bioconductor: ArrayExpress | Projects

10.1002/cam4.3367

Identification of small molecule drugs and development of a novel autophagy‐related prognostic signature for kidney renal clear cell carcinoma
Cited by: 9
Author(s): Qianwei Xing, Chengjian Ji, Bingye Zhu, Rong Cong
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0238202

Immune and sex-biased gene expression in the threatened Mojave desert tortoise, Gopherus agassizii
Cited by: 2
Author(s): Cindy Xu, Greer A. Dolby, K. Kristina Drake, Todd C. Esque, Kenro Kusumi
Software Mentions: 4
Published: over 5 years ago

10.1038/leu.2016.251

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts
Cited by: 99
Author(s): Annalisa Mupo, Monika Seiler, Vijitha Sathiaseelan, Alena Pance, Yi Yang, Anant A. Agrawal, Francesco Iorio, Rubén Bautista, Suruchi Pacharne, Konstantinos Tzelepis, Nicla Manes, Penny Wright, Elli Papaemmanuil, David G. Kent, Peter Campbell, Silvia Buonamici, Niccolò Bolli, George S. Vassiliou
Software Mentions: 4
Published: over 9 years ago

10.1186/s12935-021-01834-x

High expression of CDCA7 predicts poor prognosis for clear cell renal cell carcinoma and explores its associations with immunity
Cited by: 12
Author(s): Shouyong Liu, Yi Wang, Chenkui Miao, Zengjun Wang
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13223-021-00584-9

Expression profiling of ileal mucosa in asthma reveals upregulation of innate immunity and genes characteristic of Paneth and goblet cells
Cited by: 1
Author(s): Jan Krzysztof Nowak, Marzena Dworacka, Nazgul Gubaj, Arystan Dossimov, Zhumabek Dossimov, Jarosław Walkowiak
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0244556

Pathways of calcium regulation, electron transport, and mitochondrial protein translation are molecular signatures of susceptibility to recurrent exertional rhabdomyolysis in Thoroughbred racehorses
Cited by: 6
Author(s): Kennedy Aldrich, Deborah Velez‐Irizarry, Clara Fenger, Melissa Schott, Stephanie J. Valberg
Software Mentions: 4
Published: almost 5 years ago

10.1093/bib/bbv049

Empirical comparison of structure-based pathway methods
Cited by: 24
Author(s): Maria K. Jaakkola, Laura L. Elo
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-019-5850-7

Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks
Cited by: 6
Author(s): Kevin B. Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, D Lambert, Stephen Brown, James R. Bradford
Software Mentions: 4
Published: over 6 years ago

10.1093/bib/bbx080

‘Multi-omic’ data analysis using O-miner
Cited by: 13
Author(s): Ajanthah Sangaralingam, Abu Z. Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, A. Nagano, Helen Ross-Adams, Jun Wang, Nick R. Lemoine, Claude Chelala
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms19113687

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
Cited by: 5
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0231125

Analysis of circulating-microRNA expression in lactating Holstein cows under summer heat stress
Cited by: 14
Author(s): Jihwan Lee, Mi Kyung Lee, Jun-Kyu Son, Hyeonju Lim, Euntae Kim, Dong-Hyun Kim, Seungmin Ha, Tai-Young Hur, Seung Hwan Lee, Inchul Choi
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.02626

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways
Cited by: 80
Author(s): Benoît Ballester, Alejandra Medina-Rivera, Dominic Schmidt, Mar Gonzàlez-Porta, Matthew Carlucci, Marc E. Rothenberg, Kyle Chessman, Aline Faure, Alister P. W. Funnell, Ângela Gonçalves, Claudia Kutter, Margus Lukk, Suraj Menon, William McLaren, Klara Stefflova, Stephen Watt, Matthew T. Weirauch, Merlin Crossley, John C. Marioni, Duncan T. Odom, Paul Flicek, Michael D. Wilson
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1007961

A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene
Cited by: 17
Author(s): Michael Hecker, Nina Boxberger, Nicole Illner, Brit Fitzner, I Schröder, Alexander Winkelmann, Aleš Dudešek, Stefanie Meister, Dirk Koczan, Peter Lorenz, Hans‐Jürgen Thiesen, Uwe K. Zettl
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2105-10-S12-S7

XML-based approaches for the integration of heterogeneous bio-molecular data
Cited by: 26
Author(s): Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga, Paolo Perlasca, Giorgio Valentini, David Manset
Software Mentions: 4
Published: over 16 years ago

10.1371/journal.pone.0001061

Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor
Cited by: 52
Author(s): Caitlin B. Conboy, Christiana Spyrou, Natalie Thorne, Elizabeth J. Wade, Nuno L. Barbosa‐Morais, Michael D. Wilson, Arindam Bhattacharjee, Richard A. Young, Simon Tavaré, Jacqueline A. Lees, Duncan T. Odom
Software Mentions: 4
Published: over 18 years ago

10.1016/j.ccell.2019.08.003

Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis
Cited by: 230
Author(s): René Jackstadt, Sander R. van Hooff, Joshua D.G. Leach, Xabier Cortés-Lavaud, Jeroen Lohuis, Rachel A. Ridgway, Valérie M. Wouters, Jatin Roper, Timothy J. Kendall, Campbell S.D. Roxburgh, Paul G. Horgan, Colin Nixon, Craig Nourse, Matthias Gunzer, William Clark, Ann Hedley, Ömer H. Yılmaz, Mamunur Rashid, Peter J. Bailey, Andrew V. Biankin, Andrew D. Campbell, David J. Adams, Simon T. Barry, Colin W. Steele, Jan Paul Medema, Owen J. Sansom
Software Mentions: 4
Published: over 6 years ago

10.1016/j.jhepr.2021.100237

Aramchol downregulates stearoyl CoA-desaturase 1 in hepatic stellate cells to attenuate cellular fibrogenesis
Cited by: 26
Author(s): Dipankar Bhattacharya, Brittany Basta, José M. Mato, Amanda Craig, David Fernández–Ramos, Fernando Lopitz‐Otsoa, Darya Tsvirkun, Liat Hayardeny, Vasuretha Chandar, Robert E. Schwartz, Augusto Villanueva, Scott L. Friedman
Software Mentions: 3
Published: over 4 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: almost 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.0253859

Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome
Cited by: 8
Author(s): Sujata Srikanth, Lavanya Jain, Cinthya J. Zepeda-Mendoza, Lauren Cascio, Kelly A. Jones, Rini Pauly, Barb DuPont, Curtis Rogers, Sara M. Sarasua, Katy Phelan, Cynthia C. Morton, Luigi Boccuto
Software Mentions: 3
Published: over 4 years ago

10.3390/jof4030081

Identification of Antifungal Targets Based on Computer Modeling
Cited by: 10
Author(s): Elena Bencúrová, Shishir Gupta, Edita Sarukhanyan, Thomas Dandekar
Software Mentions: 3
Published: over 7 years ago

10.1155/2014/345106

Comparison of Merging and Meta-Analysis as Alternative Approaches for Integrative Gene Expression Analysis
Cited by: 45
Author(s): Jonatan Taminau, Cosmin Lazar, Stijn Meganck, Ann Nowé
Software Mentions: 3
Published: about 12 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: about 6 years ago

10.1371/journal.pone.0154556

The Ontology for Biomedical Investigations
Cited by: 228
Author(s): Anita Bandrowski, Ryan R. Brinkman, Mathias Brochhausen, Matthew Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, F. Gibson, Alejandra González-Beltrán, Melissa Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez‐Boussard, Mark A. Jensen, Yuling Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa Soldatova, Christian J. Stoeckert, Chris Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, Jie Zheng
Software Mentions: 3
Published: almost 10 years ago

10.1155/2017/2568706

Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize
Cited by: 34
Author(s): Nepolean Thirunavukkarasu, R.C. Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Mittal Shikha, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta K. Dash, Firoz Hossain, H. S. Gupta
Software Mentions: 3
Published: about 9 years ago

10.1128/mSystems.00025-15

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions
Cited by: 111
Author(s): Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene
Software Mentions: 3
Published: almost 10 years ago

10.1186/1471-2164-12-610

Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease
Cited by: 10
Author(s): Rudi Alberts, Hairong Chen, Claudia Pommerenke, August B. Smit, Sabine Spijker, Robert W. Williams, Robert Geffers, Dunja Bruder, Klaus Schughart
Software Mentions: 3
Published: about 14 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

10.1186/1471-2164-15-462

Effects of functional feeds on the lipid composition, transcriptomic responses and pathology in heart of Atlantic salmon (Salmo salar L.) before and after experimental challenge with Piscine Myocarditis Virus (PMCV)
Cited by: 34
Author(s): Laura Martínez-Rubio, Øystein Evensen, Aleksei Krasnov, Sven Martin Jørgensen, Simón Wadsworth, Kari Ruohonen, Jose L. González Vecino, Douglas R. Tocher
Software Mentions: 3
Published: about 12 years ago

10.1007/s12551-018-0490-8

Mining data and metadata from the gene expression omnibus
Cited by: 64
Author(s): Zichen Wang, Alexander Lachmann, Avi Ma’ayan
Software Mentions: 3
Published: about 7 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: over 8 years ago

10.3390/biom2010001

Exploring the Optimal Strategy to Predict Essential Genes in Microbes
Cited by: 4
Author(s): Jingyuan Deng, Lirong Tan, Xiaodong Lin, Yao Lu, Long Lu
Software Mentions: 3
Published: about 14 years ago

10.1155/2020/5156304

Comprehensive Analyses of miRNA-mRNA Network and Potential Drugs in Idiopathic Pulmonary Arterial Hypertension
Cited by: 8
Author(s): Chan Li, Zeyu Zhang, Qian Xu, Ruizheng Shi
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.01871-18

Structural and Nonstructural Genes Contribute to the Genetic Diversity of RNA Viruses
Cited by: 27
Author(s): Natalie D. Collins, Andrew S. Beck, Steven G. Widen, Thomas G. Wood, Stephen Higgs, Alan D.T. Barrett
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-11-455

Next generation tools for genomic data generation, distribution, and visualization
Cited by: 46
Author(s): David A. Nix, Tonya L Di Sera, Brian Dalley, Brett Milash, Robert M Cundick, Kevin S Quinn, Samir Courdy
Software Mentions: 3
Published: over 15 years ago

10.1128/mBio.02684-19

Contextual Flexibility in Pseudomonas aeruginosa Central Carbon Metabolism during Growth in Single Carbon Sources
Cited by: 49
Author(s): Stephen K. Dolan, Michael Kohlstedt, Stephen Trigg, Pedro P. Vallejo Ramirez, Clemens F. Kaminski, Christoph Wittmann, Martin Welch
Software Mentions: 3
Published: almost 6 years ago

10.1155/2015/140819

MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation
Cited by: 13
Author(s): Luman Wang, Qiaochu Mo, Jianxin Wang
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2105-11-421

Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
Cited by: 35
Author(s): Wei‐Chung Cheng, Min-Lung Tsai, Cheng-Wei Chang, Ching-Lung Huang, Chaang-Ray Chen, Wun‐Yi Shu, Yun‐Shien Lee, Tzu‐Hao Wang, Ji-Hong Hong, Chia-Yang Li, Ian C. Hsu
Software Mentions: 3
Published: over 15 years ago

10.1155/2015/146250

An Association Rule Mining Approach to Discover lncRNAs Expression Patterns in Cancer Datasets
Cited by: 7
Author(s): Paolo Cremaschi, Roberta Carriero, Stefania Astrologo, Caterina Colì, Antonella Lisa, Silvia Parolo, Silvia Bione
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2105-10-50

EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data
Cited by: 66
Author(s): Michael Dondrup, Stefan P. Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane Katja Kleindt, H. Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J. Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann
Software Mentions: 3
Published: about 17 years ago

10.1186/s13062-016-0152-3

Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes
Cited by: 14
Author(s): Suyan Tian, Howard H. Chang, Chi Wang
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-12-373

Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis
Cited by: 64
Author(s): Andrea Saß, Angela Marchbank, Elizabeth Tullis, John J. LiPuma, Eshwar Mahenthiralingam
Software Mentions: 3
Published: over 14 years ago

10.1186/s13395-015-0059-1

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging
Cited by: 72
Author(s): Jing Su, Carl Johan Ekman, Nikolay Oskolkov, Leo Lahti, Kristoffer Ström, Alvis Brāzma, Leif Groop, Johan Rung, Ola Hansson
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-8-9

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists
Cited by: 48
Author(s): Alexandre Gattiker, Riccarda Rischatsch, Philippe Demougin, Sylvia Voegeli, Fred S. Dietrich, Peter Philippsen, Michael Primig
Software Mentions: 3
Published: about 19 years ago

10.1074/jbc.RA119.010302

Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription
Cited by: 51
Author(s): Leonie Kollenstart, Anton J.L. de Groot, George M.C. Janssen, Xue Cheng, Kees Vreeken, Fabrizio Martino, Jacques Côté, Peter A. van Veelen, Haico van Attikum
Software Mentions: 3
Published: about 6 years ago

10.1186/2041-1480-2-S1-S1

Biomedical semantics in the Semantic Web
Cited by: 12
Author(s): Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano, M. Scott Marshall
Software Mentions: 3
Published: almost 15 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

10.1371/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

10.1074/jbc.M117.784629

The transcription factor Pax6 is required for pancreatic β cell identity, glucose-regulated ATP synthesis, and Ca2+ dynamics in adult mice
Cited by: 48
Author(s): Ryan K. Mitchell, Marie‐Sophie Nguyen‐Tu, Pauline Chabosseau, Rebecca Callingham, Timothy J. Pullen, Rebecca Cheung, Isabelle Leclerc, David J. Hodson, Guy A. Rutter
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13326-016-0079-8

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease
Cited by: 16
Author(s): Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann‐Apitius, Philipp Senger
Software Mentions: 3
Published: over 9 years ago

10.1172/jci.insight.148652

CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking
Cited by: 1
Author(s): Tábata Takahashi França, Ashraf Al-Sbiei, Ghada Bashir, Yassir A. Mohamed, Ranieri Coelho Salgado, Lucila Akune Barreiros, Sarah Maria da Silva Napoleão, Cristiane Seganfredo Weber, Janáira Fernandes Severo Ferreira, Carolina Sánchez Aranda, Carolina Prando, Mayra B. de Barros Dorna, Igor Jurišica, Maria J. Fernández-Cabezudo, Hans D. Ochs, Antônio Condino‐Neto, Basel K. al-Ramadi, Otávio Cabral-Marques
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-016-1210-7

Tilting the lasso by knowledge-based post-processing
Cited by: 9
Author(s): Kukatharmini Tharmaratnam, Matthew Sperrin, Thomas Jaki, Sjur Reppe, Arnoldo Frigessi
Software Mentions: 3
Published: over 9 years ago

10.1186/s13027-021-00357-4

Identification of key genes in hepatitis B associated hepatocellular carcinoma based on WGCNA
Cited by: 6
Author(s): Chang Liu, Qinghai Dai, Qian Ding, Min Wei, Xiaohong Kong
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13040-017-0136-6

Study of Meta-analysis strategies for network inference using information-theoretic approaches
Cited by: 2
Author(s): Ngoc Cam Pham, Benjamin Haibe‐Kains, Pau Bellot, Gianluca Bontempi, Patrick Meyer
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13040-016-0122-4

Elevated transcriptional levels of aldolase A (ALDOA) associates with cell cycle-related genes in patients with NSCLC and several solid tumors
Cited by: 25
Author(s): Fan Zhang, Jiediao Lin, Xiaoyu Zuo, Yingping Zhuang, Chao‐Qun Hong, Guojun Zhang, Xiaojiang Cui, Yukun Cui
Software Mentions: 3
Published: about 9 years ago

10.1186/jbiol53

Dosage compensation is less effective in birds than in mammals
Cited by: 300
Author(s): Yuichiro Itoh, Esther Melamed, Xia Yang, Kathy Kampf, Susanna Wang, Nadir Yehya, Atila van Nas, Kirstin Replogle, Mark Band, David F. Clayton, Eric E. Schadt, Aldons J. Lusis, Arthur P. Arnold
Software Mentions: 3
Published: about 19 years ago

10.1186/s13073-016-0335-7

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq
Cited by: 104
Author(s): David Redmond, Asaf Poran, Olivier Elemento
Software Mentions: 3
Published: over 9 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

10.1186/s12864-015-2051-x

Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture
Cited by: 23
Author(s): Michael Petridis, Andrej Benjak, Gregory M. Cook
Software Mentions: 3
Published: over 10 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.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: over 4 years ago

10.1074/jbc.M114.634816

Early Growth Response Genes 2 and 3 Regulate the Expression of Bcl6 and Differentiation of T Follicular Helper Cells
Cited by: 26
Author(s): Ane Ogbe, Tizong Miao, Alistair L. J. Symonds, Becky Omodho, Randeep Singh, Punamdip Bhullar, Suling Li, Ping Wang
Software Mentions: 3
Published: over 10 years ago

10.1186/s12918-014-0108-0

Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters
Cited by: 4
Author(s): Thomas Kelder, Lars Verschuren, Ben van Ommen, Alain J. van Gool, Marijana Radonjić
Software Mentions: 3
Published: over 11 years ago

10.1186/s13059-021-02323-0

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication
Cited by: 46
Author(s): Gareth Benjamin Gillard, Lars Grønvold, Line Lieblein Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F. Koop, Eric B. Rondeau, Manu Kumar Gundappa, J. Mendoza, Daniel J. Macqueen, Rori V. Rohlfs, Simen Rød Sandve, Torgeir R. Hvidsten
Software Mentions: 3
Published: almost 5 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

10.1186/1471-2164-9-390

Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays
Cited by: 100
Author(s): Alexandra B. Graf, Brigitte Gasser, Martin Dragosits, Michael Sauer, Germán Leparc, Thomas Tüchler, David P. Kreil, Diethard Mattanovich
Software Mentions: 3
Published: over 17 years ago

10.1093/gbe/evw059

Genetic Evidence of Human Adaptation to a Cooked Diet
Cited by: 26
Author(s): Rachel N. Carmody, Michael Dannemann, Adrian W. Briggs, Birgit Nickel, Emily Groopman, Richard W. Wrangham, Janet Kelso
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13059-016-0992-2

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cited by: 330
Author(s): Jonathan Cairns, Paula Freire-Pritchett, Steven W. Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel R. Zerbino, Stefan Schoenfelder, Biola M. Javierre, Cameron S. Osborne, Peter Fraser, Mikhail Spivakov
Software Mentions: 3
Published: over 9 years ago

10.1186/s12918-017-0520-3

Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology
Cited by: 13
Author(s): Joanna H. Sier, Alfred E. Thumser, Nick Plant
Software Mentions: 3
Published: about 8 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

10.1186/1471-2105-15-S1-S2

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
Cited by: 11
Author(s): Marco Masseroli, Barend Mons, Erik Bongcam‐Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano
Software Mentions: 3
Published: about 12 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

10.1186/gb-2012-13-4-r30

Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium
Cited by: 49
Author(s): Simen M. Kristoffersen, Chad P. Haase, M. Ryan Weil, Karla D. Passalacqua, Faheem Niazi, Stephen Hutchison, Brian Desany, Anne Brit Kolstø, Nicolas J. Tourasse, Timothy D. Read, Ole Andreas Økstad
Software Mentions: 3
Published: about 14 years ago

10.1186/gb-2012-13-4-r31

Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
Cited by: 33
Author(s): Marieke Simonis, Santosh S. Atanur, Sam E.V. Linsen, Victor Guryev, Frans-Paul Ruzius, Laurence Gamé, Nico Lansu, Ewart de Bruijn, Sebastiaan van Heesch, Steven J.M. Jones, Michal Pravenec, Tim Aitman, Edwin Cuppen
Software Mentions: 3
Published: about 14 years ago

10.1186/gb-2013-14-10-r110

Modeling precision treatment of breast cancer
Cited by: 263
Author(s): Anneleen Daemen, Obi L. Griffith, Laura M. Heiser, Nicholas J. Wang, Oana Enache, Zachary Sanborn, François Pépin, Steffen Durinck, James E. Korkola, Malachi Griffith, Joe S. Hur, Nam Huh, Jongsuk Chung, Leslie Cope, Mary Jo Fackler, Christopher B. Umbricht, Saraswati Sukumar, Pankaj Seth, Vikas P. Sukhatme, Lakshmi R. Jakkula, Yiling Lu, Gordon B. Mills, Raymond J. Cho, Eric A. Collisson, Laura J. van’t Veer, Paul T. Spellman, Joe W. Gray
Software Mentions: 3
Published: about 13 years ago

10.1186/gb-2008-9-10-r146

A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection
Cited by: 19
Author(s): Amanda Greenall, Guiyuan Lei, Daniel Swan, Katherine James, Liming Wang, Heiko Peters, Anil Wipat, Darren J. Wilkinson, David Lydall
Software Mentions: 3
Published: about 18 years ago

10.1186/gb-2010-11-8-r80

Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development
Cited by: 29
Author(s): Noëlle Billon, Raivo Kolde, Jüri Reimand, Miguel Caetano Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian Dani
Software Mentions: 3
Published: about 16 years ago

10.1186/s12870-015-0643-x

Changes in Lolium perenne transcriptome during cold acclimation in two genotypes adapted to different climatic conditions
Cited by: 29
Author(s): Shamila Abeynayake, Stephen Byrne, Istvàn Nagy, Kristina Jonavičienė, Thomas Etzerodt, Birte Boelt, Torben Asp
Software Mentions: 3
Published: over 10 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

10.1007/s12263-014-0439-x

White adipose tissue reference network: a knowledge resource for exploring health-relevant relations
Cited by: 10
Author(s): Thomas Kelder, Georg Summer, Martien P. M. Caspers, Evert M. van Schothorst, Jaap Keijer, Loes P. M. Duivenvoorde, К. Schimrigk, Anja Voigt, Laura Bohnert, Catalina Picó, M. Luisa Bonet, A. Dembińska-Kieć, Małgorzata Malczewska-Malec, Beata Kieć‐Wilk, Josep Maria del Bas, Antoni Caimari, Lluı́s Arola, Marjan van Erk, Ben van Ommen, Marijana Radonjić
Software Mentions: 3
Published: about 11 years ago

10.1186/s13059-016-0971-7

Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies
Cited by: 156
Author(s): Björn Bakker, Aaron Taudt, Mirjam E. Belderbos, David Porubský, Diana C.J. Spierings, Tristan de Jong, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Allan Bradley, Eveline S.J.M. de Bont, Anke van den Berg, Victor Guryev, Peter M Lansdorp, Maria Colomé-Tatché, Floris Foijer
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2229-13-14

Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem
Cited by: 34
Author(s): Hardy Hall, Brian E. Ellis
Software Mentions: 3
Published: about 13 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/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

10.1186/1471-2105-10-133

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

10.1186/1471-2229-9-67

Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set
Cited by: 39
Author(s): Laura Pascual, José Blanca, Joaquı́n Cañizares, Fernado Nuez
Software Mentions: 3
Published: over 16 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

10.12688/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: almost 8 years ago

10.1186/1471-2164-15-595

Gene network-based analysis identifies two potential subtypes of small intestinal neuroendocrine tumors
Cited by: 34
Author(s): Mark Kidd, Irvin M. Modlin, Ignat Drozdov
Software Mentions: 3
Published: about 12 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

10.1186/1471-2105-14-153

Iterative rank-order normalization of gene expression microarray data
Cited by: 106
Author(s): Eric A. Welsh, Steven Eschrich, Anders Berglund, David Fenstermacher
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2105-12-218

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript
Cited by: 36
Author(s): Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K. Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen Parkinson, Morris A. Swertz
Software Mentions: 3
Published: over 14 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.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

10.1186/2047-783X-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: about 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: almost 16 years ago

10.1186/1471-2164-10-472

Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes
Cited by: 132
Author(s): Sylvain Forêt, Robert Kucharski, Yvonne Pittelkow, Gabrielle A. Lockett, Ryszard Maleszka
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0240178

Occurrence of Brucella ceti in striped dolphins from Italian Seas
Cited by: 14
Author(s): Giuliano Garofolo, A. Petrella, Giuseppe Lucifora, Gabriella Di Francesco, Giovanni Di Guardo, Alessandra Pautasso, Barbara Iulini, Katia Varello, Federica Giorda, Maria Goria, Alessandro Dondo, Simona Zoppi, Cristina Esmeralda Di Francesco, Stefania Giglio, Furio Ferringo, Luigina Serrecchia, Mattia Anna Rita Ferrantino, Katiuscia Zilli, Anna Janowicz, Manuela Tittarelli, Walter Mignone, Cristina Casalone, Carla Grattarola
Software Mentions: 3
Published: over 5 years ago

10.1136/annrheumdis-2020-217204

Investigation of genetically regulated gene expression and response to treatment in rheumatoid arthritis highlights an association between <i>IL18RAP</i> expression and treatment response
Cited by: 10
Author(s): Svetlana Cherlin, Myles Lewis, Darren Plant, Nisha Nair, Katriona Goldmann, Evan Tzanis, Michael R. Barnes, Paul McKeigue, Jennifer H. Barrett, Costantino Pitzalis, Anne Barton, Heather J. Cordell
Software Mentions: 3
Published: over 5 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: almost 9 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

Bonuses:

Penalties:

Papers Mentioning ArrayExpress 1,962