bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0021495

MicroRNA Expression Profiling Reveals MiRNA Families Regulating Specific Biological Pathways in Mouse Frontal Cortex and Hippocampus
Cited by: 70
Author(s): Juuso Juhila, Tessa Sipilä, Katherine Icay, Daniel Nicorici, Pekka Ellonen, Aleksi Kallio, Eija Korpelainen, Dario Greco, Iiris Hovatta
Software Mentions: 4
Published: over 15 years ago

10.1186/s12864-017-3840-1

Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus
Cited by: 9
Author(s): Lauren Kordonowy, Matthew D. MacManes
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-020-6564-6

Transcriptome analysis of fungicide-responsive gene expression profiles in two Penicillium italicum strains with different response to the sterol demethylation inhibitor (DMI) fungicide prochloraz
Cited by: 15
Author(s): Tingfu Zhang, Qing Cao, Na Li, De Li Liu, Yongze Yuan
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0187287

EAMA: Empirically adjusted meta-analysis for large-scale simultaneous hypothesis testing in genomic experiments
Cited by: 3
Author(s): Sinjini Sikdar, Somnath Datta, Susmita Datta
Software Mentions: 4
Published: about 9 years ago

10.3389/fpls.2012.00202

A High-Throughput Method for Illumina RNA-Seq Library Preparation
Cited by: 134
Author(s): Ravi Kumar, Yasunori Ichihashi, Seisuke Kimura, Daniel H. Chitwood, Lauren R. Headland, Jie Peng, Julin N. Maloof, Neelima Sinha
Software Mentions: 4
Published: almost 15 years ago

10.3389/fpls.2020.587185

Comprehensive Identification and Expression Profiling of Circular RNAs During Nodule Development in Phaseolus vulgaris
Cited by: 9
Author(s): Zhihua Wu, Wen Huang, Erdai Qin, Shuo Liu, Huan Liu, Aleel K. Grennan, Hong Liu, Rui Qin
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2407-14-977

Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer
Cited by: 41
Author(s): Prabhakar Rajan, Jacqueline Stockley, Ian Sudbery, Janis Fleming, Ann Hedley, Gabriela Kalna, David Sims, Chris P. Ponting, Andreas Heger, Craig Robson, R. McMenemin, Ian Pedley, Hing Y. Leung
Software Mentions: 4
Published: almost 12 years ago

10.1080/21505594.2020.1768018

Transcriptional host–pathogen responses of Pseudogymnoascus destructans and three species of bats with white-nose syndrome
Cited by: 19
Author(s): Christina M. Davy, Michael E. Donaldson, Hana Banďouchová, Ana M. Breit, Nicole Dorville, Yvonne A. Dzal, Veronika Kováčová, Emma L. Kunkel, Natália Martínková, Kaleigh J. O. Norquay, James E. Paterson, Jan Zukal, Jiří Pikula, Craig K. R. Willis, Christopher J. Kyle
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2021.546455

Identification of an Individualized Immune-Related Prognostic Risk Score in Lung Squamous Cell Cancer
Cited by: 9
Author(s): Yuan Zhuang, Sihan Li, Chang Liu, Guang Li
Software Mentions: 4
Published: over 5 years ago

10.1080/21505594.2017.1342910

Pseudogymnoascus destructans transcriptome changes during white-nose syndrome infections
Cited by: 22
Author(s): Sophia Reeder, Jonathan M. Palmer, Jenni M. Prokkola, Thomas M. Lilley, DeeAnn M. Reeder, Kenneth A. Field
Software Mentions: 4
Published: over 9 years ago

10.3389/fonc.2019.00712

Prognostic lncRNAs, miRNAs, and mRNAs Form a Competing Endogenous RNA Network in Colon Cancer
Cited by: 33
Author(s): Qianrong Huang, Xin-Bin Pan
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0247378

Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling
Cited by: 11
Author(s): José Diógenes Jaimes, Andrea Slavíčková, Jakub Hurych, Ondřej Cinek, Ben Nichols, Lucie Vodolánová, K. Černý, Jaroslav Havlík
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.609601

Identify and Validate the Transcriptomic, Functional Network, and Predictive Validity of FBXL19-AS1 in Hepatocellular Carcinoma
Cited by: 4
Author(s): Dingdong He, Xiaokang Zhang, Xinyu Zhu, Narayani Maharjan, Yingchao Wang, Ping Luo, Chunzi Liang, Jiancheng Tu
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.11020

Differential gene expression in a tripartite interaction:Drosophila,Spiroplasmaand parasitic wasps
Cited by: 4
Author(s): Victor Manuel Higareda Alvear, Mariana Mateos, Diego Cortez, Cécilia Tamborindeguy, Esperanza Martínez‐Romero
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.7705

The clinical significance of collagen family gene expression in esophageal squamous cell carcinoma
Cited by: 30
Author(s): Jieling Li, Wang Xiao, Kai Zheng, Ying Liu, Junjun Li, Shaoqi Wang, Kaisheng Liu, Xianrang Song, Nan Li, Shouqi Xie, Shaoxiang Wang
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-015-1660-8

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus
Cited by: 59
Author(s): Michael H. Perlin, Joëlle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan M. Goldberg, Sébastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Hélène Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón, Hadi Quesneville, Tatiana Giraud, Michael E. Hood, David J. Schultz, Christina A. Cuomo
Software Mentions: 4
Published: over 11 years ago

10.1186/s12915-018-0569-5

Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance
Cited by: 16
Author(s): Jessica M Stringer, Samuel C. Forster, Zhibo Qu, Lexie Prokopuk, Moira K O'Bryan, David K. Gardner, Stefan J. White, David L. Adelson, Patrick Western
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-017-3675-9

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress
Cited by: 23
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 4
Published: over 9 years ago

10.1186/gb-2013-14-11-r131

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
Cited by: 162
Author(s): Ana C. Marques, Jim R. Hughes, Bryony Graham, Monika S. Kowalczyk, Douglas R. Higgs, Chris P. Ponting
Software Mentions: 4
Published: almost 14 years ago

10.3389/fonc.2021.650828

Integrative Analysis of a Novel Eleven-Small Nucleolar RNA Prognostic Signature in Patients With Lower Grade Glioma
Cited by: 6
Author(s): Teng Deng, Yizhen Gong, Xiwen Liao, Xiangkun Wang, Xin Zhou, Guangzhi Zhu, Ligen Mo
Software Mentions: 4
Published: over 5 years ago

10.1186/gb-2012-13-10-r88

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
Cited by: 72
Author(s): Alok K. Tewari, Galip Gürkan Yardımcı, Yoichiro Shibata, Nathan C. Sheffield, Lingyun Song, Barry S. Taylor, Stoyan Georgiev, Gerhard A. Coetzee, Uwe Ohler, Terrence S. Furey, Gregory E. Crawford, Phillip G. Febbo
Software Mentions: 4
Published: almost 15 years ago

10.3390/cancers13030577

Optimizing the Procedure to Manufacture Clinical-Grade NK Cells for Adoptive Immunotherapy
Cited by: 16
Author(s): Adrián Fernández, Alfonso Navarro-Zapata, Adela Escudero, Nerea Matamala, Beatriz Ruz-Caracuel, Isabel Mirones, Alicia Pernas, Marta Cobo, Gema Casado, Diego Lanzarot, Carlos Rodríguez-Antolín, María Vela, Cristina Ferreras, Carmen Mestre, Aurora Viejo, Alejandra Leivas, Javier Martı́nez, Lucía Fernández, Antonio Pérez‐Martínez
Software Mentions: 4
Published: almost 6 years ago

10.3390/antiox10091380

NRF2 Mediates Therapeutic Resistance to Chemoradiation in Colorectal Cancer through a Metabolic Switch
Cited by: 7
Author(s): Séan M. O’Cathail, Chieh‐Hsi Wu, Russell J. Thomas, M. Hawkins, Tim Maughan, Annabelle Lewis
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.11995

The modulatory properties of Astragalus membranaceus treatment on endometrial cancer: an integrated pharmacological method
Cited by: 4
Author(s): Qianqian Zhang, Xianghua Huang
Software Mentions: 4
Published: about 5 years ago

10.1186/gb-2014-15-2-r32

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Cited by: 112
Author(s): Benjamin L. Kidder, Gangqing Hu, Keji Zhao
Software Mentions: 4
Published: almost 13 years ago

10.1186/s12915-019-0646-4

Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons
Cited by: 15
Author(s): Pavan Agrawal, Phuong Chung, Ulrike Heberlein, Clement F. Kent
Software Mentions: 4
Published: over 7 years ago

10.15252/msb.20209569

Exploring the virulence gene interactome with <scp>CRISPR</scp> / <scp>dC</scp> as9 in the human malaria parasite
Cited by: 30
Author(s): Jessica M. Bryant, Sebastian Baumgarten, Florent Dingli, Damarys Loew, Ameya Sinha, Aurélie Claës, Peter R. Preiser, Peter C. Dedon, Artur Scherf
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.9307

Succession of bacterial communities on carrion is independent of vertebrate scavengers
Cited by: 8
Author(s): Cody R. Dangerfield, Ethan Frehner, Evan R. Buechley, Çağan H. Şekercioğlu, William J. Brazelton
Software Mentions: 4
Published: over 6 years ago

10.1186/gb-2013-14-2-r15

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta
Cited by: 217
Author(s): Stephen R. Fairclough, Zehua Chen, Eric M. Kramer, Qiandong Zeng, Sarah Young, Hugh M. Robertson, Emina Begović, Daniel J. Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B. Franz Lang, Brian J. Haas, Chad Nusbaum, Nicole King
Software Mentions: 4
Published: almost 14 years ago

10.15252/msb.20209593

DOMINO: a network‐based active module identification algorithm with reduced rate of false calls
Cited by: 35
Author(s): Hagai Levi, Ran Elkon, Ron Shamir
Software Mentions: 4
Published: almost 6 years ago

10.15252/msb.20188323

Genome‐wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy
Cited by: 22
Author(s): Avinash Sahu, Joo S. Lee, Zhiyong Wang, Gao Zhang, Ramiro Iglesias-Bartolomé, Tian Tian, Zhi Wei, Benchun Miao, Nishanth Ulhas Nair, Olga Ponomarova, Adam Friedman, Arnaud Amzallag, Tabea Moll, Gyulnara G. Kasumova, Patricia Greninger, Regina K. Egan, Leah J. Damon, Dennie T. Frederick, Livnat Jerby‐Arnon, Allon Wagner, Kuoyuan Cheng, Seung Gu Park, Welles Robinson, Kevin Gardner, Genevieve M. Boland, Sridhar Hannenhalli, Meenhard Herlyn, Cyril H. Benes, Keith T. Flaherty, Ji Luo, J. Silvio Gutkind, Eytan Ruppin
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0233543

A transcriptome-based approach to identify functional modules within and across primary human immune cells
Cited by: 10
Author(s): Saraï Mola, Sylvain Foisy, Gabrielle Boucher, François Major, Claudine Beauchamp, Mohamad Karaky, Philippe Goyette, Sylvie Lesage, John D. Rioux
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2021.614497

Molecular and Clinical Characterization of CCT2 Expression and Prognosis via Large-Scale Transcriptome Profile of Breast Cancer
Cited by: 6
Author(s): Qiang Liu, Yihang Qi, Xiangyi Kong, Xiangyu Wang, Wenxiang Zhang, Jie Zhai, Yazhe Yang, Yi Fang, Jing Wang
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-014-0410-6

Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
Cited by: 278
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 4
Published: over 12 years ago

10.1038/s41380-018-0271-6

Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal trauma
Cited by: 106
Author(s): Katharina Gapp, Gretchen van Steenwyk, Pierre-Luc Germain, Wayo Matsushima, Konrad L. M. Rudolph, Francesca Manuella, Martin Roszkowski, Grégoire Vernaz, Tanay Ghosh, Paweł Pelczar, Isabelle M. Mansuy, Eric A. Miska
Software Mentions: 4
Published: about 8 years ago

10.3389/fonc.2019.00606

Inactivation of Prostaglandin E2 as a Mechanism for UGT2B17-Mediated Adverse Effects in Chronic Lymphocytic Leukemia
Cited by: 10
Author(s): Éric P. Allain, Michèle Rouleau, Trang Le, Katrina Vanura, Lyne Villeneuve, Patrick Caron, Véronique Turcotte, Éric Lévesque, Chantal Guillemette
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0137782

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization
Cited by: 23
Author(s): Zhilong Jia, Xiang Zhang, Naiyang Guan, Xiaochen Bo, Michael R. Barnes, Zhigang Luo
Software Mentions: 4
Published: about 11 years ago

10.1186/s12870-018-1293-6

Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch)
Cited by: 20
Author(s): Marco Cirilli, D. Giovannini, Angelo Ciacciulli, Remo Chiozzotto, Stefano Gattolin, Laura Rossini, A. Liverani, D. Bassi
Software Mentions: 4
Published: over 8 years ago

10.3389/fonc.2019.01181

Circular RNA-Associated Competing Endogenous RNA Network and Prognostic Nomogram for Patients With Colorectal Cancer
Cited by: 42
Author(s): Wei Song, Tao Fu
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12870-017-1108-1

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription
Cited by: 17
Author(s): Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-018-1575-1

VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies
Cited by: 92
Author(s): Mengjie Chen, Xiang Zhou
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13059-014-0554-4

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
Cited by: 1,433
Author(s): Wei Li, Xu Han, Tengfei Xiao, Le Cong, Michael I. Love, Feng Zhang, Rafael A. Irizarry, Jun S. Liu, Myles Brown, X Shirley Liu
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12864-020-07091-y

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning
Cited by: 10
Author(s): Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernando Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert J. Henry, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2020.556497

Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma
Cited by: 19
Author(s): Xing Niu, Jun Xu, Jinwen Liu, Lijie Chen, Xue Qin, Ming Zhong
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2020.613333

Construction of Bone Metastasis-Specific Regulation Network Based on Prognostic Stemness-Related Signatures in Breast Invasive Carcinoma
Cited by: 2
Author(s): Runzhi Huang, Zhenyu Li, Jiayao Zhang, Zhiwei Zeng, Jiaqi Zhang, Mingxiao Li, Siqao Wang, Shuyuan Xian, Yuna Xue, Xi Chen, Jie Li, Wing Yan Elizabeth Cheng, Bin Wang, Penghui Yan, Daoke Yang, Zongqiang Huang
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13568-021-01225-5

Manipulating the soil microbiomes during a community recovery process with plant beneficial species for the suppression of Fusarium wilt of watermelon
Cited by: 14
Author(s): Xu Zhang, Cong Xue, D. C. Fang, Xiangming He, Mengyu Wei, Chenjin Zhuo, Junyao Jin, Biao Shen, Rong Li, Ning Ling, Qirong Shen
Software Mentions: 4
Published: over 5 years ago

10.1534/genetics.120.303460

Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in Drosophila pseudoobscura
Cited by: 16
Author(s): Zachary L. Fuller, Spencer Koury, Christopher J. Leonard, Randee E. Young, Kobe Ikegami, Jonathan Westlake, Stephen Richards, Stephen W. Schaeffer, Nitin Phadnis
Software Mentions: 4
Published: about 6 years ago

10.1039/c8mo00042e

Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data
Cited by: 78
Author(s): Benjamin Alexander-Dann, Lavinia Lorena Pruteanu, Erin Oerton, Naomi L. Sharma, Ioana Berindan‐Neagoe, Dezső Módos
Software Mentions: 4
Published: almost 9 years ago

10.3389/fnmol.2018.00288

Dysregulation of MicroRNAs and Target Genes Networks in Peripheral Blood of Patients With Sporadic Amyotrophic Lateral Sclerosis
Cited by: 84
Author(s): Maria Liguori, Nicoletta Nuzziello, Alessandro Introna, Arianna Consiglio, Flavio Licciulli, Eustachio D’Errico, Antonio Scarafino, Eugenio Distaso, Isabella Laura Simone
Software Mentions: 4
Published: about 8 years ago

10.1186/s13024-018-0303-3

Inhibition of monocyte-like cell extravasation protects from neurodegeneration in DBA/2J glaucoma
Cited by: 44
Author(s): Pete A. Williams, Catherine E. Braine, Krishnakumar Kizhatil, Nicole E. Foxworth, Nicholas G. Tolman, Jeffrey M. Harder, R. Scott, Gregory L. Sousa, Alyssa Panitch, Gareth R. Howell, Simon W. M. John
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13024-020-00394-4

Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice
Cited by: 40
Author(s): Nicholas F. Fitz, Cody M. Wolfe, Brittany E. Playso, Richard J. Biedrzycki, Yi Lü, Kyong Nyon Nam, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.202780

circRNA expression profiling of colon tissue from mesalazine-treated mouse of inflammatory bowel disease reveals an important circRNA-miRNA-mRNA pathway
Cited by: 8
Author(s): Wei Zhou, Haiyin Zhang, Y. B. Pan, Yingbin Xu, Yongqing Cao
Software Mentions: 4
Published: over 5 years ago

10.3389/fmolb.2021.608369

Identification of a DNA Repair Gene Signature and Establishment of a Prognostic Nomogram Predicting Biochemical-Recurrence-Free Survival of Prostate Cancer
Cited by: 9
Author(s): Gongwei Long, Wei Ouyang, Yucong Zhang, Guoliang Sun, Jiahua Gan, Zhiquan Hu, Heng Li
Software Mentions: 4
Published: over 5 years ago

10.1111/mmi.12977

<scp>K</scp>dm<scp>A</scp>, a histone<scp>H</scp>3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in<scp>A</scp>spergillus nidulans
Cited by: 41
Author(s): Agnieszka Gacek‐Matthews, Luke M. Noble, Clemens Gruber, Harald Berger, Michael Sulyok, Ana T. Marcos, Joseph Strauss, Alex Andrianopoulos
Software Mentions: 4
Published: over 11 years ago

10.7717/peerj.3859

How to normalize metatranscriptomic count data for differential expression analysis
Cited by: 31
Author(s): Heiner Klingenberg, Peter Meinicke
Software Mentions: 4
Published: about 9 years ago

10.3389/fnmol.2018.00178

Stable STIM1 Knockdown in Self-Renewing Human Neural Precursors Promotes Premature Neural Differentiation
Cited by: 21
Author(s): Renjitha Gopurappilly, Bipan Kumar Deb, Pragnya Chakraborty, Gaiti Hasan
Software Mentions: 4
Published: over 8 years ago

10.3390/ani11092705

Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF
Cited by: 2
Author(s): Gercino Ferreira Virgínio Júnior, Ana Paula da Silva, Ariany Faria de Toledo, Milaine Poczynek, Amanda Moelemberg Cezar, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0069401

TCW: Transcriptome Computational Workbench
Cited by: 16
Author(s): Carol Soderlund, William M. Nelson, Mark R. Willer, David R. Gang
Software Mentions: 4
Published: over 13 years ago

10.1186/s12885-018-4757-z

Association of tamoxifen resistance and lipid reprogramming in breast cancer
Cited by: 98
Author(s): Susanne Hultsch, Matti Kankainen, Lassi Paavolainen, Ruusu-Maaria Kovanen, Elina Ikonen, Sara Kangaspeska, Vilja Pietiäinen, Olli Kallioniemi
Software Mentions: 4
Published: about 8 years ago

10.3390/cancers13061421

Efficacy of Targeted Radionuclide Therapy Using [131I]ICF01012 in 3D Pigmented BRAF- and NRAS-Mutant Melanoma Models and In Vivo NRAS-Mutant Melanoma
Cited by: 5
Author(s): Hussein Akil, Mercédès Quintana, J. Raymond, Tommy Billoux, Valentin Benboubker, Sophie Besse, Philippe Auzeloux, Véronique Delmas, Valérie Petit, Lionel Larue, M. D’Incan, Françoise Degoul, Jacques Rouanet
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-862

De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes
Cited by: 51
Author(s): Peter J.P. Croucher, Michael S. Brewer, Christopher J. Winchell, Geoff Oxford, Rosemary G. Gillespie
Software Mentions: 4
Published: almost 14 years ago

10.1007/s00438-020-01735-0

Major latex protein-like encoding genes contribute to Rhizoctonia solani defense responses in sugar beet
Cited by: 16
Author(s): Louise Holmquist, Fredrik Dölfors, Johan Fogelqvist, Jonathan Cohn, Thomas Kraft, Christina Dixelius
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2019.03044

Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti
Cited by: 34
Author(s): Víctor M. Flores‐Núñez, Citlali Fonseca-García, Damaris Desgarennes, Emiley A. Eloe‐Fadrosh, Tanja Woyke, Laila P. Partida‐Martínez
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0157022

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Cited by: 660
Author(s): Hugo Varet, Loraine Brillet-Guéguen, Jean‐Yves Coppée, Marie‐Agnès Dillies
Software Mentions: 4
Published: over 10 years ago

10.3390/ani11082165

Comprehensive Transcriptomic Comparison between Porcine CD8− and CD8+ Gamma Delta T Cells Revealed Distinct Immune Phenotype
Cited by: 7
Author(s): Sang–Wook Kim, Bee-Oh Lim, Sameer-ul-Salam Mattoo, Eunyoung Oh, Chang-Gi Jeong, Won-Il Kim, Kyung-Tai Lee, Sang-Myeong Lee, Junmo Kim
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1003997

Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
Cited by: 110
Author(s): Zeynep Kalender Atak, Valentina Gianfelici, Gert Hulselmans, Kim De Keersmaecker, Arun George Devasia, Ellen Geerdens, Nele Mentens, Sabina Chiaretti, Kaat Durinck, Anne Uyttebroeck, Peter Vandenberghe, Iwona Włodarska, Jacqueline Cloos, Robin Foà, Franki Speleman, Jan Cools, Stein Aerts
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0216679

Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel
Cited by: 8
Author(s): Fatma Zohra Djazouli Alim, Elena V. Romanova, Yea Ling Tay, Ahmad Yamin bin Abdul Rahman, Kok‐Gan Chan, Kar‐Wai Hong, Mark F. Rogers, Bruce R. Southey, Michael Greenwood, André Souza Mecawi, Mohammad Rais Mustafa, Nicole Mahy, Colin Campbell, José Antunes‐Rodrigues, Jonathan V. Sweedler, David Murphy, Charles C.T. Hindmarch
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-019-5767-1

Transcriptomic responses to diet quality and viral infection in Apis mellifera
Cited by: 23
Author(s): Lindsay Rutter, Jimena Carrillo-Tripp, Bryony C. Bonning, Dianne Cook, Amy L. Toth, Adam Doležal
Software Mentions: 4
Published: over 7 years ago

10.3390/molecules21111431

Comparative Transcriptomic Analysis of Grape Berry in Response to Root Restriction during Developmental Stages
Cited by: 20
Author(s): Lu Feng, Qiong Lin, Di Wu, Shiping Wang, Dengliang Wang, Chongde Sun
Software Mentions: 4
Published: about 10 years ago

10.18632/aging.103454

Weighted correlation gene network analysis reveals a new stemness index-related survival model for prognostic prediction in hepatocellular carcinoma
Cited by: 14
Author(s): Qiujing Zhang, Jia Wang, Menghan Liu, Qingqing Zhu, Qiang Li, Chao Xie, Congcong Han, Yali Wang, Min Gao, Jie Liu
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers12082210

Human FBXL8 Is a Novel E3 Ligase Which Promotes BRCA Metastasis by Stimulating Pro-Tumorigenic Cytokines and Inhibiting Tumor Suppressors
Cited by: 10
Author(s): Shu Chun Chang, Wei‐Hsiu Hsu, Emily Chia Yu Su, Chin Sheng Hung, Jeak Ling Ding
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-018-5160-5

Analysis and correction of compositional bias in sparse sequencing count data
Cited by: 62
Author(s): M. S. Binoj Kumar, Eric V. Slud, Kwame Okrah, Stephanie Hicks, Sridhar Hannenhalli, Héctor Corrada Bravo
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2021.605095

Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene Expression
Cited by: 4
Author(s): Pui Shan Wong, Koichi Tamano, Sachiyo Aburatani
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1008797

UVR8-mediated inhibition of shade avoidance involves HFR1 stabilization in Arabidopsis
Cited by: 23
Author(s): Eleni Tavridou, Emanuel Schmid‐Siegert, Christian Fankhauser, Roman Ulm
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-015-1799-3

RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress
Cited by: 67
Author(s): Longxing Hu, Huiying Li, Liang Chen, Yanhong Lou, Erick Amombo, Jinmin Fu
Software Mentions: 4
Published: over 11 years ago

10.3390/cancers12123786

Stroma Transcriptomic and Proteomic Profile of Prostate Cancer Metastasis Xenograft Models Reveals Prognostic Value of Stroma Signatures
Cited by: 9
Author(s): Sofia Karkampouna, Maria Rosaria De Filippo, Charlotte K.Y. Ng, Irena Klima, Eugenio Zoni, Martin Spahn, Frank Stein, Per Haberkant, George N. Thalmann, Marianna Kruithof-de Julio
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2021.672168

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy
Cited by: 18
Author(s): Sandra Hellberg, Johanna Raffetseder, Olof Rundquist, Rasmus Magnusson, Georgia Papapavlou, Maria C. Jenmalm, Jan Ernerudh, Mika Gustafsson
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2018.02533

Adenosinergic Signaling Alters Natural Killer Cell Functional Responses
Cited by: 72
Author(s): Andrea M. Chambers, Jiao Wang, Kyle B. Lupo, Hao Yu, Nadia A. Lanman, Sandro Matosevic
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-018-5184-x

Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification
Cited by: 7
Author(s): Yung-Chih Lai, Ya-Chen Liang, Ting‐Xin Jiang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 4
Published: about 8 years ago

10.3390/cancers12051325

Tumor Cell Associated Hyaluronan-CD44 Signaling Promotes Pro-Tumor Inflammation in Breast Cancer
Cited by: 18
Author(s): Patrice M Witschen, Thomas S. Chaffee, Nicholas J. Brady, Danielle N. Huggins, Todd P. Knutson, Rebecca S. LaRue, Sarah A. Munro, Lyubov Tiegs, James B. McCarthy, Andrew C. Nelson, Kathryn L. Schwertfeger
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers13030548

Identification of RCC Subtype-Specific microRNAs–Meta-Analysis of High-Throughput RCC Tumor microRNA Expression Data
Cited by: 11
Author(s): Arkadiusz Kajdasz, Weronika Majer, Katarzyna Kluzek, Jacek Sobkowiak, Tomasz Milecki, Natalia Derebecka, Zbigniew Kwias, Hans A.R. Bluyssen, Joanna Wesoły
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-15-133

Virus-independent and common transcriptome responses of leafhopper vectors feeding on maize infected with semi-persistently and persistent propagatively transmitted viruses
Cited by: 33
Author(s): Bryan J. Cassone, Saranga Wijeratne, Andrew P. Michel, Lucy R. Stewart, Yuting Chen, Pearlly S. Yan, Margaret G. Redinbaugh
Software Mentions: 4
Published: over 12 years ago

10.3389/fimmu.2020.580219

Host Transcriptomic Response Following Administration of Rotavirus Vaccine in Infants’ Mimics Wild Type Infection
Cited by: 4
Author(s): Alberto Gómez‐Carballa, Ruth Barral-Arca, Miriam Cebey-López, María José Currás-Tuala, Sara Pischedda, José Gómez-Rial, Dominic Habgood-Coote, Jethro Herberg, Myrsini Kaforou, Federico Martinón‐Torres, Antonio Salas
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0225382

Biomarker discovery in inflammatory bowel diseases using network-based feature selection
Cited by: 17
Author(s): Mostafa M. Abbas, John Matta, Thanh Le, Halima Bensmail, Tayo Obafemi-Ajayi, Vasant Honavar, Yasser EL-Manzalawy
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1005755

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer
Cited by: 12
Author(s): Najeeb Halabi, Alejandra Martinez, Halema Al-Farsi, Eliane Mery-Lamarche, Laurence Puydenus, Pascal Pujol, Hanif Khalak, Cameron Mclurcan, Gwénaël Ferron, Denis Querleu, Iman K. Al-Azwani, Eman K. Al-Dous, Yasmin Ali Mohamoud, Joel A. Malek, Arash Rafii
Software Mentions: 4
Published: almost 11 years ago

10.26508/lsa.201900535

The molecular clock protein Bmal1 regulates cell differentiation in mouse embryonic stem cells
Cited by: 12
Author(s): Amador Gallardo, Ana Rodríguez Molina, Helena G Asenjo, Jordi Martorell-Marugán, Rosa Montes, Verónica Ramos-Mejía, Antonio Sánchez–Pozo, Pedro Carmona-Sáez, Lourdes López-Onieva, David Landeira
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-018-4457-8

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon
Cited by: 10
Author(s): Li Liu, Shuchao Ren, Junqiang Guo, Qingyi Wang, Xiaotuo Zhang, Peiran Liao, Shipeng Li, Ramanjulu Sunkar, Yun Zheng
Software Mentions: 4
Published: over 8 years ago

10.3389/fimmu.2019.03065

Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells
Cited by: 17
Author(s): Jessica Vázquez, Deborah Chasman, Gladys López, Chanel T. Tyler, Irene M. Ong, Aleksandar K. Stanic
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-016-0947-7

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
Cited by: 858
Author(s): Aaron T. L. Lun, Karsten Bach, John C. Marioni
Software Mentions: 4
Published: over 10 years ago

10.7717/peerj.7696

The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers
Cited by: 4
Author(s): Shuaibin Lian, Liansheng Li, Yongjie Zhou, Zixiao Liu, Lei Wang
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-016-2973-y

Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch)
Cited by: 15
Author(s): Kanjana Worarad, Tomohiro Suzuki, Kazuo Ishii, Toshinori Kozaki, Masayuki Iigo, Kenji Yamane
Software Mentions: 4
Published: about 10 years ago

10.1186/s12859-018-2261-8

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Cited by: 43
Author(s): Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson
Software Mentions: 4
Published: over 8 years ago

10.1038/s41375-021-01221-5

Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia
Cited by: 5
Author(s): Cédric Schleiss, Raphaël Carapito, Luc‐Matthieu Fornecker, Leslie Muller, Nicodème Paul, Ouria Tahar, Angélique Pichot, Manuela Tavian, Alina Nicolae, Laurent Miguet, Laurent Mauvieux, Raoul Herbrecht, Sarah Cianférani, Jean–Noël Freund, Myriam Maumy-Bertrand, Seiamak Bahram, Frédèric Bertrand, Laurent Vallat
Software Mentions: 4
Published: over 5 years ago

10.1038/leu.2016.251

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts
Cited by: 99
Author(s): Annalisa Mupo, Monika Seiler, Vijitha Sathiaseelan, Alena Pance, Yi Yang, Anant A. Agrawal, Francesco Iorio, Rubén Bautista, Suruchi Pacharne, Konstantinos Tzelepis, Nicla Manes, Penny Wright, Elli Papaemmanuil, David G. Kent, Peter Campbell, Silvia Buonamici, Niccolò Bolli, George S. Vassiliou
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pgen.1009097

Diversified regulation of circadian clock gene expression following whole genome duplication
Cited by: 9
Author(s): Alexander C. West, Marianne Iversen, Even H. Jørgensen, Simen Rød Sandve, David G. Hazlerigg, Shona H. Wood
Software Mentions: 4
Published: about 6 years ago

10.3389/fimmu.2021.667177

CXCL8 Associated Dendritic Cell Activation Marker Expression and Recruitment as Indicators of Favorable Outcomes in Colorectal Cancer
Cited by: 20
Author(s): Enhao Li, Xiaobao Yang, Yuzhang Du, Guanzheng Wang, David Chan, Di Wu, Peiqing Xu, Peihong Ni, Dakang Xu, Yiqun Hu
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-3809-0

Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data
Cited by: 20
Author(s): Susan A. Yoon, Dougu Nam
Software Mentions: 4
Published: over 9 years ago

10.3389/fimmu.2021.663736

MicroRNA Expression Differences in Blood-Derived CD19+ B Cells of Methotrexate Treated Rheumatoid Arthritis Patients
Cited by: 8
Author(s): Fatima Heinicke, Xiao Zhong, Siri Tennebø Flåm, Johannes Breidenbach, Magnus Leithaug, Marthe Thoresen Mæhlen, Siri Lillegraven, Anna‐Birgitte Aga, Ellen Sauar Norli, Maria D Mjaavatten, Espen A. Haavardsholm, Manuela Zucknick, Simon Rayner, Benedicte A. Lie
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.709466

Human Placental Trophoblasts Infected by Listeria monocytogenes Undergo a Pro-Inflammatory Switch Associated With Poor Pregnancy Outcomes
Cited by: 15
Author(s): Lauren J. Johnson, Siavash Azari, Amy Webb, Xiaoli Zhang, Mikhail A. Gavrilin, James L. Marshall, Kara M. Rood, Stéphanie Seveau
Software Mentions: 4
Published: over 5 years ago

10.1186/s40170-020-00229-2

Metabolic plasticity of IDH1-mutant glioma cell lines is responsible for low sensitivity to glutaminase inhibition
Cited by: 13
Author(s): Victor Ruiz‐Rodado, Adrian Lita, Tyrone Dowdy, Orieta Celiku, Alejandra Cavazos Saldana, Herui Wang, Chunzhang Yang, Raj Chari, Aiguo Li, Wei Zhang, Hua Song, Meili Zhang, Susie Ahn, Dionne L. Davis, Xiang Chen, Zhengping Zhuang, Christel Herold‐Mende, Kylie J. Walters, Mark R. Gilbert, Mioara Larion
Software Mentions: 4
Published: about 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568