-33

An approach to analyse the specific impact of rapamycin on mRNA-ribosome association
Cited by: 16
Author(s): Raphaël Genolet, Tanguy Araud, Laetitia Maillard, Pascale Jaquier-Gubler, Joseph Curran
Software Mentions: 1
Published: over 17 years ago

10.1155/2021/8020067

Identification of Immune-Related Genes in Sepsis due to Community-Acquired Pneumonia
Cited by: 1
Author(s): Yanyan Li, Jiqin Wang, Yuzhen Li, Chunyan Liu, Xia Gong, Yijie Zhuang, Liang Chen, Kai Sun
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2105-10-330

BASE - 2nd generation software for microarray data management and analysis
Cited by: 50
Author(s): Johan Vallon‐Christersson, Nicklas Nordborg, Martin Svensson, Jari Häkkinen
Software Mentions: 1
Published: over 16 years ago

10.1016/j.csbj.2017.10.001

Challenges in the Setup of Large-scale Next-Generation Sequencing Analysis Workflows
Cited by: 41
Author(s): Pranav Kulkarni, Peter Frommolt
Software Mentions: 1
Published: about 9 years ago

10.1016/j.csbj.2016.10.003

Determining the Molecular Pathways Underlying the Protective Effect of Non-Steroidal Anti-Inflammatory Drugs for Alzheimer's Disease: A Bioinformatics Approach
Cited by: 12
Author(s): Alejo J. Nevado‐Holgado, Simon Lovestone
Software Mentions: 1
Published: about 9 years ago

10.1016/j.csbj.2018.02.001

An Artificial Neural Network Integrated Pipeline for Biomarker Discovery Using Alzheimer's Disease as a Case Study
Cited by: 42
Author(s): Dimitrios Zafeiris, Sergio Rutella, Graham Ball
Software Mentions: 1
Published: about 8 years ago

10.1186/cc12893

Induced expression and functional effects of aquaporin-1 in human leukocytes in sepsis
Cited by: 31
Author(s): Alice G. Vassiliou, Nikolaos A. Maniatis, Stylianos E. Orfanos, Zafeiria Mastora, Edison Jahaj, Triantafyllos Paparountas, Apostolos Armaganidis, Charis Roussos, Vassilis Aidinis, Αναστασία Κοτανίδου
Software Mentions: 1
Published: about 13 years ago

10.2174/138920208786847935

Meta Analysis of Gene Expression Data within and Across Species
Cited by: 34
Author(s): Ana Carolina Fierro, Filip Vandenbussche, Kristof Engelen, Yves Van de Peer, Kathleen Marchal
Software Mentions: 1
Published: about 17 years ago

10.1186/1755-8794-2-11

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

10.1038/srep45828

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

10.1186/s12920-016-0227-0

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

10.1186/1471-2350-8-36

Cerebellar gene expression profiles of mouse models for Rett syndrome reveal novel MeCP2 targets
Cited by: 110
Author(s): ChaRandle Jordan, Hong Hua Li, Helen H. Kwan, Uta Francke
Software Mentions: 1
Published: over 18 years ago

10.1016/j.dib.2016.11.049

Microarray dataset on the genome-wide expression profile of an M. smegmatis amtR mutant (JR258) compared to M. smegmatis mc 2 155
Cited by: 2
Author(s): Michael Petridis, Gregory M. Cook
Software Mentions: 1
Published: about 9 years ago

10.1186/2051-5960-2-23

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

10.1016/j.dib.2018.11.135

Gene ontology analysis of transcriptome data from DMBA-induced mammary tumors of rats fed a high-corn oil and a high-extra virgin olive oil diet
Cited by: 1
Author(s): Raquel Escrich, Marta Cubedo, Eduard Escrich, Raquel Moral
Software Mentions: 1
Published: about 7 years ago

10.1186/s12916-017-0929-y

A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes
Cited by: 40
Author(s): Jean‐Philippe Foy, Louis Bazire, Sandra Ortiz-Cuàran, Sophie Deneuve, Janice Kielbassa, Emilie Thomas, Alain Viari, Alain Puisieux, P. Goudot, Chloé Bertolus, Nicolas Foray, Youlia Kirova, Pierre Verrelle, Pierre Saintigny
Software Mentions: 1
Published: over 8 years ago

10.1093/database/bax101

CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system
Cited by: 21
Author(s): Yi-Fang Lee, Chien‐Yueh Lee, Liang‐Chuan Lai, Mong‐Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang
Software Mentions: 1
Published: about 8 years ago

10.1093/database/bax071

SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets
Cited by: 12
Author(s): Jin Li, Ching-San Tseng, Antonio Federico, Franjo Ivankovic, Yu-Shan Huang, Alfredo Ciccodicola, Maurice S. Swanson, Peng Yu
Software Mentions: 1
Published: about 9 years ago

10.1093/database/baz058

Chickspress: a resource for chicken gene expression
Cited by: 15
Author(s): Fiona M. McCarthy, Ken Pendarvis, Amanda M. Cooksey, Cathy Gresham, Matt Bomhoff, Sean Davey, Eric Lyons, Tad S. Sonstegard, Susan M. Bridges, Shane C. Burgess
Software Mentions: 1
Published: about 7 years ago

10.1186/s12916-016-0609-3

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

10.1093/database/bay116

YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast
Cited by: 1
Author(s): Wei Wu, Hao Ping Tu, Yu Chu, Torbjörn E. M. Nordling, Yan Yuan Tseng, Hungjiun Liaw
Software Mentions: 1
Published: about 8 years ago

10.1186/s12879-016-1533-z

The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
Cited by: 13
Author(s): Steven T. Pullan, Jon C. Allnutt, Rebecca Devine, Kim A. Hatch, Rose E. Jeeves, Charlotte L. Hendon-Dunn, Philip Marsh, Joanna Bacon
Software Mentions: 1
Published: over 9 years ago

10.1093/database/bax098

PCOSBase: a manually curated database of polycystic ovarian syndrome
Cited by: 9
Author(s): Nor Afiqah‐Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti‐Azura Mohamed‐Hussein
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-017-01156-x

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

10.1093/database/bay054

RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins
Cited by: 4
Author(s): Jin Li, Su-Ping Deng, Jacob Vieira, James Thomas, Valerio Costa, Ching-San Tseng, Franjo Ivankovic, Alfredo Ciccodicola, Peng Yu
Software Mentions: 1
Published: about 8 years ago

10.1186/s13195-014-0070-5

PLD3 is accumulated on neuritic plaques in Alzheimer’s disease brains
Cited by: 35
Author(s): Jun‐ichi Satoh, Yoshihiro Kino, Yoji Yamamoto, Natsuki Kawana, Tsuyoshi Ishida, Yuko Saito, Kunimasa Arima
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-017-04709-2

DACH1 suppresses breast cancer as a negative regulator of CD44
Cited by: 29
Author(s): Hanxiao Xu, Shengnan Yu, Xun Yuan, Jing Xiong, Dong Kuang, Richard G. Pestell, Kongming Wu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-017-05872-2

Functional and Transcriptomic Characterization of Peritoneal Immune-Modulation by Addition of Alanyl-Glutamine to Dialysis Fluid
Cited by: 12
Author(s): Rebecca Herzog, Lilian Kuster, Julia Powers Becker, Tobias Gluexam, Dietmar Pils, Andreas Spittler, Manoj Bhasin, Seth L. Alper, Andreas Vychytil, Christoph Aufricht, Klaus Kratochwill
Software Mentions: 1
Published: over 8 years ago

10.1186/s12865-017-0238-4

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

10.1093/database/baz023

YESdb: integrative analysis of environmental stress in yeast
Cited by: 1
Author(s): Evi Berchtold, Gergely Csaba, Ralf Zimmer
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-06810-y

Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1
Cited by: 13
Author(s): James McCaffrey, Nicholas J.A. Webb, Toryn Poolman, Maryline Fresquet, Cressida Moxey, Leo Zeef, Ian J. Donaldson, David Ray, Rachel Lennon
Software Mentions: 1
Published: over 8 years ago

10.1186/1748-7188-4-5

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

10.1186/1471-2164-13-49

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

10.1186/1471-2164-15-438

RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Cited by: 26
Author(s): Marta Vergara-Irigaray, María Fookes, Nicholas R. Thomson, Christoph M. Tang
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-11-433

Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization
Cited by: 10
Author(s): Ming Zhang, Yudong Zhang, Li Liu, Lijuan Yu, Shirley Tsang, Jian Tan, Wenhua Yao, Manjit S. Kang, Yong-Qiang An, Xing Fan
Software Mentions: 1
Published: over 15 years ago

10.1093/database/bay059

IsopiRBank: a research resource for tracking piRNA isoforms
Cited by: 14
Author(s): Huan Zhang, Asim Ali, Jianing Gao, Rongjun Ban, Xiaohua Jiang, Yuanwei Zhang, Qinghua Shi
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.24644

MiR-21 over-expression and Programmed Cell Death 4 down-regulation features malignant pleural mesothelioma
Cited by: 12
Author(s): Lorenzo Nicolè, Rocco Cappellesso, Tiziana Sanavia, Vincenza Guzzardo, Ambrogio Fassina
Software Mentions: 1
Published: almost 8 years ago

10.1093/database/bav022

Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer
Cited by: 4
Author(s): Ji Hyun Lee, Sungyong You, Do Young Hyeon, Byeongsoo Kang, Hyerim Kim, Kyoung Mii Park, Byung-Woo Han, Daehee Hwang, Sung Hoon Kim
Software Mentions: 1
Published: almost 11 years ago

10.1093/database/bat074

HypoxiaDB: a database of hypoxia-regulated proteins
Cited by: 29
Author(s): Pankaj Khurana, R. Sugadev, Jaspreet Jain, Shashi Bala Singh
Software Mentions: 1
Published: about 13 years ago

10.1093/database/baaa073

A curated database reveals trends in single-cell transcriptomics
Cited by: 130
Author(s): Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-017-12498-x

A dual targeted β-defensin and exome sequencing approach to identify, validate and functionally characterise genes associated with bull fertility
Cited by: 21
Author(s): Ronan Whiston, Emma K. Finlay, Matthew S. McCabe, Paul Cormican, Paul Flynn, A.R. Cromie, P. J. Hansen, A. Bruce Lyons, Seán Fair, Patrick Lonergan, Cliona O’ Farrelly, Kieran G. Meade
Software Mentions: 1
Published: over 8 years ago

10.1016/j.devcel.2016.10.015

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances
Cited by: 188
Author(s): Orsolya Symmons, Leslie Pan, Silvia Remeseiro, Tuğçe Aktaş, Felix A. Klein, Wolfgang Huber, François Spitz
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-016-2771-6

Transcriptomic response of yeast cells to ATX1 deletion under different copper levels
Cited by: 12
Author(s): Ayca Cankorur-Cetinkaya, Serpil Eraslan, Betül Kırdar
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-8-447

Application of a correlation correction factor in a microarray cross-platform reproducibility study
Cited by: 7
Author(s): Kellie J. Archer, Catherine I. Dumur, G. Scott Taylor, Michael D. Chaplin, Anthony Guiseppi‐Elie, Geraldine M. Grant, Andrea Ferreira‐Gonzalez, Carleton T. Garrett
Software Mentions: 1
Published: about 18 years ago

10.1016/j.devcel.2014.12.024

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State
Cited by: 70
Author(s): Shilu Amin, Ian J. Donaldson, Denise A. Zannino, James Hensman, Magnus Rattray, Marta Losa, François Spitz, Franck Ladam, Charles G. Sagerström, Nicoletta Bobola
Software Mentions: 1
Published: about 11 years ago

10.1242/dev.168146

Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes
Cited by: 17
Author(s): Toru Suzuki, Chisato Kikuguchi, Saori Nishijima, Takeshi Nagashima, Akinori Takahashi, Mariko Okada, Tadashi Yamamoto
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-10-215

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

10.1186/s12859-015-0854-z

Evaluation of O2PLS in Omics data integration
Cited by: 91
Author(s): Said el Bouhaddani, Jeanine J. Houwing-Duistermaat, Perttu Salo, Markus Perola, Geurt Jongbloed, Hae‐Won Uh
Software Mentions: 1
Published: about 10 years ago

10.1242/dev.112623

Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo
Cited by: 53
Author(s): Isabel Olivera-Martínez, Nicholas J. Schurch, Roman A. Li, Junfang Song, Pamela A. Halley, Raman M Das, David W. Burt, Geoffrey J. Barton, Kate G. Storey
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-8-343

Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model
Cited by: 12
Author(s): Ryoko Morioka, Shigehiko Kanaya, Masami Yokota Hirai, Mitsuru Yano, Nagahisa Ogasawara, Kazuki Saito
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-11-682

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

10.1186/1471-2105-12-S10-S2

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses
Cited by: 14
Author(s): Mikhail G. Dozmorov, Jonathan D. Wren
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-9-208

RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina
Cited by: 14
Author(s): Ravi Kiran Reddy Kalathur, Nicolas Gagnière, Guillaume Berthommier, Laetitia Poidevin, Wolfgang Raffelsberger, Raymond Ripp, Thierry Léveillard, Olivier Poch
Software Mentions: 1
Published: almost 18 years ago

10.1242/dmm.021626

Pulmonary transcriptome analysis in the rabbit model of surgically-induced diaphragmatic hernia treated with fetal tracheal occlusion
Cited by: 17
Author(s): Alexander C. Engels, Paul Brady, Molka Kammoun, Julio Finalet Ferreiro, Philip DeKoninck, Masayuki Endo, Jaan Toelen, Joris Robert Vermeesch, Jan Deprest
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-10-575

Using transcriptome profiling to characterize QTL regions on chicken chromosome 5
Cited by: 13
Author(s): Guillaume Le Mignon, Colette Désert, Frédérique Pitel, Sophie Leroux, Olivier Demeure, Grégory Guernec, Behnam Abasht, Madeleine Douaire, Pascale Le Roy, Sandrine Lagarrigue
Software Mentions: 1
Published: about 16 years ago

10.1016/j.drudis.2012.07.014

Transcriptional data: a new gateway to drug repositioning?
Cited by: 193
Author(s): Francesco Iorio, Timothy Rittman, Hong Ge, Michael P. Menden, Julio Sáez-Rodríguez
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-5-68

PEDRo: A database for storing, searching and disseminating experimental proteomics data
Cited by: 66
Author(s): Kevin Garwood, Thomas J. McLaughlin, Chris Garwood, Scott Joens, Norman Morrison, Christopher F Taylor, Kathleen M. Carroll, Caroline A. Evans, Anthony D. Whetton, Sarah R. Hart, David Stead, Zhikang Yin, Alistair J. P. Brown, Andrew Hesketh, Keith F. Chater, Lena Hansson, Muriel Mewissen, Peter Ghazal, Julie A. Howard, Kathryn S. Lilley, Simon J. Gaskell, Andy Brass, Simon J. Hubbard, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: over 21 years ago

10.1186/1471-2164-16-S1-S2

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data
Cited by: 41
Author(s): Anna L Swan, Dov J. Stekel, Charlie Hodgman, David Allaway, Mohammed Hussein Al-Qahtani, Ali Mobasheri, Jaume Bacardit
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-11-S1-S6

Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha
Cited by: 116
Author(s): Winston Koh, Chen Tian Sheng, Betty Tan, Qian Yi Lee, Vladimir A. Kuznetsov, Lim Sai Kiang, Vivek Tanavde
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-9-291

Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium
Cited by: 66
Author(s): Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens, Salvatore Bozzaro
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-11-478

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes
Cited by: 11
Author(s): Michael Klutstein, Zahava Siegfried, Ariel Gispan, Shlomit Farkash-Amar, Guy Zinman, Ziv Bar‐Joseph, Giora Simchen, Itamar Simon
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-9-285

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
Cited by: 78
Author(s): Michael Boedigheimer, Russell D. Wolfinger, Michael Bass, Pierre R. Bushel, Jeff W. Chou, Matthew N. Cooper, J. Christopher Corton, Jennifer Fostel, Susan Hester, Janice S. Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit, Karol L. Thompson
Software Mentions: 1
Published: over 17 years ago

10.15252/emmm.201708163

An <scp>FGFR</scp> 3/ <scp>MYC</scp> positive feedback loop provides new opportunities for targeted therapies in bladder cancers
Cited by: 40
Author(s): Mélanie Mahé, Florent Dufour, Hélène Neyret–Kahn, Aura Ileana Moreno-Vega, C Béraud, Ming Shi, Iméne Hamaidi, Virginia Sánchez-Quiles, Clémentine Krucker, Marion Dorland‐Galliot, Élodie Chapeaublanc, Rémy Nicolle, Hervé Lang, Célio Pouponnot, Thierry Massfelder, François Radvanyi, Isabelle Bernard‐Pierrot
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.25736

A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing’s family of tumors
Cited by: 3
Author(s): Andrew J. Annalora, Shawn T. O’Neil, Jeremy D Bushman, James Summerton, Carol S. Marcus, Patrick L. Iversen
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.26330

Whole genome duplication is an early event leading to aneuploidy in IDH-wild type glioblastoma
Cited by: 15
Author(s): Blandine Boisselier, Frédéric Dugay, Marc‐Antoine Belaud‐Rotureau, Anne Coutolleau, Emmanuel Garcion, Philippe Meneï, Philippe Guardiola, Audrey Rousseau
Software Mentions: 1
Published: about 7 years ago

10.1080/22221751.2019.1645572

Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity
Cited by: 19
Author(s): Natalie D. Collins, Steven G. Widen, Li Li, Daniele M. Swetnam, Pei–Yong Shi, Robert B. Tesh, Vanessa V. Sarathy
Software Mentions: 1
Published: about 7 years ago

10.1530/ERC-13-0098

Clinical and functional impact of TARBP2 over-expression in adrenocortical carcinoma
Cited by: 51
Author(s): Stefano Caramuta, Linkiat Lee, Deniz M. Özata, Pınar Akçakaya, Hong Xie, Anders Höög, Jan Zedenius, Martin Bäckdahl, Catharina Larsson, Weng‐Onn Lui
Software Mentions: 1
Published: over 12 years ago

10.1530/ERC-17-0399

GnRH antagonist treatment of malignant adrenocortical tumors
Cited by: 14
Author(s): Milena Doroszko, Marcin Chruściel, Joanna Stelmaszewska, T. Ślęzak, Sławomir Anisimowicz, Ursula Plöckinger, Marcus Quinkler, Marco Bonomi, Sławomir Wołczyński, Ilpo Huhtaniemi, Jorma Toppari, Nafis Rahman
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-21915-8

Morphine induces changes in the gut microbiome and metabolome in a morphine dependence model
Cited by: 144
Author(s): Fuyuan Wang, Jingjing Meng, Li Zhang, Timothy J. Johnson, Chi Chen, Sabita Roy
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-12-137

Assessing affymetrix GeneChip microarray quality
Cited by: 70
Author(s): Matthew N. McCall, Peter Murakami, Margus Lukk, Wolfgang Huber, Rafael A. Irizarry
Software Mentions: 1
Published: almost 15 years ago

10.1111/1462-2920.12726

Adaptation of anaerobic cultures ofEscherichia coli K-12 in response to environmental trimethylamine-N-oxide
Cited by: 9
Author(s): Katie J. Denby, Matthew D. Rolfe, Ellen Crick, Guido Sanguinetti, Robert K. Poole, Jeffrey Green
Software Mentions: 1
Published: about 11 years ago

10.1111/j.1462-2920.2011.02461.x

Genomic variations define divergence of water/wildlife‐associated Campylobacter jejuni niche specialists from common clonal complexes
Cited by: 54
Author(s): Philip J. Hepworth, Kevin E. Ashelford, Jason Hinds, Katherine A. Gould, Adam A. Witney, Nicola Williams, Howard Leatherbarrow, Nigel P. French, Richard J. Birtles, Chriselle Mendonca, Nick Dorrell, Brendan W. Wren, Paul Wigley, Neil Hall, Craig Winstanley
Software Mentions: 1
Published: almost 15 years ago

10.1038/s41598-018-24437-5

Deviations of the immune cell landscape between healthy liver and hepatocellular carcinoma
Cited by: 130
Author(s): Nataliya Rohr-Udilova, Florian Klinglmüller, Rolf Schulte‐Hermann, Judith Stift, Merima Herac, Martina Salzmann, Francesca Finotello, Gerald Timelthaler, Georg Oberhuber, Matthias Pinter, Thomas Reiberger, Erika Jensen‐Jarolim, Robert Eferl, Michael Trauner
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-9-171

Transcriptional regulation by Poly(ADP-ribose) polymerase-1 during T cell activation
Cited by: 41
Author(s): Luis Sáenz, Juan José Lozano, Rut Valdor, Alberto Baroja‐Mazo, Pablo Ramı́rez, Pascual Parrilla, Pedro Aparicio, Lauro Sumoy, José Yélamos
Software Mentions: 1
Published: almost 18 years ago

10.1038/s41598-018-24769-2

Profiling of 179 miRNA Expression in Blood Plasma of Lung Cancer Patients and Cancer-Free Individuals
Cited by: 32
Author(s): Ivan A. Zaporozhchenko, Evgeny S. Morozkin, Anastasia A. Ponomaryova, Elena Y. Rykova, Н. В. Чердынцева, А. А. Жеравин, O. A. Pashkovskaya, Evgeny Pokushalov, Valentin V. Vlassov, Pavel P. Laktionov
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13072-015-0018-4

Role of Ccr4-Not complex in heterochromatin formation at meiotic genes and subtelomeres in fission yeast
Cited by: 40
Author(s): Cristina Cotobal, María Rodríguez-López, Caia D. S. Duncan, Ayesha Hasan, Akira Yamashita, Masayuki Yamamoto, Jürg Bähler, Juan Mata
Software Mentions: 1
Published: over 10 years ago

10.1186/s13072-016-0078-0

Chromatin variation associated with liver metabolism is mediated by transposable elements
Cited by: 30
Author(s): Juan Du, Amy Leung, Candi Trac, Michael Lee, Brian W. Parks, Aldons J. Lusis, Rama Natarajan, Dustin E. Schones
Software Mentions: 1
Published: over 9 years ago

10.1186/1756-8935-3-6

A paucity of heterochromatin at functional human neocentromeres
Cited by: 86
Author(s): Alicia Alonso, Dan Hasson, Fanny Cheung, Peter E. Warburton
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-10-350

Type I interferon receptor-independent and -dependent host transcriptional responses to mouse hepatitis coronavirus infection in vivo
Cited by: 17
Author(s): Matthijs Raaben, Marian J. A. Groot Koerkamp, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-13-323

Flexible and efficient genome tiling design with penalized uniqueness score
Cited by: 3
Author(s): Yang Du, Eduard Muráni, Siriluck Ponsuksili, Klaus Wimmers
Software Mentions: 1
Published: about 13 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Penalties:

Papers Mentioning ArrayExpress 1,962