bioconductor: ArrayExpress | Projects

10.1186/s12943-015-0358-5

Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Cited by: 198
Author(s): Sören Müller, Susanne Raulefs, Philipp Bruns, Fabian Afonso-Grunz, Anne Plötner, Rolf Thermann, Carsten Jäger, Anna Melissa Schlitter, Bo Kong, Ivonne Regel, W. Kurt Roth, Björn Rotter, Klaus Hoffmeier, Günter Kahl, Ina Koch, Fabian J. Theis, Jörg Kleeff, Peter Winter, Christoph Michalski
Software Mentions: 4
Published: over 10 years ago

10.1186/s12859-019-3072-2

HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis
Cited by: 3
Author(s): Hongryul Ahn, Il Bong Jung, Han–Jung Chae, Dong‐Won Kang, Wi Hoon Jung, Sun Kim
Software Mentions: 4
Published: about 6 years ago

10.1186/s12870-014-0254-y

Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans
Cited by: 77
Author(s): Dharani Dhar Burra, Oliver Berkowitz, Pete E. Hedley, Jenny Morris, Svante Resjö, Fredrik Levander, Erland Liljeroth, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: over 11 years ago

10.3390/ijms21114115

Minor Splicing Factors Zrsr1 and Zrsr2 Are Essential for Early Embryo Development and 2-Cell-Like Conversion
Cited by: 16
Author(s): Isabel Gómez-Redondo, Priscila Ramos‐Ibeas, Eva Pericuesta, Raúl Fernández‐González, Ricardo Laguna‐Barraza, Alfonso Gutiérrez‐Adán
Software Mentions: 4
Published: over 5 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

10.1186/1475-2859-8-37

Interactive visualization of clusters in microarray data: an efficient tool for improved metabolic analysis of E. coli
Cited by: 7
Author(s): Theresa Scharl, Gerald Striedner, Florentina Pötschacher, Friedrich Leisch, Karl Bayer
Software Mentions: 4
Published: over 16 years ago

10.1038/s41598-019-50885-8

Improved gene co-expression network quality through expression dataset down-sampling and network aggregation
Cited by: 25
Author(s): Franziska Liesecke, Johan-Owen De Craene, Sébastien Besseau, Vincent Courdavault, Marc Clastre, Valentin Vergès, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.22423

Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome
Cited by: 2
Author(s): Shana Claeys, Geertrui Denecker, Robrecht Cannoodt, Candy Kumps, Kaat Durinck, Franki Speleman, Katleen De Preter
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-018-32972-4

Cytoplasmic location of NR4A1 in aggressive lymphomas is associated with a favourable cancer specific survival
Cited by: 4
Author(s): Karoline Fechter, Julia Feichtinger, Katharina Prochazka, Julia Judith Unterluggauer, Katrin Pansy, Elisabeth Steinbauer, Martin Pichler, Johannes Haybaeck, Andreas Prokesch, Hildegard Greinix, Christine Beham–Schmid, Peter Neumeister, Gerhard G. Thallinger, Alexander Deutsch
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-25302-1

Egr2-independent, Klf1-mediated induction of PD-L1 in CD4+ T cells
Cited by: 8
Author(s): Shuzo Teruya, Tomohisa Okamura, Takashi Komai, Mariko Inoue, Yukiko Iwasaki, Shuji Sumitomo, Hirofumi Shoda, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 4
Published: over 7 years ago

10.1186/s12885-021-08111-0

A novel 10 glycolysis-related genes signature could predict overall survival for clear cell renal cell carcinoma
Cited by: 20
Author(s): Qianwei Xing, Taidui Zeng, Shouyong Liu, Hong Cheng, Limin Ma, Yi Wang
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-15-884

A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions
Cited by: 46
Author(s): Beatrix Bicskei, James E. Bron, Kevin A. Glover, John B. Taggart
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0256353

Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes
Cited by: 6
Author(s): Claus M. Zacho, Martina Abenhus Bager, Ashot Margaryan, Peter Gravlund, Anders Galatius, Arne Redsted Rasmussen, Morten E. Allentoft
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.22689

Systematic assessment of cervical cancer initiation and progression uncovers genetic panels for deep learning-based early diagnosis and proposes novel diagnostic and prognostic biomarkers
Cited by: 32
Author(s): Nguyen Phuoc Long, Kyung Hee Jung, Sang Jun Yoon, Nguyễn Hoàng Anh, Tran Diem Nghi, Yun Pyo Kang, Pengcheng Zhang, Jung Eun Min, Sung Kyung Hong, Sung Won Kwon
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0114461

Inference of the Oxidative Stress Network in Anopheles stephensi upon Plasmodium Infection
Cited by: 10
Author(s): Jatin Shrinet, Umesh K. Nandal, T. Adak, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 4
Published: about 11 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

10.1038/srep29832

Identification of host transcriptional networks showing concentration-dependent regulation by HPV16 E6 and E7 proteins in basal cervical squamous epithelial cells
Cited by: 7
Author(s): Stephen Smith, Cinzia G. Scarpini, Ian J. Groves, Richard Odle, Nicholas Coleman
Software Mentions: 4
Published: over 9 years ago

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

10.26508/lsa.202000809

Reduced RNA turnover as a driver of cellular senescence
Cited by: 9
Author(s): Nowsheen Mullani, Yevheniia Porozhan, Adèle Mangelinck, Christophe Rachez, Mickaël Costallat, Éric Batsché, Michèle Goodhardt, Giovanni Cenci, Carl Mann, Christian Muchardt
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41597-019-0205-4

The Personal Genome Project-UK, an open access resource of human multi-omics data
Cited by: 18
Author(s): Olga Chervova, Lucía Conde, José Afonso Guerra-Assunção, Ismail Moghul, A. D. B. Webster, Alison Berner, Elizabeth Larose Cadieux, Yuan Tian, Vitaly Voloshin, Tiago S. Jesus, Rifat Hamoudi, Javier Herrero, Stephan Beck
Software Mentions: 4
Published: about 6 years ago

10.1186/s12859-017-1536-9

Network-based analysis of transcriptional profiles from chemical perturbations experiments
Cited by: 11
Author(s): Francesca Mulas, Amy Li, David H. Sherr, Stefano Monti
Software Mentions: 4
Published: almost 9 years ago

10.7717/peerj.9812

Using bioinformatics and metabolomics to identify altered granulosa cells in patients with diminished ovarian reserve
Cited by: 6
Author(s): Ruifen He, Zhongying Zhao, Yongxiu Yang, Xiaolei Liang
Software Mentions: 4
Published: over 5 years ago

10.1530/REP-19-0293

Blastocyst transfer in mice alters the placental transcriptome and growth
Cited by: 4
Author(s): Katerina Menelaou, Malwina Prater, Simon James Tunster, Georgina E T Blake, Colleen Geary Joo, James C. Cross, Russell S. Hamilton, Erica D. Watson
Software Mentions: 4
Published: almost 6 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

10.26508/lsa.201800283

Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements
Cited by: 13
Author(s): Verena Thormann, Laura V. Glaser, Maika C. Rothkegel, Marina Borschiwer, Melissa Bothe, Alisa Fuchs, Sebastiaan H. Meijsing
Software Mentions: 4
Published: almost 7 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

10.1371/journal.pone.0246508

Relationships between fox populations and rabies virus spread in northern Canada
Cited by: 17
Author(s): Susan A. Nadin-Davis, Emilie Falardeau, Alex Flynn, Hugh Whitney, H. Dawn Marshall
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.ppat.1009768

Trichuris muris infection drives cell-intrinsic IL4R alpha independent colonic RELMα+ macrophages
Cited by: 6
Author(s): Ruth Forman, Larisa Logunova, Hannah Smith, Kelly Wemyss, Iris Mair, Louis Boon, Judith E. Allen, Werner Müller, Joanne L. Pennock, Kathryn J. Else
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-017-16747-x

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
Cited by: 193
Author(s): Peter W. Eide, Jarle Bruun, Ragnhild Lothe, Anita Sveen
Software Mentions: 4
Published: about 8 years ago

10.18632/oncotarget.23280

Validation of a hypoxia related gene signature in multiple soft tissue sarcoma cohorts
Cited by: 32
Author(s): Lingjian Yang, Laura Forker, Joely J. Irlam, Nischalan Pillay, Ananya Choudhury, Catharine M L West
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0038946

Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study
Cited by: 51
Author(s): Swanhild U. Meyer, Sebastian Kaiser, Carola Wagner, Christian Thirion, Michael W. Pfaffl
Software Mentions: 4
Published: over 13 years ago

10.3390/genes6010001

Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1
Cited by: 53
Author(s): Kristina B. V. Døssing, Tina Binderup, Bogumił Kaczkowski, Anders Jacobsen, Maria Rossing, Ole Winther, Birgitte Federspiel, Ulrich Knigge, Andreas Kjær, Lennart Friis‐Hansen
Software Mentions: 4
Published: about 11 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

10.3389/fpls.2015.00718

A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones
Cited by: 20
Author(s): Itziar Frades, Kibrom B. Abreha, Estelle Proux‐Wéra, Åsa Lankinen, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: over 10 years ago

10.7150/jca.44413

Comprehensive Analysis of the Tumor Microenvironment in Cutaneous Melanoma associated with Immune Infiltration
Cited by: 17
Author(s): Pan Wang, Xinyu Zhang, Nan Sun, Zhihong Zhao, Jie He
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-015-1964-8

A genetic framework for H2O2 induced cell death in Arabidopsis thaliana
Cited by: 40
Author(s): Eve Kaurilind, Enjun Xu, Mikael Brosché
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0015147

Analysis of Ultra Low Genome Conservation in Clostridium difficile
Cited by: 58
Author(s): Joy Scaria, Lalit Ponnala, Tavan Janvilisri, Weiwei Yan, Lukas A. Mueller, Yung-Fu Chang
Software Mentions: 4
Published: about 15 years ago

10.3389/fnmol.2021.699562

Spatial RNA Sequencing Identifies Robust Markers of Vulnerable and Resistant Human Midbrain Dopamine Neurons and Their Expression in Parkinson’s Disease
Cited by: 20
Author(s): Julio Águila, Shu Cheng, Nigel Kee, Mengshu Cao, Menghan Wang, Qiaolin Deng, Eva Hedlund
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0234939

Effect of bovine leukemia virus (BLV) infection on bovine mammary epithelial cells RNA-seq transcriptome profile
Cited by: 4
Author(s): Lucia Martínez Cuesta, Juan Pedro Lirón, María Victoria Nieto Farias, Guillermina Laura Dolcini, María Carolina Ceriani
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-10-389

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability
Cited by: 18
Author(s): Herman M. J. Sontrop, Perry D. Moerland, René van den Ham, Marcel J. T. Reinders, Wim Verhaegh
Software Mentions: 4
Published: about 16 years ago

10.3389/fnmol.2018.00363

Assessing Transcriptome Quality in Patch-Seq Datasets
Cited by: 33
Author(s): Shreejoy J. Tripathy, Lilah Toker, Claire Bomkamp, B. Ogan Mancarci, Manuel Belmadani, Paul Pavlidis
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2020.00495

Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator
Cited by: 7
Author(s): Natalia M. Vior, Eva Cea-Torrescassana, Tom H. Eyles, Govind Chandra, Andrew W. Truman
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0225658

Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses
Cited by: 15
Author(s): Dominika Borowska, Richard Kuo, Richard Bailey, Kellie Watson, Pete Kaiser, Lonneke Vervelde, Mark P. Stevens
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2016.01688

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways
Cited by: 19
Author(s): Sadegh Azimzadeh Jamalkandi, Sayed‐Hamidreza Mozhgani, Hamid Gholami Pourbadie, Mehdi Mirzaie, Farshid Noorbakhsh, Behrouz Vaziri, Alireza Gholami, Naser Ansari-Pour, Mohieddin Jafari
Software Mentions: 4
Published: about 9 years ago

10.3389/fimmu.2018.03075

Pregnancy Epigenetic Signature in T Helper 17 and T Regulatory Cells in Multiple Sclerosis
Cited by: 22
Author(s): Andrea Iannello, Simona Rolla, Alessandro Maglione, Giulio Ferrero, Valentina Bardina, Ilenia Inaudi, Stefania De Mercanti, Francesco Novelli, Lucrezia D'Antuono, Simona Cardaropoli, Tullia Todros, Maria Vittoria Turrini, Cinzia Cordioli, Giorgia Puorro, Angela Marsili, Roberta Lanzillo, Vincenzo Brescia Morra, Francesca Cordero, Michele De Bortoli, Luca Durelli, Andrea Visconti, Santina Cutrupi, Marinella Clerico
Software Mentions: 4
Published: almost 7 years ago

10.1155/2013/983805

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases
Cited by: 10
Author(s): Alberto Anguita, Miguel García-Remesal, Diana de la Iglesia, Víctor Maojo
Software Mentions: 4
Published: about 13 years ago

10.3389/fimmu.2021.636108

Impact of Tenascin-C on Radiotherapy in a Novel Syngeneic Oral Squamous Cell Carcinoma Model With Spontaneous Dissemination to the Lymph Nodes
Cited by: 5
Author(s): Caroline Spenlé, Thomas Loustau, Hélène Burckel, Gilles Riegel, Chérine Abou Faycal, Chengbei Li, Alev Yılmaz, Luciana Petti, Fanny Steinbach, Constance Ahowesso, Camille Jost, Nicodème Paul, Raphaël Carapito, Georges Noël, Fabienne Anjuère, Nathalie Salomé, Gertraud Orend
Software Mentions: 4
Published: over 4 years ago

10.3389/fmolb.2021.719982

Identification of Mast Cell-Based Molecular Subtypes and a Predictive Signature in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Hanxiang Liu, Yi Yang
Software Mentions: 4
Published: over 4 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

10.3389/fimmu.2017.01199

Plasmodium berghei NK65 in Combination with IFN-γ Induces Endothelial Glucocorticoid Resistance via Sustained Activation of p38 and JNK
Cited by: 9
Author(s): Karolina Zielińska, Lode De Cauwer, Sofie Knoops, Kristof Van der Molen, Alexander Sneyers, Jonathan Thommis, J. Brian de Souza, Ghislain Opdenakker, Karolien De Bosscher, Philippe E. Van den Steen
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0071462

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: over 12 years ago

10.3389/fgene.2019.00159

A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures
Cited by: 22
Author(s): Adib Shafi, Tin Nguyen, Azam Peyvandipour, Hung Son Nguyen, Sorin Drăghici
Software Mentions: 4
Published: almost 7 years ago

10.1007/s00401-017-1743-5

Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing
Cited by: 120
Author(s): Philipp Euskirchen, Franck Bielle, Karim Labreche, Wigard P. Kloosterman, Shai Rosenberg, Maïlys Daniau, Charlotte Schmitt, Julien Masliah‐Planchon, Franck Bourdeaut, Caroline Dehais, Yannick Marie, Jean‐Yves Delattre, Ahmed Idbaïh
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2020.566734

Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging
Cited by: 4
Author(s): Yujuan Gui, Mélanie Thomas, Pierre Garcia, Mona Karout, Rashi Halder, Alessandro Michelucci, Heike Kollmus, Cuiqi Zhou, Shlomo Melmed, Klaus Schughart, Rudi Balling, Michel Mittelbronn, Joseph H. Nadeau, Robert W. Williams, Thomas Sauter, Manuel Buttini, Lasse Sinkkonen
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2018.02902

Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens
Cited by: 35
Author(s): Joannah R. Fergusson, Michael D. Morgan, Mélanie Bruchard, Leonie F. A. Huitema, Balthasar A. Heesters, Vincent van Unen, Jan Piet van Hamburg, Nicole N. van der Wel, Daisy I. Picavet, Frits Koning, Sander W. Tas, Mark S. Anderson, John C. Marioni, Georg A. Holländer, Hergen Spits
Software Mentions: 4
Published: almost 7 years ago

10.3390/jcm8060849

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection
Cited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-021-07646-7

Transcriptomic analysis reveals pronounced changes in gene expression due to sub-lethal pyrethroid exposure and ageing in insecticide resistance Anopheles coluzzii
Cited by: 18
Author(s): Victoria A. Ingham, Faye Brown, Hilary Ranson
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2105-15-S1-S6

CorrelaGenes: a new tool for the interpretation of the human transcriptome
Cited by: 1
Author(s): Paolo Cremaschi, Sergio Rovida, Lucia Sacchi, Antonella Lisa, Francesca Calvi, Alessandra Montecucco, Giuseppe Biamonti, Silvia Bione, Gianni Sacchi
Software Mentions: 4
Published: about 12 years ago

10.1093/bioinformatics/bty125

AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes
Cited by: 28
Author(s): Wanseon Lee, Katharine Plant, Peter Humburg, Julian C. Knight
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0238076

Deletion of Mediator 1 suppresses TGFβ signaling leading to changes in epidermal lineages and regeneration
Cited by: 3
Author(s): Yuko Oda, Thai Nguyen, Akiko Hata, Mark B. Meyer, J. Wesley Pike, Daniel Bikle
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-021-04070-2

Large-scale labeling and assessment of sex bias in publicly available expression data
Cited by: 10
Author(s): Emily Flynn, Annie C. Y. Chang, Russ B. Altman
Software Mentions: 4
Published: almost 5 years ago

10.1093/bioinformatics/btx143

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data
Cited by: 26
Author(s): Robert Petryszak, Nuno A. Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, Alvis Brāzma
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0021681

An Evaluation Protocol for Subtype-Specific Breast Cancer Event Prediction
Cited by: 8
Author(s): Herman M. J. Sontrop, Wim Verhaegh, Marcel J. T. Reinders, Perry D. Moerland
Software Mentions: 4
Published: over 14 years ago

10.1371/journal.pone.0256657

Microbiota composition and mucosal immunity in patients with asymptomatic diverticulosis and controls
Cited by: 10
Author(s): Tessel Meike van Rossen, Rogier E. Ooijevaar, J. Kuyvenhoven, Anat Eck, Herman Bril, René Buijsman, Marja A. Boermeester, H. B. A. C. Stockmann, Niels de Korte, Andries E. Budding
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0090322

Poly(ADP-Ribose)Polymerase Activity Controls Plant Growth by Promoting Leaf Cell Number
Cited by: 29
Author(s): Philipp Schulz, Karel Jansseune, Thomas Degenkolbe, Michaël Méret, Hannes Claeys, Aleksandra Skirycz, Markus Teige, Lothar Willmitzer, Matthew A. Hannah
Software Mentions: 4
Published: almost 12 years ago

10.1186/s13040-015-0052-6

DNA microarray integromics analysis platform
Cited by: 11
Author(s): Tomasz Waller, Tomasz Gubała, Krzysztof Sarapata, Monika Piwowar, Wiktor Jurkowski
Software Mentions: 4
Published: over 10 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

10.1186/1752-0509-6-54

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks
Cited by: 96
Author(s): Florian Martin, Timothy M. Thomson, Alain Sewer, David A. Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 4
Published: over 13 years ago

10.3389/fcell.2019.00299

Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data
Cited by: 23
Author(s): Geng Chen, Jiwei Chen, Huanlong Liu, Shuangguan Chen, Yang Zhang, Peng Li, Danielle Thierry-Mieg, Jean Thierry‐Mieg, William B. Mattes, Baitang Ning, Tieliu Shi
Software Mentions: 4
Published: about 6 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

10.1371/journal.pone.0254562

DNA methylation analyses identify an intronic ZDHHC6 locus associated with time to recurrent stroke in the Vitamin Intervention for Stroke Prevention (VISP) clinical trial
Cited by: 4
Author(s): Nicole M. Davis Armstrong, Weimin Chen, Fang‐Chi Hsu, Michael S. Brewer, Natàlia Cullell, Israel Fernández‐Cadenas, Stephen R. Williams, Michèle M. Sale, Bradford B. Worrall, Keith L. Keene
Software Mentions: 4
Published: over 4 years ago

10.3389/fcvm.2021.627873

Essential Genes and MiRNA–mRNA Network Contributing to the Pathogenesis of Idiopathic Pulmonary Arterial Hypertension
Cited by: 7
Author(s): Shengyu Hao, Pan Jiang, Liang Xie, Guiling Xiang, Zilong Liu, Weiping Hu, Qiao Wu, Liyan Jiang, Yi Xiao, Shanqun Li
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0232120

Corticosterone and testosterone treatment influence expression of gene pathways linked to meiotic segregation in preovulatory follicles of the domestic hen
Cited by: 2
Author(s): E. Wróbel, Alexandra B. Bentz, W. Walter Lorenz, Steven T. Gardner, Mary T. Mendonça, Kristen J. Navara
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pmed.1002194

Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study
Cited by: 401
Author(s): H. Raza Ali, L Chlon, Paul D.P. Pharoah, Florian Markowetz, Carlos Caldas
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0203266

Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress
Cited by: 54
Author(s): R.C. Sharma, Garima Singh, Sitangshu Bhattacharya, Ashutosh Singh
Software Mentions: 4
Published: over 7 years ago

10.12688/f1000research.6925.1

GOsummaries: an R Package for Visual Functional Annotation of Experimental Data
Cited by: 71
Author(s): Raivo Kolde, Jaak Vilo
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0229606

Postprandial transfer of colostral extracellular vesicles and their protein and miRNA cargo in neonatal calves
Cited by: 13
Author(s): Benedikt Kirchner, Dominik Buschmann, Vijay Paul, Michael W. Pfaffl
Software Mentions: 4
Published: almost 6 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

10.1016/j.exphem.2019.08.009

Machine learning predicts putative hematopoietic stem cells within large single-cell transcriptomics data sets
Cited by: 32
Author(s): Fiona Hamey, Berthold Göttgens
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/btu027

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
Cited by: 15
Author(s): Marta Rosikiewicz, Marc Robinson‐Rechavi
Software Mentions: 4
Published: almost 12 years ago

10.3389/fphar.2019.00747

Bioinformatic Study of Transcriptome Changes in the Mice Lumbar Spinal Cord After the 30-Day Spaceflight and Subsequent 7-Day Readaptation on Earth: New Insights Into Molecular Mechanisms of the Hypogravity Motor Syndrome
Cited by: 8
Author(s): M. S. Kuznetsov, Artur Nicolaevich Lisukov, Albert A. Rizvanov, O. V. Tyapkina, Oleg Gusev, P. N. Rezvyakov, I. B. Kozlovskaya, E. E. Nikolskiy, Р. Р. Исламов
Software Mentions: 4
Published: over 6 years ago

10.12688/f1000research.13254.2

Simulation and visualization of multiple KEGG pathways using BioNSi
Cited by: 2
Author(s): Adva Yeheskel, Adam Reiter, Metsada Pasmanik‐Chor, Amir Rubinstein
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.635794

Multi-Transcript Level Profiling Revealed Distinct mRNA, miRNA, and tRNA-Derived Fragment Bio-Signatures for Coping Behavior Linked Haplotypes in HPA Axis and Limbic System
Cited by: 3
Author(s): Kevin Gley, Frieder Hadlich, Nares Trakooljul, Fiete Haack, Eduard Muráni, Ulrike Gimsa, Klaus Wimmers, Siriluck Ponsuksili
Software Mentions: 4
Published: over 4 years ago

10.1093/jxb/eru094

Identification of predominant genes involved in regulation and execution of senescence-associated nitrogen remobilization in flag leaves of field grown barley
Cited by: 63
Author(s): Julien Hollmann, Per L. Gregersen, Karin Krupinska
Software Mentions: 4
Published: almost 12 years ago

10.1093/gigascience/giab034

A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers
Cited by: 5
Author(s): Mariya Dimitrova, Rikke Louise Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
Software Mentions: 4
Published: over 4 years ago

10.1093/gigascience/giaa151

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data
Cited by: 438
Author(s): Matthew D. Young, Sam Behjati
Software Mentions: 4
Published: about 5 years ago

10.1186/gb-2005-6-6-r54

Cited by: 148
Author(s): Nils Rostoks, Justin O. Borevitz, Pete E. Hedley, Joanne Russell, Sharon Mudie, Jenny Morris, Linda Cardle, David Marshall, Robbie Waugh
Software Mentions: 4
Published: about 21 years ago

10.1016/j.gpb.2018.08.002

PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System
Cited by: 19
Author(s): Huan Qi, Zhenhong Jiang, Kang Zhang, Shiping Yang, Fei He, Ziding Zhang
Software Mentions: 4
Published: over 7 years ago

10.1186/s13059-019-1706-3

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C
Cited by: 25
Author(s): Yousra Ben Zouari, Anne Molitor, Natalia Sikorska, Véra Pancaldi, Tom Sexton
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-016-1053-6

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms
Cited by: 114
Author(s): Roderick C. Slieker, Maarten van Iterson, René Luijk, Marian Beekman, Daria V. Zhernakova, Matthijs Moed, Hailiang Mei, M.A. van Galen, Patrick Deelen, Marc Jan Bonder, Alexandra Zhernakova, André G. Uitterlinden, Ettje F. Tigchelaar, Coen D. A. Stehouwer, Casper G. Schalkwijk, Carla Kallen, Albert Hofman, Diana van Heemst, Eco J. C. de Geus, Jenny van Dongen, Joris Deelen, Leonard H van den Berg, Joyce B. J. van Meurs, Ritsert C. Jansen, Peter A.C. ’t Hoen, Lude Franke, Cisca Wijmenga, Jan H. Veldink, Morris A. Swertz, Marleen M.J. van Greevenbroek, Cornelia M. van Duijn, Dorret I. Boomsma, P. Eline Slagboom, Bastiaan T. Heijmans
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-015-0735-9

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population
Cited by: 39
Author(s): Joke Baute, Dorota Herman, Frederik Coppens, Jolien De Block, Bram Slabbinck, Matteo Dell’Acqua, Mario Enrico Pè, Steven Maere, Hilde Nelissen, Dirk Inzé
Software Mentions: 4
Published: over 10 years ago

10.1186/gb-2011-12-8-r76

The head-regeneration transcriptome of the planarian Schmidtea mediterranea
Cited by: 110
Author(s): Thomas Sandmann, Matthias Christian Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer
Software Mentions: 4
Published: about 15 years ago

10.1186/s13059-014-0555-3

Determining the quality and complexity of next-generation sequencing data without a reference genome
Cited by: 27
Author(s): Seyed Yahya Anvar, Lusine Khachatryan, Martijn Vermaat, M.A. van Galen, Irina Pulyakhina, Yavuz Ariyürek, Ken Kraaijeveld, Johan T. den Dunnen, Peter de Knijff, Peter A C ‘t Hoen, Jeroen F. J. Laros
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0240183

Transcriptome analysis revealed misregulated gene expression in blastoderms of interspecific chicken and Japanese quail F1 hybrids
Cited by: 0
Author(s): Satoshi Ishishita, Shoji Tatsumoto, Keiji Kinoshita, Mitsuo Nunome, Takayuki Suzuki, Yasuhiro Go, Yoichi Matsuda
Software Mentions: 4
Published: about 5 years ago

10.1186/gb-2013-14-12-r147

Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties
Cited by: 77
Author(s): Aurélien A. Sérandour, Gordon D. Brown, Joshua D. Cohen, Jason S. Carroll
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0243911

The pharmacodynamic and differential gene expression analysis of PPAR α/δ agonist GFT505 in CDAHFD-induced NASH model
Cited by: 12
Author(s): Linfu Liu, Chuang Liu, Menglong Zhao, Qianru Zhang, Ying Lu, Ping Liu, Hua Yang, Jinliang Yang, Xiaoxin Chen, Yuqin Yao
Software Mentions: 4
Published: about 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.pone.0122143

Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer
Cited by: 27
Author(s): Pushpinder Bawa, Sajna Zackaria, Mohit Verma, Saurabh Gupta, Srivatsan Raghunathan, Bibha Chaudhary, Subhashini Srinivasan
Software Mentions: 4
Published: over 10 years ago

10.1038/s41396-017-0043-3

Energy limitation of cyanophage development: implications for marine carbon cycling
Cited by: 54
Author(s): Richard John Puxty, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 4
Published: almost 8 years ago

10.1128/mSystems.00187-19

Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate
Cited by: 10
Author(s): Joseph P. Webb, V S Springthorpe, Luca Rossoni, David-Paul Minde, Swen Langer, Heather Walker, Amias Alstrom-Moore, Tony R. Larson, Kathryn S. Lilley, Graham R. Eastham, Gill Stephens, Gavin H. Thomas, David J. Kelly, Jeffrey Green
Software Mentions: 4
Published: over 6 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962