bioconductor: gcrma | Projects | Ecosyste.ms: Papers

10.3390/cancers11010091

The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis
Cited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: over 5 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

10.1371/journal.pone.0204123

Prediction of early breast cancer patient survival using ensembles of hypoxia signatures
Cited by: 8
Author(s): Inna Y. Gong, Natalie S. Fox, Vincent Huang, Paul C. Boutros
Software Mentions: 12
Published: about 6 years ago

10.3389/fmolb.2021.681526

Identification of Key Biomarkers and Immune Infiltration in Systemic Juvenile Idiopathic Arthritis by Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Min Zhang, Rongxin Dai, Qianqian Zhao, Lina Zhou, Yunfei An, Xuemei Tang, Xiaodong Zhao
Software Mentions: 12
Published: about 3 years ago

10.1007/s12032-017-0963-9

The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data
Cited by: 107
Author(s): Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Software Mentions: 12
Published: over 7 years ago

10.3389/fimmu.2021.698236

Comprehensive Analysis of Clinical Significance, Immune Infiltration and Biological Role of m6A Regulators in Early-Stage Lung Adenocarcinoma
Cited by: 3
Author(s): Bolun Zhou, Shugeng Gao
Software Mentions: 12
Published: about 3 years ago

10.1186/1471-2164-9-419

Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: Comparison of rat and mouse
Cited by: 74
Author(s): Paul C. Boutros, Rui Yan, Ivy D. Moffat, Raimo Pohjanvirta, Allan B. Okey
Software Mentions: 11
Published: almost 17 years ago

10.1186/1756-0500-3-81

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
Cited by: 17
Author(s): Colin S. Gillespie, Guiyuan Lei, Richard J. Boys, Amanda Greenall, Darren J. Wilkinson
Software Mentions: 11
Published: over 14 years ago

10.1186/gb-2004-5-10-r80

Cited by: 10,848
Author(s): Robert Gentleman, Vincent J. Carey, Douglas M. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Maria Iacus, Rafael A. Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony Rossini, Günther Sawitzki, Colin A. Smith, Gordon K. Smyth, Luke Tierney, Jean Yee Hwa Yang, Jianhua Zhang
Software Mentions: 10
Published: almost 21 years ago

10.7717/peerj.1845

A molecular classification of human mesenchymal stromal cells
Cited by: 42
Author(s): Florian Rohart, Elizabeth A. Mason, Nicholas Matigian, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Suzanne Butcher, Jatin Patel, Kerry Atkinson, Kiarash Khosrotehrani, Nicholas M. Fisk, Kim‐Anh Lê Cao, Christine A. Wells
Software Mentions: 10
Published: over 8 years ago

10.1371/journal.pone.0018337

mRNA Levels in Control Rat Liver Display Strain-Specific, Hereditary, and AHR-Dependent Components
Cited by: 7
Author(s): Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, Raimo Pohjanvirta
Software Mentions: 9
Published: over 13 years ago

10.3389/fimmu.2021.592303

Machine Learning Identifies Complicated Sepsis Course and Subsequent Mortality Based on 20 Genes in Peripheral Blood Immune Cells at 24 H Post-ICU Admission
Cited by: 35
Author(s): Shayantan Banerjee, Akram Mohammed, Hector R. Wong, Nades Palaniyar, Rishikesan Kamaleswaran
Software Mentions: 9
Published: over 3 years ago

10.3390/cancers11101606

A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning
Cited by: 12
Author(s): Johannes A Vey, Lorenz A. Kapsner, Maximilian Fuchs, Philipp Unberath, Giulia Veronesi, Meik Kunz
Software Mentions: 8
Published: almost 5 years ago

10.7554/eLife.05005

Predicting effective microRNA target sites in mammalian mRNAs
Cited by: 5,158
Author(s): Vikram Agarwal, George W. Bell, Jin Wu Nam, David P. Bartel
Software Mentions: 8
Published: about 9 years ago

10.1186/1471-2105-12-464

From hybridization theory to microarray data analysis: performance evaluation
Cited by: 4
Author(s): Fabrice Berger, Enrico Carlon
Software Mentions: 8
Published: almost 13 years ago

10.3390/cells9030786

Systematic Identification of Housekeeping Genes Possibly Used as References in Caenorhabditis elegans by Large-Scale Data Integration
Cited by: 13
Author(s): Jingxin Tao, Youjin Hao, Xudong Li, Huachun Yin, Xiner Nie, Jie Zhang, Bo-Ying Xu, Chen Qiao, Bo Li
Software Mentions: 8
Published: over 4 years ago

10.1186/gm385

Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies
Cited by: 14
Author(s): Maud H.W. Starmans, Melania Pintilie, Thomas John, Sandy D. Der, Frances A. Shepherd, Igor Jurišica, Philippe Lambin, Ming‐Sound Tsao, Paul C. Boutros
Software Mentions: 8
Published: almost 13 years ago

10.18632/oncotarget.26668

mTOR inhibition affects Yap1-β-catenin-induced hepatoblastoma growth and development
Cited by: 11
Author(s): Laura Molina, Hong Yang, Adeola O. Adebayo Michael, Michael Oertel, Aaron Bell, Sucha Singh, Xin Chen, Junyan Tao, Satdarshan P. Monga
Software Mentions: 8
Published: over 5 years ago

10.7150/ijms.48244

Identification of Key Genes and Pathways in Myeloma side population cells by Bioinformatics Analysis
Cited by: 21
Author(s): Yang Qin, Kaihu Li, Xin Li, Jing Liu
Software Mentions: 8
Published: almost 5 years ago

10.3389/fcell.2021.646774

CRISPR-cas9 Screening Identified Lethal Genes Enriched in Cell Cycle Pathway and of Prognosis Significance in Breast Cancer
Cited by: 6
Author(s): Xi Sun, Zheng Wang, Xiaosong Chen, Kunwei Shen
Software Mentions: 6
Published: over 3 years ago

10.1186/gm496

A robust prognostic signature for hormone-positive node-negative breast cancer
Cited by: 18
Author(s): Obi L. Griffith, François Pépin, Oana Enache, Laura M. Heiser, Eric A. Collisson, Paul T. Spellman, Joe W. Gray
Software Mentions: 6
Published: almost 12 years ago

10.18632/oncotarget.22636

3D-cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimic<i>in-vivo</i>conditions
Cited by: 11
Author(s): Gabriele Gamerith, Johannes Michael Rainer, Julia Huber, Hubert Hackl, Zlatko Trajanoski, Stefan Koeck, Edith Lorenz, Johann Kern, Reinhard Kofler, Jens M. Kelm, Heinz Zwierzina, Arno Amann
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0019024

Functional Genomics Unique to Week 20 Post Wounding in the Deep Cone/Fat Dome of the Duroc/Yorkshire Porcine Model of Fibroproliferative Scarring
Cited by: 21
Author(s): Loren H. Engrav, Christopher K. Tuggle, Kathleen F. Kerr, Kehao Zhu, Surawej Numhom, Oliver Couture, Richard P. Beyer, Anne M. Hocking, Gretchen J. Carrougher, Maria Luiza Christóvão Ramos, Matthew B. Klein, Nicole S. Gibran
Software Mentions: 6
Published: over 13 years ago

10.1371/journal.pone.0066826

A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development
Cited by: 31
Author(s): Alicia N. Schep, Boris Adryan
Software Mentions: 6
Published: over 11 years ago

10.1371/journal.pcbi.1000193

Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm
Cited by: 236
Author(s): Jun Yan, Haifang Wang, Yuting Liu, Chunxuan Shao
Software Mentions: 6
Published: almost 16 years ago

10.1186/1743-422X-11-126

Reactive astrogliosis in response to hemorrhagic fever virus: microarray profile of Junin virus-infected human astrocytes
Cited by: 8
Author(s): Olga A. Kolokoltsova, Nadezhda E. Yun, Slobodan Paessler
Software Mentions: 6
Published: about 10 years ago

10.1080/21623945.2019.1595269

Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians
Cited by: 17
Author(s): Aditya Saxena, Prabhat Tiwari, Nitin Wahi, Arpana Soni, Ram Chandra Bansiwal, Anshul Kumar, Balram Sharma, Prakash P Punjabi, Nidhi Gupta, Babita Malik, Krishna Mohan Medicherla, Prashanth Suravajhala, Sandeep Kumar Mathur
Software Mentions: 6
Published: almost 6 years ago

10.1186/1471-2105-15-170

Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences
Cited by: 24
Author(s): Natalie S. Fox, Maud H.W. Starmans, Syed Haider, Philippe Lambin, Paul C. Boutros
Software Mentions: 6
Published: over 10 years ago

10.1186/1471-2164-10-439

Relative power and sample size analysis on gene expression profiling data
Cited by: 64
Author(s): Maarten van Iterson, Peter A C ‘t Hoen, Paola Pedotti, Guido Hooiveld, Johan T. den Dunnen, Gjb van Ommen, JM Boer, R.M. Menezes
Software Mentions: 6
Published: about 15 years ago

10.3390/microarrays3040212

The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma
Cited by: 1
Author(s): Andrew R. Dalby, Ian Bailey
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0118731

Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis
Cited by: 77
Author(s): Katherine C. H. Amrine, Bárbara Blanco-Ulate, Dario Cantu
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2164-11-723

Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications
Cited by: 66
Author(s): José M. Otero, Wanwipa Vongsangnak, Mohammad Ali Asadollahi, Roberto Olivares-Hernandes, Jérôme Maury, Laurent Farinelli, Loïc Barlocher, Magne Østerås, Michel Schalk, Anthony Clark, Jens Nielsen
Software Mentions: 5
Published: almost 14 years ago

10.1038/srep13135

Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NFκB Signaling and Inflammatory Lung Injury
Cited by: 119
Author(s): Sara M. Camp, Ermelinda Ceco, Carrie Evenoski, Sergei M. Danilov, Tong Zhou, Eddie T. Chiang, Liliana Moreno‐Vinasco, Brandon Mapes, Jieling Zhao, Gamze Gürsoy, Mary Elizabeth Brown, Djanybek Adyshev, Shahid Siddiqui, Hector Quijada, Saad Sammani, Eleftheria Letsiou, Laleh Saadat, Mohammed Yousef, Ting Wang, Jie Liang, Joe G.N. Garcia
Software Mentions: 5
Published: about 9 years ago

10.1186/s13073-021-00924-9

The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches
Cited by: 8
Author(s): Julie M. Steinbrink, Rachel A. Myers, Kaiyuan Hua, Melissa D. Johnson, Jessica Seidelman, Ephraim L. Tsalik, Ricardo Henao, Geoffrey S. Ginsburg, Christopher W. Woods, Barbara D. Alexander, Micah T. McClain
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-57110-6

Single-cell transcriptional profiles in human skeletal muscle
Cited by: 160
Author(s): Aliza Rubenstein, Gregory R. Smith, Ulrika Raue, Gwénaëlle Begue, Kiril Minchev, Frederique Ruf-Zamojski, Venugopalan D. Nair, Xingyu Wang, Lan Zhou, Elena Zaslavsky, Todd A. Trappe, Scott Trappe, Stuart C. Sealfon
Software Mentions: 5
Published: over 4 years ago

10.1186/1752-0509-6-2

Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control
Cited by: 15
Author(s): Kevin M. D’Auria, Gina M. Donato, Mary C. Gray, Glynis L. Kolling, Cirle A. Warren, Lauren M Cave, Michael D. Solga, Joanne Lannigan, Jason A. Papin, Erik L. Hewlett
Software Mentions: 5
Published: almost 13 years ago

10.7554/eLife.34042

Differential 3’ processing of specific transcripts expands regulatory and protein diversity across neuronal cell types
Cited by: 21
Author(s): Saša Jereb, Hun‐Way Hwang, Eric Van Otterloo, Eve-Ellen Govek, John Fak, Yuan Yuan, Mary E. Hatten, Robert B. Darnell
Software Mentions: 5
Published: over 6 years ago

10.3390/cancers11010053

Prognostic Gene Discovery in Glioblastoma Patients using Deep Learning
Cited by: 34
Author(s): Kelvin Wong, Robert Rostomily, Stephen T.C. Wong
Software Mentions: 5
Published: over 5 years ago

10.1186/s13062-015-0051-z

Test on existence of histology subtype-specific prognostic signatures among early stage lung adenocarcinoma and squamous cell carcinoma patients using a Cox-model based filter
Cited by: 25
Author(s): Suyan Tian, Chi Wang, Ming-Wen An
Software Mentions: 5
Published: over 9 years ago

10.1093/jxb/eraa108

Crosstalk between heterotrimeric G protein-coupled signaling pathways and WRKY transcription factors modulating plant responses to suboptimal micronutrient conditions
Cited by: 16
Author(s): Tai‐Hsi Wu, Shalini Krishnamoorthi, Honzhen Goh, Richalynn Leong, Amy Catherine Sanson, Daisuke Urano
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-018-33234-z

Low dose dimethyl sulfoxide driven gross molecular changes have the potential to interfere with various cellular processes
Cited by: 65
Author(s): Sinem Tunçer, Rafig Gurbanov, Ilir Sheraj, Ege Solel, Okan Esentürk, Sreeparna Banerjee
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0050253

Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level
Cited by: 2
Author(s): Andrew R. Dalby, Ibrahim Emam, Raimo Franke
Software Mentions: 5
Published: almost 12 years ago

10.1038/s41598-018-27376-3

Transcriptional analysis of adipose tissue during development reveals depot-specific responsiveness to maternal dietary supplementation
Cited by: 16
Author(s): Hernan P. Fainberg, Mark Birtwistle, Reham I. Alagal, Ahmad Alhaddad, Mark Pope, Graeme R. Davies, Rachel Woods, Marcos Castellanos, Sean May, Catharine A. Ortori, David A. Barrett, V.E.A. Perry, Frank Wiens, Bernd Stahl, Eline van der Beek, Harold S. Sacks, Helen Budge, Michael Symonds
Software Mentions: 4
Published: over 6 years ago

10.2478/intox-2014-0010

Systems toxicology approaches enable mechanistic comparison of spontaneous and cigarette smoke-related lung tumor development in the A/J mouse model
Cited by: 14
Author(s): Karsta Luettich, Yu‐Tao Xiang, Anita Iskandar, Alain Sewer, Florian Martin, Marja Talikka, Patrick Vanscheeuwijck, An Berges, Emilija Veljkovic, Ignacio González-Suárez, Walter K. Schlage, Walter K. Schlage, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 4
Published: over 10 years ago

10.1186/1471-2164-14-S1-S9

Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information
Cited by: 2
Author(s): Ellis Patrick, Michael Buckley, David M. Lin, Jean Yee Hwa Yang
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2105-8-146

Analysis of probe level patterns in Affymetrix microarray data
Cited by: 15
Author(s): A. Cambon, Abdelnaby Khalyfa, Nigel G. F. Cooper, Caryn M. Thompson
Software Mentions: 4
Published: over 17 years ago

10.1186/1471-2164-11-50

Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data
Cited by: 17
Author(s): Jun Yin, Sarah McLoughlin, Ian B. Jeffery, Antonino Glaviano, Breandán N. Kennedy, Desmond G. Higgins
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2164-9-110

Search for the genes involved in oocyte maturation and early embryo development in the hen
Cited by: 47
Author(s): Sébastien Elis, Florence Batellier, Isabelle Couty, Sandrine Balzergue, Marie‐Laure Martin‐Magniette, Philippe Monget, Élisabeth Blesbois, Marina Govoroun
Software Mentions: 4
Published: over 16 years ago

10.1186/1471-2164-10-363

Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor
Cited by: 56
Author(s): Anita Zamboni, Pamela Gatto, Alessandro Cestaro, S. Pilati, Roberto Viola, Fulvio Mattivi, C. Moser, Riccardo Velasco
Software Mentions: 4
Published: about 15 years ago

10.1186/1471-2105-8-273

The utility of MAS5 expression summary and detection call algorithms
Cited by: 144
Author(s): Stuart D Pepper, Emma Saunders, Laura Edwards, Claire Wilson, Crispin Miller
Software Mentions: 4
Published: about 17 years ago

10.1155/2013/187509

Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Based on Omics Data
Cited by: 8
Author(s): Ai-Di Zhang, Shao‐Xing Dai, Jing‐Fei Huang
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2105-13-56

'maskBAD' - a package to detect and remove Affymetrix probes with binding affinity differences
Cited by: 5
Author(s): Michael Dannemann, Michael Lachmann, Anna Lorenc
Software Mentions: 4
Published: over 12 years ago

10.1038/s41598-021-91864-2

Meta-analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo-resistance in AML
Cited by: 2
Author(s): Parastoo Modarres, Farzaneh Mohamadi Farsani, Amir Abas Nekouie, Sadeq Vallian
Software Mentions: 4
Published: over 3 years ago

10.1002/cam4.3833

The immune landscape during the tumorigenesis of cervical cancer
Cited by: 18
Author(s): Yiying Wang, Mengdi He, Guodong Zhang, Kankan Cao, Moran Yang, Hongwei Zhang, Haiou Liu
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.3737

Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño
Cited by: 16
Author(s): M. Rocío Aguilar-Rangel, Ricardo A. Chávez Montes, Eric González‐Segovia, Jeffrey Ross‐Ibarra, June Simpson, Ruairidh J. H. Sawers
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-39733-x

HER2 and p95HER2 differentially regulate miRNA expression in MCF-7 breast cancer cells and downregulate MYB proteins through miR-221/222 and miR-503
Cited by: 15
Author(s): Andrej Gorbatenko, Rolf Søkilde, Ester E. Sørensen, Inga Newie, Helena Persson, Beatriz Morancho, Joaquı́n Arribas, Thomas Litman, Carlos Rovira, Stine Falsig Pedersen
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2407-12-223

Estimation of groin recurrence risk in patients with squamous cell vulvar carcinoma by the assessment of marker gene expression in the lymph nodes
Cited by: 11
Author(s): Magdalena Kowalewska, Jakub Radziszewski, Krzysztof Goryca, Mateusz Bujko, Małgorzata Oczko‐Wojciechowska, Michał Jarząb, Janusz A. Siedlecki, Mariusz Bidziński
Software Mentions: 4
Published: over 12 years ago

10.7554/eLife.02734

Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer
Cited by: 102
Author(s): Sakari Vanharanta, Christina B. Marney, Weiqun Shu, Manuel Valiente, Yilong Zou, Aldo Mele, Robert B. Darnell, Joan Massagué
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pgen.1002676

LINT, a Novel dL(3)mbt-Containing Complex, Represses Malignant Brain Tumour Signature Genes
Cited by: 30
Author(s): Karin Meier, Eve-Lyne Mathieu, Florian Finkernagel, L. Maximilian Reuter, Maren Scharfe, Gunther Doehlemann, Michael Jarek, Alexander Brehm
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2407-9-413

Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KITmutations and expression
Cited by: 21
Author(s): Jerzy Ostrowski, Marcin Polkowski, Agnieszka Paziewska, Magdalena Skrzypczak, Krzysztof Goryca, Tymon Rubel, Katarzyna Kokoszyńska, Piotr Rutkowski, Zbigniew Nowecki, Anna Jerzak vel Dobosz, Dorota Jarosz, W. Ruka, Lucjan Wyrwicz
Software Mentions: 4
Published: almost 15 years ago

10.1371/journal.pgen.1006593

Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer’s disease
Cited by: 99
Author(s): Fiona Kerr, Oyinkan Sofola-Adesakin, Dobril Ivanov, Jemma Gatliff, Beatriz Gomez Perez‐Nievas, Hélène Bertrand, Pedro Martı́nez, Rebecca Callard, Inge Snoeren, Helena M. Cochemé, Jennifer Adcott, Mobina Khericha, Jorge Iván Castillo-Quan, Geoff Wells, Wendy Noble, Janet M. Thornton, Linda Partridge
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1003188

Suv4-20h Histone Methyltransferases Promote Neuroectodermal Differentiation by Silencing the Pluripotency-Associated Oct-25 Gene
Cited by: 29
Author(s): Dario Nicetto, Matthias Hahn, Julia Jeannine Jung, Tobias D. Schneider, Tobias Straub, Róbert Dávid, Gunnar Schotta, Ralph A.W. Rupp
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0054144

Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory
Cited by: 139
Author(s): José M. Otero, Donatella Cimini, Kiran Raosaheb Patil, Simon Guldberg Poulsen, Lisbeth Olsson, Jens Nielsen
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-213X-9-30

Extensive molecular differences between anterior- and posterior-half-sclerotomes underlie somite polarity and spinal nerve segmentation
Cited by: 17
Author(s): Daniel Hughes, Roger J. Keynes, David Tannahill
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pone.0017080

The Light Responsive Transcriptome of the Zebrafish: Function and Regulation
Cited by: 92
Author(s): Benjamin D. Weger, Meltem Sahinbas, G. Otto, Philipp Mracek, Olivier Armant, Dirk Dolle, Kajori Lahiri, Daniela Vallone, Laurence Ettwiller, Robert Geisler, Nicholas S. Foulkes, Thomas Dickmeis
Software Mentions: 4
Published: over 13 years ago

10.1186/1471-2105-15-238

Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models
Cited by: 92
Author(s): Florian Martin, Alain Sewer, Marja Talikka, Yu‐Tao Xiang, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: about 10 years ago

10.1002/1878-0261.12788

Adipose tissue from metabolic syndrome mice induces an aberrant miRNA signature highly relevant in prostate cancer development
Cited by: 5
Author(s): Cintia Massillo, Rocío Belén Duca, Ezequiel Lacunza, Guillermo Nicolás Dalton, Paula Lucía Farré, Nicolás Taha, Flavia Piccioni, Georgina Daniela Scalise, Kevin Gardner, Adriana De Siervi
Software Mentions: 3
Published: about 4 years ago

10.18632/oncotarget.8713

Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung adenocarcinoma
Cited by: 43
Author(s): Naiara da Costa Cinegaglia, Sónia C. S. Andrade, Tomáš Tokár, Maísa Pinheiro, Fabio Severino, Rogério Antônio de Oliveira, Érica Nishida Hasimoto, Daniele Cristina Catâneo, Antônio José Maria Catâneo, Júlio Defaveri, Cleonilson Protásio de Souza, Márcia Maria Chiquitelli Marques, Robson Francisco Carvalho, Luiz Lehmann Coutinho, Jefferson Luiz Gross, Sílvia Regina Rogatto, Wan L. Lam, Igor Jurišica, Patrícia P. Reis
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-11-315

A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays
Cited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masanori Kawakita, Takayuki Sakaguchi, Nori Kurata
Software Mentions: 3
Published: over 14 years ago

10.1155/2012/650842

ArraySearch: A Web-Based Genomic Search Engine
Cited by: 1
Author(s): Tyler J. Wilson, Xijin Ge
Software Mentions: 3
Published: almost 13 years ago

10.1172/jci.insight.146098

SLFN11 captures cancer-immunity interactions associated with platinum sensitivity in high-grade serous ovarian cancer
Cited by: 9
Author(s): C Winkler, Matthew King, Julie Berthe, Domenico Ferraioli, Anna Garuti, Federica Grillo, Jaime Rodriguez‐Canales, Lorenzo Ferrando, Nicolás Chopin, Isabelle Ray‐Coquard, Oona Delpuech, Davide Bedognetti, Alberto Ballestrero, Elisabetta Leo, Gabriele Zoppoli
Software Mentions: 3
Published: about 3 years ago

10.1111/j.1365-313X.2008.03727.x

The transcriptome of syncytia induced by the cyst nematode<i>Heterodera schachtii</i>in Arabidopsis roots
Cited by: 197
Author(s): Dagmar Szakasits, Petra Heinen, Krzysztof Wieczorek, Julia Hofmann, Florian Wagner, David P. Kreil, Peter Sykacek, Florian M. W. Grundler, Holger Bohlmann
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pbio.1001386

Smooth Muscle Tension Induces Invasive Remodeling of the Zebrafish Intestine
Cited by: 50
Author(s): Christoph Seiler, Gangarao Davuluri, Joshua Abrams, Fitzroy J. Byfield, Paul A. Janmey, Michael Pack
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0039653

A Novel SND1-BRAF Fusion Confers Resistance to c-Met Inhibitor PF-04217903 in GTL16 Cells though MAPK Activation
Cited by: 45
Author(s): Nathan V. Lee, Maruja E. Lira, Adam Pavlı́ček, Jingjing Ye, Dana Buckman, Shubha Bagrodia, Sreesha P. Srinivasa, Yongjun Zhao, Samuel Aparicio, Paul A. Rejto, James G. Christensen, Keith A. Ching
Software Mentions: 3
Published: over 12 years ago

10.1186/gb-2006-7-2-r12

Cited by: 382
Author(s): Tobias Sargeant, Matthias Marti, Elisabet Caler, Jane M. Carlton, Ken M. Simpson, Terence P. Speed, Alan F. Cowman
Software Mentions: 3
Published: almost 19 years ago

10.1371/journal.pone.0048855

Deep Sequencing Reveals Differences in the Transcriptional Landscapes of Fibers from Two Cultivated Species of Cotton
Cited by: 40
Author(s): Jean-Marc Lacape, Michel Claverie, Ramón Vidal, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Manuel Ruiz, M. Fleur du Pré, Danny Llewellyn, Yves Al-Ghazi, John Jacobs, Alexis Dereeper, Stéphanie Huguet, Marc Giband, Claire Lanaud
Software Mentions: 3
Published: almost 12 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: over 8 years ago

10.1371/journal.pone.0001151

Gene Expression Analysis of In Vivo Fluorescent Cells
Cited by: 35
Author(s): Konstantin Khodosevich, Dragoš Inta, Peter H. Seeburg, Hannah Monyer
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.pone.0131103

The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis
Cited by: 13
Author(s): Kim L. Johnson, Sascha Ramm, Christian Kappel, Sally Ward, Ottoline Leyser, Tomoaki Sakamoto, Takeshi Kurata, Michael W. Bevan, Michael Lenhard
Software Mentions: 3
Published: over 9 years ago

10.3390/cancers11101482

An Integrated Bioinformatics Analysis Repurposes an Antihelminthic Drug Niclosamide for Treating HMGA2-Overexpressing Human Colorectal Cancer
Cited by: 13
Author(s): Stephen Wan Leung, Chia Jung Chou, Tsui-Chin Huang, Pei Ming Yang
Software Mentions: 3
Published: about 5 years ago

10.1186/gb-2005-6-2-r16

Cited by: 335
Author(s): Sung Choe, Michael Boutros, Alan D. Michelson, George M. Church, Marc S. Halfon
Software Mentions: 3
Published: almost 20 years ago

10.1371/journal.pgen.1005969

Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators
Cited by: 49
Author(s): So Yeon Kwon, Valentina Grisan, Boyun Jang, John Herbert, Paul Badenhorst
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1000574

Alternative Splicing of NURF301 Generates Distinct NURF Chromatin Remodeling Complexes with Altered Modified Histone Binding Specificities
Cited by: 53
Author(s): So Yeon Kwon, Hua Xiao, Carl Wu, Paul Badenhorst
Software Mentions: 3
Published: about 15 years ago

10.1371/journal.pone.0017118

Distinct Early Molecular Responses to Mutations Causing vLINCL and JNCL Presage ATP Synthase Subunit C Accumulation in Cerebellar Cells
Cited by: 52
Author(s): Yi Cao, John F. Staropoli, Sunita Biswas, Janice A. Espinola, Marcy E. MacDonald, Jongmin Lee, Susan L. Cotman
Software Mentions: 3
Published: over 13 years ago

10.7554/eLife.15635

Sox9 and Sox8 protect the adult testis from male-to-female genetic reprogramming and complete degeneration
Cited by: 65
Author(s): Francisco Barrionuevo, Alicia Hurtado, Gwang-Jin Kim, Francisca M. Real, Mohammed Bakkali, Janel L. Kopp, Maike Sander, Gerd Scherer, Miguel Burgos, Rafael Jiménez
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0015706

Gene Expression of Axon Growth Promoting Factors in the Deer Antler
Cited by: 26
Author(s): Wolfgang Pita-Thomas, Carmen M. Fernandez‐Martos, Mónica Yunta, Rodrigo M. Maza, Rosa Navarro-Ruíz, Marcos Javier Lopez-Rodríguez, David Reigada, Manuel Nieto‐Sampedro, Manuel Nieto‐Díaz
Software Mentions: 3
Published: almost 14 years ago

10.1186/ar2855

Insights in to the pathogenesis of axial spondyloarthropathy based on gene expression profiles
Cited by: 45
Author(s): Srilakshmi M Sharma, Dongseok Choi, Stephen R. Planck, Christina A. Harrington, Carrie R. Austin, J. A. Lewis, Tessa N. Diebel, Tammy M. Martin, Justine R. Smith, James T. Rosenbaum
Software Mentions: 3
Published: almost 16 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

10.1186/s13059-021-02352-9

Ten-eleven translocation protein 1 modulates medulloblastoma progression
Cited by: 2
Author(s): Hyerim Kim, Yunhee Kang, Yujing Li, Li Chen, Li Lin, Nicholas Johnson, Dan Zhu, M. Hope Robinson, Leon F. McSwain, Benjamin G Barwick, Xianrui Yuan, Xin Liao, Jie Zhao, Zhiping Zhang, Qiang Shu, Jianjun Chen, Emily G. Allen, Anna Marie Kenney, Robert C. Castellino, Erwin G. Van Meir, Karen N. Conneely, Paula M. Vertino, Peng Jin, Jian Li
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2180-10-159

Revealing fosfomycin primary effect on Staphylococcus aureus transcriptome: modulation of cell envelope biosynthesis and phosphoenolpyruvate induced starvation
Cited by: 32
Author(s): Marko Petek, Špela Baebler, Drago Kuzman, Ana Rotter, Zdravko Podlesek, Kristina Gruden, Maja Ravnikar, U. Urleb
Software Mentions: 3
Published: almost 15 years ago

10.1186/1471-2229-10-59

Transcriptional responses to polycyclic aromatic hydrocarbon-induced stress in Arabidopsis thalianareveal the involvement of hormone and defense signaling pathways
Cited by: 89
Author(s): David Weisman, Merianne Alkio, Adán Colón‐Carmona
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2180-8-209

Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro
Cited by: 53
Author(s): Philip A. Bronstein, Melanie J. Filiatrault, Christopher R. Myers, Michael Rutzke, David J. Schneider, Samuel Cartinhour
Software Mentions: 3
Published: almost 17 years ago

10.1186/2193-1801-3-381

Coregulation of FANCA and BRCA1 in human cells
Cited by: 5
Author(s): Anneke Haitjema, Berber M. Mol, Irsan Kooi, Maarten P.G. Massink, Jens Al Jørgensen, Davy Rockx, Martin A. Rooimans, Johan P. de Winter, Hanne Meijers-Heijboer, Hans Joenje, Josephine C. Dorsman
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2172-13-58

DNA methylation profile of Aire-deficient mouse medullary thymic epithelial cells
Cited by: 7
Author(s): Guoying Wu, Keiji Hirabayashi, Shinya Sato, Nobuko Akiyama, Taishin Akiyama, Kunio Shiota, Shusuke Yagi
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0113660

Diffusion of Information throughout the Host Interactome Reveals Gene Expression Variations in Network Proximity to Target Proteins of Hepatitis C Virus
Cited by: 9
Author(s): Ettore Mosca, Roberta Alfieri, Luciano Milanesi
Software Mentions: 3
Published: almost 10 years ago

10.1080/21623945.2020.1776082

The common pathophysiologic threads between Asian Indian diabetic’s ‘Thin Fat Phenotype’ and partial lipodystrophy: the peripheral adipose tissue transcriptomic evidences
Cited by: 3
Author(s): Aditya Saxena, Prabhat Tiwari, Nitin Wahi, Anshul Kumar, Sandeep Kumar Mathur
Software Mentions: 3
Published: almost 5 years ago

10.7150/jca.54565

Systematic Analysis of 4-gene Prognostic Signature in Patients with Diffuse Gliomas Based on Gene Expression Profiles
Cited by: 1
Author(s): Chunhai Huang, Zujian Xiong, Qi Yang, Xuejun Li
Software Mentions: 3
Published: almost 4 years ago

10.1093/braincomms/fcab053

Activating transcription factor 4-dependent lactate dehydrogenase activation as a protective response to amyloid beta toxicity
Cited by: 8
Author(s): Teresa Niccoli, Fiona Kerr, Inge Snoeren, Daniel K. Fabian, Benjamin Aleyakpo, Dobril Ivanov, Oyinkan Sofola-Adesakin, Adam Cryar, Jennifer Adcott, Janet Thornton, Linda Partridge
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0013091

Modeling Oncogenic Signaling in Colon Tumors by Multidirectional Analyses of Microarray Data Directed for Maximization of Analytical Reliability
Cited by: 293
Author(s): Magdalena Skrzypczak, Krzysztof Goryca, Tymon Rubel, Agnieszka Paziewska, Michał Mikula, Dorota Jarosz, Jacek Pachlewski, Jacek Olędzki, Jerzy Ostrowsk
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0010247

Evaluation of the Psoriasis Transcriptome across Different Studies by Gene Set Enrichment Analysis (GSEA)
Cited by: 153
Author(s): Mayte Suárez‐Fariñas, Michelle A. Lowes, Lisa C. Zaba, James G. Krueger
Software Mentions: 3
Published: over 14 years ago

Projects: bioconductor: gcrma

Papers Mentioning gcrma 186