bioconductor: RankProd | Projects

10.1186/1756-0500-3-277

EMA - A R package for Easy Microarray data analysis
Cited by: 45
Author(s): Nicolas Servant, Eléonore Gravier, Pierre Gestraud, Cécile Laurent, Caroline Paccard, Anne Biton, Isabel Martínez Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé
Software Mentions: 20
Published: about 14 years ago

10.1093/bioinformatics/bty947

SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data
Cited by: 19
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 18
Published: almost 6 years ago

10.1186/1748-7188-4-7

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity
Cited by: 71
Author(s): Koji Kadota, Yuji Nakai, Kentaro Shimizu
Software Mentions: 13
Published: over 15 years ago

10.1186/s12859-021-04268-4

A comprehensive database for integrated analysis of omics data in autoimmune diseases
Cited by: 10
Author(s): Jordi Martorell-Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez‐López, Fátima Al‐Shahrour, Víctor González‐Rumayor, María Peña‐Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón‐Riquelme, Pedro Carmona-Sáez
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pone.0041169

Global Transcriptome Analysis in Influenza-Infected Mouse Lungs Reveals the Kinetics of Innate and Adaptive Host Immune Responses
Cited by: 93
Author(s): Claudia Pommerenke, Esther Wilk, Barkha Srivastava, Annika Schulze, Natalia Novoselova, Robert Geffers, Klaus Schughart
Software Mentions: 11
Published: over 12 years ago

10.18632/aging.102087

Identification of hub genes in prostate cancer using robust rank aggregation and weighted gene co-expression network analysis
Cited by: 71
Author(s): Zhenyu Song, Chongxi Fan, Zhiyuan Zhuo, Zhe Ma, Wenzhi Li, Gang Chen
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pcbi.1008947

Chromosomal neighbourhoods allow identification of organ specific changes in gene expression
Cited by: 1
Author(s): Rishi Das Roy, Outi Hallikas, Mona M. Christensen, Élodie Renvoisé, Jukka Jernvall
Software Mentions: 10
Published: about 3 years ago

10.15252/msb.20198849

High‐fat diet in a mouse insulin‐resistant model induces widespread rewiring of the phosphotyrosine signaling network
Cited by: 24
Author(s): Antje Dittmann, Norman J. Kennedy, Nina L Soltero, Nader Morshed, Miyeko Mana, Ömer H. Yılmaz, Roger J. Davis, Forest M. White
Software Mentions: 9
Published: over 5 years ago

10.3389/fimmu.2019.02796

Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries
Cited by: 8
Author(s): Anastas Pashov, Velizar Shivarov, Maya Dimitrov Hadzhieva, V. Kostov, Dilyan Ferdinandov, Karen‐Marie Heintz, Shina Pashova, Milena Todorova, Tchavdar Vassilev, Thomas Kieber‐Emmons, Leonardo A. Meza‐Zepeda, Eivind Hovig
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pone.0165545

omicsNPC: Applying the Non-Parametric Combination Methodology to the Integrative Analysis of Heterogeneous Omics Data
Cited by: 11
Author(s): Nestoras Karathanasis, Ioannis Tsamardinos, Vincenzo Lagani
Software Mentions: 9
Published: about 8 years ago

10.1371/journal.pone.0031630

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis
Cited by: 33
Author(s): Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Susanna Donatelli, Raffaele Calogero
Software Mentions: 8
Published: almost 13 years ago

10.3390/microorganisms8020270

In Vitro Zika Virus Infection of Human Neural Progenitor Cells: Meta-Analysis of RNA-Seq Assays
Cited by: 15
Author(s): Rossella Gratton, Paola Maura Tricarico, Almerinda Agrelli, Heverton Valentim Colaço da Silva, Lucas Coêlho Bernardo, Sérgio Crovella, Antônio Victor Campos Coelho, Ronald Moura, Lucas André Cavalcanti Brandão
Software Mentions: 7
Published: almost 5 years ago

10.3390/medicina55060269

A Robust Approach for Identification of Cancer Biomarkers and Candidate Drugs
Cited by: 10
Author(s): Shahjaman, Rezanur Rahman, S. M. Shahinul Islam, Md. Nurul Haque Mollah
Software Mentions: 7
Published: over 5 years ago

10.3390/v13020244

HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles
Cited by: 5
Author(s): Antônio Victor Campos Coelho, Rossella Gratton, João Paulo Britto de Melo, José Leandro Andrade‐Santos, Rafael Lima Guimarães, Sérgio Crovella, Paola Maura Tricarico, Lucas André Cavalcanti Brandão
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12859-018-2437-2

Adaptively capturing the heterogeneity of expression for cancer biomarker identification
Cited by: 1
Author(s): Xueping Xie, Yufeng Xie, Yitong Liu, Hongqiang Wang
Software Mentions: 6
Published: about 6 years ago

10.1186/s13073-016-0282-3

Identification of key regulators of pancreatic cancer progression through multidimensional systems-level analysis
Cited by: 45
Author(s): Deepa Rajamani, Manoj Bhasin
Software Mentions: 6
Published: over 8 years ago

10.3389/fphar.2016.00142

Comparative Transcriptome Analysis Identifies CCDC80 as a Novel Gene Associated with Pulmonary Arterial Hypertension
Cited by: 22
Author(s): Shota Sasagawa, Yuhei Nishimura, Hirofumi Sawada, Eric Erquan Zhang, Shiko Okabe, Soichiro Murakami, Yoshifumi Ashikawa, Mizuki Yuge, Koki Kawaguchi, Reiko Kawase, Yoshihide Mitani, Kazuo Maruyama, Toshio Tanaka
Software Mentions: 6
Published: over 8 years ago

10.1186/1471-2164-12-326

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis
Cited by: 19
Author(s): Franc Llorens, Manuela Hummel, Xavier Pastor, Anna Ferrer, Raquel Pluvinet, Ana Vivancos, Ester Castillo, Susana Iraola, A.M. Mosquera, E. A. Gonzalez, Juan José Lozano, Matthew Ingham, Juliane C. Dohm, María Noguera, Robert Kofler, José Antonio del Rı́o, Mònica Bayés, Heinz Himmelbauer, Lauro Sumoy
Software Mentions: 5
Published: over 13 years ago

10.12688/f1000research.10465.1

Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity
Cited by: 5
Author(s): William Lau, Rachel Sparks, John S. Tsang
Software Mentions: 5
Published: almost 8 years ago

10.1007/s00394-016-1230-0

Cocoa polyphenols and fiber modify colonic gene expression in rats
Cited by: 14
Author(s): Malén Massot-Cladera, Àngels Franch, Margarida Castell, Francisco J. Pérez-Cano
Software Mentions: 5
Published: over 8 years ago

10.1186/1752-0509-7-12

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework
Cited by: 12
Author(s): Gaurav Kumar, Edmond J. Breen, Shoba Ranganathan
Software Mentions: 5
Published: almost 12 years ago

10.1371/journal.pone.0170762

Semi-quantitative proteomics of mammalian cells upon short-term exposure to non-ionizing electromagnetic fields
Cited by: 13
Author(s): Arnold Kuzniar, Charlie Laffeber, Berina Eppink, Karel Bezstarosti, Dick H. W. Dekkers, H. Woelders, A.P.M. Zwamborn, Jeroen Demmers, Joyce H.G. Lebbink, Roland Kanaar
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0216847

Significantly different expression levels of microRNAs associated with vascular invasion in hepatocellular carcinoma and their prognostic significance after surgical resection
Cited by: 13
Author(s): Sung Kyu Song, Woon Yong Jung, Yun Chan Kang, Chul‐Woon Chung, YongKeun Park
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0151127

MiRComb: An R Package to Analyse miRNA-mRNA Interactions. Examples across Five Digestive Cancers
Cited by: 35
Author(s): María Vila-Casadesús, Meritxell Gironella, Juan José Lozano
Software Mentions: 5
Published: over 8 years ago

10.1186/gb-2012-13-10-r95

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers
Cited by: 60
Author(s): Anneleen Decock, Maté Ongenaert, Jasmien Hoebeeck, Katleen De Preter, Gert Van Peer, Wim Van Criekinge, Ruth Ladenstein, Johannes H. Schulte, Rosa Noguera, Raymond Stallings, An Van Damme, Geneviève Laureys, Joëlle Vermeulen, Tom Van Maerken, Frank Speleman, Jo Vandesompele
Software Mentions: 5
Published: almost 13 years ago

10.1371/journal.pone.0166067

Immunohistochemical Typing of Adenocarcinomas of the Pancreatobiliary System Improves Diagnosis and Prognostic Stratification
Cited by: 31
Author(s): Carlos Fernández Moro, Alejandro Fernandez-Woodbridge, Melroy D’Souza, Qianni Zhang, Benedek Bozóky, Senthil Vasan Kandaswamy, Piera Catalano, Rainer Heuchel, Sonia Shtembari, Marco Del Chiaro, Olof Danielsson, Mikael Björnstedt, Matthias Löhr, Bengt Isaksson, Caroline Verbeke, Béla Bozóky
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.50541

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
Cited by: 62
Author(s): Rita A Batista, Jordi Moreno‐Romero, Yue Qiu, Joram van Boven, Juan Santos‐González, Duarte D. Figueiredo, Claudia Köhler
Software Mentions: 5
Published: almost 5 years ago

10.1186/1471-2105-15-14

Fold change rank ordering statistics: a new method for detecting differentially expressed genes
Cited by: 99
Author(s): Doulaye Dembélé, Philippe Kastner
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pone.0161504

Comparison of Normal and Pre-Eclamptic Placental Gene Expression: A Systematic Review with Meta-Analysis
Cited by: 58
Author(s): Obed Brew, Mark Sullivan, Anthony C. Woodman
Software Mentions: 5
Published: about 8 years ago

10.1186/s12864-015-1787-7

Identification and functional analysis of early gene expression induced by circadian light-resetting in Drosophila
Cited by: 20
Author(s): Adeolu B. Adewoye, Charalambos P. Kyriacou, Eran Tauber
Software Mentions: 5
Published: over 9 years ago

10.1186/s12885-017-3103-1

Meta-analysis of gene expression in relapsed childhood B-acute lymphoblastic leukemia
Cited by: 21
Author(s): Yock-Ping Chow, Hamidah Alias, Rahman Jamal
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0111819

Expression Analysis of All Protease Genes Reveals Cathepsin K to Be Overexpressed in Glioblastoma
Cited by: 39
Author(s): Urška Verbovšek, Helena Motaln, Ana Rotter, Nadia A. Atai, Kristina Gruden, C. J. F. Van Noorden, Tamara T. Lah
Software Mentions: 5
Published: about 10 years ago

10.1038/sdata.2016.4

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
Cited by: 10
Author(s): Anneleen Decock, Maté Ongenaert, Wim Van Criekinge, Franki Speleman, Jo Vandesompele
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2105-11-408

Comparison study of microarray meta-analysis methods
Cited by: 85
Author(s): Anna Campain, Jean Yee Hwa Yang
Software Mentions: 4
Published: over 14 years ago

10.1111/acel.12479

Characterization of the direct targets of <scp>FOXO</scp> transcription factors throughout evolution
Cited by: 158
Author(s): Ashley E. Webb, Anshul Kundaje, Anne Brunet
Software Mentions: 4
Published: over 8 years ago

10.1155/2013/848952

Integration of Data from Omic Studies with the Literature-Based Discovery towards Identification of Novel Treatments for Neovascularization in Diabetic Retinopathy
Cited by: 4
Author(s): Aleš Maver, Dimitar Hristovski, Thomas C. Rindflesch, Borut Peterlin
Software Mentions: 4
Published: almost 12 years ago

10.18632/aging.203505

Transcriptomic analysis of elderly women with low muscle mass: association with immune system pathway
Cited by: 1
Author(s): Levi H. Jales Neto, Bidossessi Wilfried Hounkpe, Geórgea Hermogenes Fernandes, Liliam Takayama, Valéria F. Caparbo, Neuza Lopes, Alexandre C. Pereira, Rosa Maria Rodrigues Pereira
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0104504

Identification of Significant Features by the Global Mean Rank Test
Cited by: 17
Author(s): Martin Klammer, J. Nikolaj Dybowski, Daniel Hoffmann, Christoph Schaab
Software Mentions: 4
Published: over 10 years ago

10.3389/fphar.2016.00126

EP300 Protects from Light-Induced Retinopathy in Zebrafish
Cited by: 13
Author(s): Reiko Kawase, Yuhei Nishimura, Yoshifumi Ashikawa, Shota Sasagawa, Soichiro Murakami, Mizuki Yuge, Shiko Okabe, Koki Kawaguchi, Hiroshi Yamamoto, Kazumi Moriyuki, Shinsaku Yamane, Kazuhiro Tsuruma, Masamitsu Shimazawa, Hideaki Hara, Toshio Tanaka
Software Mentions: 4
Published: over 8 years ago

10.1186/s12920-018-0403-5

Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers
Cited by: 12
Author(s): S Schultz, Harald Bartsch, Karl Sotlar, Karina Petat-Dutter, Michael Bonin, Steffen Kahlert, Nadia Harbeck, Ulrich Vogel, Harald Seeger, Tanja Fehm, Hans Neubauer
Software Mentions: 4
Published: about 6 years ago

10.1111/jcmm.14585

Differential coexpression networks in bronchiolitis and emphysema phenotypes reveal heterogeneous mechanisms of chronic obstructive pulmonary disease
Cited by: 11
Author(s): Jiangyue Qin, Ting Yang, Ni Zeng, Chun Wan, Lijuan Gao, Xiaoou Li, Lei Chen, Yongchun Shen, Fuqiang Wen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0076746

Meta-Analysis Identifies NF-κB as a Therapeutic Target in Renal Cancer
Cited by: 37
Author(s): Suraj Peri, Karthik Devarajan, Dong‐Hua Yang, Alfred G. Knudson, Siddharth Balachandran
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0034534

MicroRNA Dysregulation in the Spinal Cord following Traumatic Injury
Cited by: 113
Author(s): Mónica Yunta, Manuel Nieto‐Díaz, Francisco J. Esteban, Marcos Caballero-López, Rosa Navarro-Ruíz, David Reigada, D. Wolfgang Pita-Thomas, Ángela del Águila, Teresa Muñoz‐Galdeano, Rodrigo M. Maza
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2407-14-739

MicroRNA expression as risk biomarker of breast cancer metastasis: a pilot retrospective case-cohort study
Cited by: 42
Author(s): Augusto L F Marino, Adriane Feijó Evangelista, René Aloísio da Costa Vieira, Taciane Macedo, Lígia Maria Kerr, Lucas Faria Abrahão-Machado, Adhemar Longatto‐Filho, Henrique C. S. Silveira, Márcia Maria Chiquitelli Marques
Software Mentions: 4
Published: about 10 years ago

10.1111/jcmm.15441

Molecular classification and immunologic characteristics of immunoreactive high‐grade serous ovarian cancer
Cited by: 1
Author(s): Zheran Liu, Huimeng Wu, Jiachen Deng, Haoqing Wang, Zixuan Wang, An‐Gang Yang, Bowen Liang, Ji Luo, Jianyong Li, Ye Xu, Xiaoli Tang, Fang Fu, Libin Deng
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0036210

Hypocotyl Transcriptome Reveals Auxin Regulation of Growth-Promoting Genes through GA-Dependent and -Independent Pathways
Cited by: 128
Author(s): Elisabeth J. Chapman, Kathleen Greenham, Cristina Castillejo, Ryan C. Sartor, Agniezska Bialy, Tai Sun, Mark Estelle
Software Mentions: 4
Published: over 12 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: about 6 years ago

10.1371/journal.pone.0227193

Transcriptome analysis of early pregnancy vitamin D status and spontaneous preterm birth
Cited by: 22
Author(s): Aishwarya P. Yadama, Hooman Mirzakhani, Thomas F. McElrath, Augusto A. Litonjua, Scott T. Weiss
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-015-0460-0

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data
Cited by: 20
Author(s): Wuming Gong, Naoko Koyano-Nakagawa, Tongbin Li, Daniel J. Garry
Software Mentions: 4
Published: over 9 years ago

10.18632/aging.102034

A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass
Cited by: 5
Author(s): Xuehui Li, Lei Wei, Qiongye Dong, Liyang Liu, Michael Q. Zhang, Zhen Xie, Xiaowo Wang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0008830

Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve
Cited by: 51
Author(s): Eric C. Wooten, Lakshmanan K. Iyer, Maria Claudia Montefusco, Alyson Kelley Hedgepeth, David A. Payne, Navin K. Kapur, David E. Housman, Michael E. Mendelsohn, Gordon S. Huggins
Software Mentions: 4
Published: almost 15 years ago

10.3934/Neuroscience.2019.4.333

Identification of biomarkers associated with Parkinson’s disease by gene expression profiling studies and bioinformatics analysis
Cited by: 10
Author(s): Marios G. Krokidis
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-15-91

Transcriptomic profiling of TK2 deficient human skeletal muscle suggests a role for the p53 signalling pathway and identifies growth and differentiation factor-15 as a potential novel biomarker for mitochondrial myopathies
Cited by: 98
Author(s): Susana G. Kalko, Sonia Paco, Cristina Jou, Maria Angels Rodríguez, Marija Meznarič, Mihael Rogac, Maja Jekovec-Vrhovšek, Monica Sciacco, Maurizio Moggio, Gigliola Fagiolari, Boél De Paepe, Linda De Meırleır, Isidre Ferrer, Manuel Roig-Quilis, Francina Munell, Julio Montoya, Ester López‐Gallardo, Eduardo Ruiz‐Pesini, Rafael Artuch, Raquel Montero, Ferrán Torner, A. Nascimento, C. Ortez, J. Colomer, Cecilia Jiménez‐Mallebrera
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0016679

Specific Age-Associated DNA Methylation Changes in Human Dermal Fibroblasts
Cited by: 113
Author(s): Carmen M. Koch, Christoph V. Suschek, Qiong Lin, Simone Bork, Maria Goergens, Sylvia Joussen, Norbert Pallua, Anthony D. Ho, Martin Zenke, Wolfgang Wagner
Software Mentions: 3
Published: almost 14 years ago

10.1002/brb3.1879

Identifying functionally relevant candidate genes for inflexible ethanol intake in mice and humans using a guilt‐by‐association approach
Cited by: 8
Author(s): Luana Martins de Carvalho, Pablo Augusto de Souza Fonseca, Isadora Marques Paiva, Samara Damasceno, Agatha Sondertoft Braga Pedersen, Daniel Almeida da Silva e Silva, Corinde E. Wiers, Nora D. Volkow, Ana Lúcia Brunialti Godard
Software Mentions: 3
Published: about 4 years ago

10.1155/2021/7326853

Identification of Genes Universally Differentially Expressed in Gastric Cancer
Cited by: 6
Author(s): Yidan Shi, Lishuang Qi, Haifeng Chen, Jiahui Zhang, Qingzhou Guan, Jun He, Meifeng Li, Zheng Guo, Haidan Yan, Ping Li
Software Mentions: 3
Published: almost 4 years ago

10.1186/1748-7188-3-8

A weighted average difference method for detecting differentially expressed genes from microarray data
Cited by: 104
Author(s): Koji Kadota, Yuji Nakai, Kentaro Shimizu
Software Mentions: 3
Published: over 16 years ago

10.3389/fendo.2018.00158

Integrated Characterization of MicroRNA and mRNA Transcriptome in Papillary Thyroid Carcinoma
Cited by: 13
Author(s): Azliana Mohamad Yusof, A. Rahman A. Jamal, Rohaizak Muhammad, Shahrun Niza Abdullah Suhaimi, Isa Mohamed Rose, Sazuita Saidin, Nurul Syakima Ab Mutalib
Software Mentions: 3
Published: over 6 years ago

10.18632/oncotarget.14302

Activating transcription factor 3 is crucial for antitumor activity and to strengthen the antiviral properties of Onconase
Cited by: 20
Author(s): Anna Vert, Jessica Castro, Marc Ribó, Antoni Benito, María Vilanova
Software Mentions: 3
Published: almost 8 years ago

10.3389/fgene.2021.580390

Systematic Identification of circRNA–miRNA–mRNA Regulatory Network in Esophageal Squamous Cell Carcinoma
Cited by: 6
Author(s): Yi Shen, Yi Shao, Chen Niu, Xiaoli Ruan, Zhaoping Zang, Rena Nakyeyune, Xiuhua Guo, Fen Liu
Software Mentions: 3
Published: over 3 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: over 7 years ago

10.1186/1471-2164-13-105

Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures
Cited by: 41
Author(s): Ana I. Manzano, Jack J. W. A. van Loon, Peter C. M. Christianen, Juana María González-Rubio, F. Javier Medina, Raúl Herranz
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0093489

The Mechanisms Underlying α-Amanitin Resistance in Drosophila melanogaster: A Microarray Analysis
Cited by: 17
Author(s): Chelsea L. Mitchell, Michael C. Saul, Liang Liu, Hairong Wei, Thomas Werner
Software Mentions: 3
Published: over 10 years ago

10.1186/s40478-019-0712-8

Inhibition of mitochondrial respiration prevents BRAF-mutant melanoma brain metastasis
Cited by: 30
Author(s): Terje Sundstrøm, Lars Prestegarden, Francisco Azuaje, Synnøve Nymark Aasen, Gro Vatne Røsland, Jobin K. Varughese, Marzieh Bahador, Simon Bernatz, Yannick Braun, Patrick N. Harter, Kai Ove Skaftnesmo, Elizabeth S. Ingham, Lisa M. Mahakian, Sarah Tam, Clifford G. Tepper, Kjell Petersen, Katherine W. Ferrara, Karl Johan Tronstad, Morten Lund‐Johansen, Rudi Beschorner, Rolf Bjerkvig, Frits Thorsen
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.7579

A nuclear-directed human pancreatic ribonuclease (PE5) targets the metabolic phenotype of cancer cells
Cited by: 15
Author(s): Anna Vert, Jessica Castro, Marc Ribó, Antoni Benito, María Vilanova
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0086329

Investigation of Radiosensitivity Gene Signatures in Cancer Cell Lines
Cited by: 43
Author(s): John Hall, Rohan Iype, Joana Senra, Janet Taylor, Lucile Armenoult, Kenneth Oguejiofor, Yaoyong Li, Ian J. Stratford, Peter L. Stern, Mark J. O’Connor, Crispin Miller, Catharine M L West
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0127702

A New Combinatorial Optimization Approach for Integrated Feature Selection Using Different Datasets: A Prostate Cancer Transcriptomic Study
Cited by: 7
Author(s): Nisha Puthiyedth, Carlos Riveros, Regina Berretta, Pablo Moscato
Software Mentions: 3
Published: over 9 years ago

10.1038/srep37651

Immune signatures of protective spleen memory CD8 T cells
Cited by: 11
Author(s): Lilia Brinza, Sophia Djebali, Martine Tomkowiak, Julien Mafille, Céline Loiseau, Pierre Emmanuel Jouve, Simon Bernard, Laurent Buffat, Bruno Lina, Michèle Ottmann, Manuel Rosa‐Calatrava, Stéphane Schicklin, Nathalie Bonnefoy, Grégoire Lauvau, Morgan Grau, Mélanie Wencker, Christophe Arpin, Thierry Walzer, Yann Leverrier, Jacqueline Marvel
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-020-74100-1

Early-pregnancy transcriptome signatures of preeclampsia: from peripheral blood to placenta
Cited by: 9
Author(s): Aishwarya P. Yadama, Enrico Maiorino, Vincent J. Carey, Thomas F. McElrath, Augusto A. Litonjua, Joseph Loscalzo, Scott T. Weiss, Hooman Mirzakhani
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0024235

In-Vivo Expression Profiling of Pseudomonas aeruginosa Infections Reveals Niche-Specific and Strain-Independent Transcriptional Programs
Cited by: 45
Author(s): Piotr Bielecki, Jacek Puchałka, Melissa L. Wos‐Oxley, Holger Loessner, Justyna Glik, Marek Kawecki, Mariusz Nowak, Burkhard Tümmler, Siegfried Weiß, Vítor A. P. Martins dos Santos
Software Mentions: 3
Published: about 13 years ago

10.1038/srep28396

Identification of long non-coding RNAs involved in neuronal development and intellectual disability
Cited by: 42
Author(s): Eva D’haene, Eva Jacobs, Pieter-Jan Volders, Tim De Meyer, Björn Menten, Sarah Vergult
Software Mentions: 3
Published: over 8 years ago

10.1038/tp.2016.101

Epigenetic differences in monozygotic twins discordant for major depressive disorder
Cited by: 37
Author(s): Karim Malki, Elena Koritskaya, Fraser Harris, Kevin Bryson, Mark Herbster, Maria Grazia Tosto
Software Mentions: 3
Published: over 8 years ago

10.1186/s12870-015-0568-4

Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease
Cited by: 43
Author(s): Nidhi Rawat, Sandhya.P. Kiran, Dongliang Du, Fred G. Gmitter, Zhanao Deng
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0097821

PIWI Proteins Are Dispensable for Mouse Somatic Development and Reprogramming of Fibroblasts into Pluripotent Stem Cells
Cited by: 22
Author(s): Elaine Cheng, Dongwan Kang, Zhong Wang, Haifan Lin
Software Mentions: 3
Published: about 10 years ago

10.1186/s12885-015-1337-3

Transcriptional changes associated with resistance to inhibitors of epidermal growth factor receptor revealed using metaanalysis
Cited by: 3
Author(s): Sidra Younis, Qamar Javed, Miroslav Blumenberg
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0136473

Transcriptomic Analysis and Meta-Analysis of Human Granulosa and Cumulus Cells
Cited by: 21
Author(s): Tanja Burnik Papler, Eda Vrtačnik Bokal, Aleš Maver, Andreja Nataša Kopitar, Luca Lovrečić
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0005415

A Molecular Function Map of Ewing's Sarcoma
Cited by: 160
Author(s): Maximilian Kauer, Jozef Ban, Reinhard Kofler, Robert L. Walker, Sean Davis, Paul S. Meltzer, Heinrich Kovar
Software Mentions: 3
Published: over 15 years ago

10.1038/srep17822

Role of innate immunity-triggered pathways in the pathogenesis of Sickle Cell Disease: a meta-analysis of gene expression studies
Cited by: 33
Author(s): Bidossessi Wilfried Hounkpe, Maiara Marx Luz Fiusa, Marina Pereira Colella, Loredana Costa, Rafaela de Oliveira Benatti, Sara T Olalla Saad, Fernando Ferreira Costa, Magnun Nueldo Nunes Santos, Erich Vinícius De Paula
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2202-9-93

Bioinformatic and statistical analysis of the optic nerve head in a primate model of ocular hypertension
Cited by: 40
Author(s): Kenneth S Kompass, Olga A. Agapova, Wenjun Li, Paul L. Kaufman, Carol A. Rasmussen, M. Rosario Hernandez
Software Mentions: 3
Published: about 16 years ago

10.3390/ph12040156

C3orf70 Is Involved in Neural and Neurobehavioral Development
Cited by: 8
Author(s): Yoshifumi Ashikawa, Takashi Shiromizu, Koki Miura, Yoshiyuki Adachi, Takaaki Matsui, Yasumasa Bessho, Toshio Tanaka, Yuhei Nishimura
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.830

The effect of listening to music on human transcriptome
Cited by: 32
Author(s): Chakravarthi Kanduri, Pirre Raijas, Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0130128

Oviductal Transcriptome Is Modified after Insemination during Spontaneous Ovulation in the Sow
Cited by: 37
Author(s): Rebeca López‐Úbeda, Francisco Alberto García–Vázquez, Raquel Romar, J. Gadea, Marta Muñoz, Richard Hunter, Pilar Coy
Software Mentions: 3
Published: over 9 years ago

10.1038/sdata.2015.10

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
Cited by: 48
Author(s): Serdar Turkarslan, Eliza J.R. Peterson, Tige R. Rustad, K Minch, David J Reiss, Robert Morrison, Shuyi Ma, Nathan D. Price, David R. Sherman, Nitin S. Baliga
Software Mentions: 3
Published: over 9 years ago

10.3390/genes8120368

scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells
Cited by: 73
Author(s): Yuan Cao, Junjie Zhu, Peilin Jia, Zhongming Zhao
Software Mentions: 3
Published: almost 7 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: about 4 years ago

10.1186/gb-2008-9-7-r112

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
Cited by: 98
Author(s): Sascha Laubinger, Georg Zeller, Stefan R. Henz, Timo Sachsenberg, Christian Widmer, Naïra Naouar, Marnik Vuylsteke, Bernhard Schölkopf, Gunnar Rätsch, Detlef Weigel
Software Mentions: 3
Published: almost 17 years ago

10.3389/fphar.2016.00162

Downregulation of GSTK1 Is a Common Mechanism Underlying Hypertrophic Cardiomyopathy
Cited by: 38
Author(s): Shota Sasagawa, Yuhei Nishimura, Shiko Okabe, Soichiro Murakami, Yoshifumi Ashikawa, Mizuki Yuge, Koki Kawaguchi, Reiko Kawase, Ryuji Okamoto, Ito M, Toshio Tanaka
Software Mentions: 3
Published: over 8 years ago

10.3389/fphar.2016.00119

E2F4 Promotes Neuronal Regeneration and Functional Recovery after Spinal Cord Injury in Zebrafish
Cited by: 11
Author(s): Shota Sasagawa, Yuhei Nishimura, Yuka Hayakawa, Soichiro Murakami, Yoshifumi Ashikawa, Mizuki Yuge, Shiko Okabe, Koki Kawaguchi, Reiko Kawase, Toshio Tanaka
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0230905

Identification of human peripheral blood monocyte gene markers for early screening of solid tumors
Cited by: 11
Author(s): Siyang Chen, Menghan Liu, Bowen Liang, Shanghua Ge, Jie Peng, Haiyue Huang, Ye Xu, Xiaoli Tang, Libin Deng
Software Mentions: 3
Published: over 4 years ago

10.1186/s13637-015-0034-5

Gene expression analysis supports tumor threshold over 2.0 cm for T-category breast cancer
Cited by: 2
Author(s): Hiroko Kato Solvang, Arnoldo Frigessi, Fatemeh Kaveh, Margit Riis, Torben Lüders, Ida Rashida Khan Bukholm, Vessela N. Kristensen, Bettina Kulle Andreassen
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13048-016-0252-9

The oviductal transcriptome is influenced by a local ovarian effect in the sow
Cited by: 3
Author(s): Rebeca López‐Úbeda, Marta Muñoz, Luis Alberto Vieira, Richard Hunter, Pilar Coy, Sebastián Cánovas
Software Mentions: 3
Published: over 8 years ago

10.1007/s11010-016-2776-0

Differential expression of store-operated calcium- and proliferation-related genes in hepatocellular carcinoma cells following TRPC1 ion channel silencing
Cited by: 14
Author(s): Çiğdem Selli, Dominic Pearce, Andrew H. Sims, Metiner Tosun
Software Mentions: 2
Published: over 8 years ago

10.3389/fnins.2016.00601

Variation in Gene Expression in Autism Spectrum Disorders: An Extensive Review of Transcriptomic Studies
Cited by: 62
Author(s): Ashley Ansel, Joshua P. Rosenzweig, Philip D. Zisman, Michal L. Melamed, Benjamin Gesundheit
Software Mentions: 2
Published: almost 8 years ago

10.3389/fnins.2016.00396

Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2−/− Hippocampus
Cited by: 27
Author(s): Giovanni Provenzano, Zelia Corradi, Katia Monsorno, Tarcisio Fedrizzi, Laura Ricceri, María Luisa Scattoni, Yuri Bozzi
Software Mentions: 2
Published: about 8 years ago

10.1007/s10126-016-9704-x

Functional Genomic Analysis of the Impact of Camelina (Camelina sativa) Meal on Atlantic Salmon (Salmo salar) Distal Intestine Gene Expression and Physiology
Cited by: 20
Author(s): Tyler D. Brown, Tiago S. Hori, Xi Xue, Chang Lin Ye, D. M. Anderson, Matthew L. Rise
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-14-25

Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia colitranscriptome
Cited by: 29
Author(s): Bei‐Wen Ying, Shigeto Seno, Fuyuro Kaneko, Hideo Matsuda, Tetsuya Yomo
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2164-13-220

Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells
Cited by: 115
Author(s): Toma Tebaldi, Angela Re, Gabriella Viero, Ilaria Pegoretti, Andrea Passerini, Enrico Blanzieri, Alessandro Quattrone
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-015-2069-0

Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains
Cited by: 28
Author(s): John J. Varga, Mariette Barbier, Xavier Mulet, Piotr Bielecki, Jennifer A. Bartell, Joshua P. Owings, Inmaculada Martínez-Ramos, Lauren E. Hittle, Michael R. Davis, F. Heath Damron, George W. Liechti, Jacek Puchałka, Vítor A. P. Martins dos Santos, Robert K. Ernst, Jason A. Papin, Sebastián Albertí, Antonio Oliver, Joanna B. Goldberg
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0068136

Genome-Wide Responses of Female Fruit Flies Subjected to Divergent Mating Regimes
Cited by: 8
Author(s): Dave T. Gerrard, Claudia Fricke, Dominic A. Edward, Dylan R. Edwards, Tracey Chapman
Software Mentions: 2
Published: over 11 years ago

10.1186/s40001-018-0328-7

Membrane-bound estrogen receptor alpha initiated signaling is dynamin dependent in breast cancer cells
Cited by: 9
Author(s): István Marczell, Petra Balogh, G Nyírő, Anna L. Kiss, Balázs Kovács, Gábor Békési, Kàroly Rácz, Attila Patócs
Software Mentions: 2
Published: over 6 years ago

Projects: bioconductor: RankProd

Papers Mentioning RankProd 213