bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3390/ijms22073674

Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis?
Cited by: 3
Author(s): Cleonardo Augusto Silva, André M. Ribeiro-dos-Santos, Wanderson Gonçalves e Gonçalves, Pablo Diego do Carmo Pinto, Rafael Pompeu Pantoja, Tatiana Vinasco-Sandoval, André M. Ribeiro-dos-Santos, Mara H. Hutz, Amanda Ferreira Vidal, Gilderlanio Santana de Araújo, Sidney Emanuel Batista dos Santos
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0065598

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates
Cited by: 292
Author(s): Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Ian Maze, Jian Feng, Eric J. Nestler
Software Mentions: 4
Published: over 13 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

10.18632/oncotarget.10052

Network-based identification of microRNAs as potential pharmacogenomic biomarkers for anticancer drugs
Cited by: 71
Author(s): Jie Li, Kecheng Lei, Zengrui Wu, Weihua Li, Guixia Liu, Jianwen Liu, Feixiong Cheng, Yun Tang
Software Mentions: 4
Published: over 10 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

10.3389/fmicb.2019.02195

Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces
Cited by: 5
Author(s): Yu-Wen Lai, Chi Nam Ignatius Pang, Leona T. Campbell, Wen Chen, Marc R. Wilkins, Dee Carter
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms22052481

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species
Cited by: 5
Author(s): Jodi B Callwood, Kalpalatha Melmaiee, Krishnanand P. Kulkarni, Amaranatha R. Vennapusa, Diarra Aicha, Michael J. Moore, Nicholi Vorsa, Purushothaman Natarajan, Umesh K. Reddy, Sathya Elavarthi
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms21218333

Transcriptional Effects of Psychoactive Drugs on Genes Involved in Neurogenesis
Cited by: 7
Author(s): Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Trang T. T. Truong, Zoe Liu, Bruna Panizzutti, Mark F. Richardson, Laura J. Gray, Michael Berk, Olivia Dean, Ken Walder
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0122143

Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer
Cited by: 27
Author(s): Pushpinder Bawa, Sajna Zackaria, Mohit Verma, Saurabh Gupta, Srivatsan Raghunathan, Bibha Chaudhary, Subhashini Srinivasan
Software Mentions: 4
Published: over 11 years ago

10.3390/ijms21249560

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses
Cited by: 2
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 4
Published: almost 6 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/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

10.3389/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

10.3389/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

10.3389/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

10.3390/ijms21124470

Differences between Well-Differentiated Neuroendocrine Tumors and Ductal Adenocarcinomas of the Pancreas Assessed by Multi-Omics Profiling
Cited by: 8
Author(s): Teresa Starzyńska, Jakub Karczmarski, Agnieszka Paziewska, Maria Kulecka, Katarzyna Kuśnierz, Natalia Żeber‐Lubecka, Filip Ambrożkiewicz, Michał Mikula, Beata Kos‐Kudła, Jerzy Ostrowski
Software Mentions: 4
Published: over 6 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/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

10.3390/ijms21124453

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: over 6 years ago

10.1038/s41421-018-0030-5

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation
Cited by: 64
Author(s): Yuli Li, Ruijia Wang, Xiaogang Xun, Jing Wang, Lisui Bao, Ramesha Thimmappa, Jun Ding, Jingwei Jiang, Liheng Zhang, Tianqi Li, Jia Lv, Chuang Mu, Xiaoli Hu, Lingling Zhang, Jing Liu, Yuqiang Li, Lijie Yao, Wenqian Jiao, Yangfan Wang, Shanshan Lian, Zelong Zhao, Yaoyao Zhan, Xiaoting Huang, Huan Liao, Wang Jia, Hongzhen Sun, Xue Mi, Yu Xia, Qiang Xing, Wei Lü, Anne Osbourn, Zunchun Zhou, Yaqing Chang, Zhenmin Bao, Shi Wang
Software Mentions: 4
Published: over 8 years ago

10.1534/g3.119.400757

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize
Cited by: 9
Author(s): Pengfei Qiao, Lin Meng, Miguel Vasquez, Susanne Matschi, James Chamness, Matheus Baseggio, Laurie G. Smith, Mert R. Sabuncu, Michael A. Gore, Michael J. Scanlon
Software Mentions: 4
Published: almost 7 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

10.3390/ijms21082800

Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)
Cited by: 13
Author(s): Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Tengyu Wei, Shuisheng Li, Haoran Lin, Xiaochun Liu
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms22063125

A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora
Cited by: 12
Author(s): Isabel Marques, Isabel Fernandes, Octávio S. Paulo, Fernando C. Lidon, Fábio M. DaMatta, José C. Ramalho, Ana I. Ribeiro‐Barros
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms20225710

The Biological Effects of Complete Gasoline Engine Emissions Exposure in a 3D Human Airway Model (MucilAirTM) and in Human Bronchial Epithelial Cells (BEAS-2B)
Cited by: 13
Author(s): Pavel Rőssner, Tereza Červená, Michal Vojtíšek-Lom, Kristýna Vrbová, Antonín Ambrož, Zuzana Nováková, Fatima Elzeinová, Hasmik Margaryan, V. Beránek, Martin Pechout, David Macoun, Jǐŕı Kléma, Andrea Rössnerová, Miroslav Cigánek, Jan Topinka
Software Mentions: 4
Published: almost 7 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

10.3390/ijms20236040

Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms20143583

Ureaplasma Species Modulate Cytokine and Chemokine Responses in Human Brain Microvascular Endothelial Cells
Cited by: 6
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Nicolas Schlegel, Kirsten Glaser
Software Mentions: 4
Published: over 7 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

10.3390/ijms20143480

Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
Cited by: 34
Author(s): Ziwen Li, Xianghai An, Taotao Zhu, Tingwei Yan, Wu Shu, Youhui Tian, Jinping Li, Xiangyuan Wan
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms19010271

Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells’ Proliferation through Regulating the Cell Cycle
Cited by: 21
Author(s): Yiren Jiao, Bo Huang, Yu Chen, Guang-liang Hong, Jian Xu, Chen Hu, Chong Wang
Software Mentions: 4
Published: almost 9 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><i>A</i></scp><i>spergillus nidulans</i>
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

10.3390/ijms18030627

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens
Cited by: 14
Author(s): Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert T. Greenlee, Deborah Multerer, Stacey Honda, Yihe G. Daida, Heather Spencer Feigelson, Andrew G. Glass, Fergus J. Couch, Thomas E. Rohan, Iddo Z. Ben‐Dov
Software Mentions: 4
Published: over 9 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

10.3389/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

10.3390/ijms19010031

Transcriptome Analysis of Tomato Leaf Spot Pathogen Fusarium proliferatum: De novo Assembly, Expression Profiling, and Identification of Candidate Effectors
Cited by: 15
Author(s): Meiling Gao, Siyu Yao, Yang Liu, Haining Yu, Pao Xu, Wenhui Sun, Zhongji Pu, Hongman Hou, Yongming Bao
Software Mentions: 4
Published: almost 9 years ago

10.3390/ijms20123101

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation
Cited by: 29
Author(s): Saurabh Gupta, Yanni Dong, Paul P. Dijkwel, Bernd Mueller‐Roeber, Tsanko Gechev
Software Mentions: 4
Published: over 7 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

10.1371/journal.pone.0144409

The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells
Cited by: 14
Author(s): Thomas Whisenant, Eigen Peralta, Lauren Aarreberg, Nana Gao, Steven R. Head, Phillip Ordoukhanian, James R. Williamson, Daniel R. Salomon
Software Mentions: 4
Published: almost 11 years ago

10.7554/eLife.04235

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: about 12 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

10.7554/eLife.47013

An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans
Cited by: 27
Author(s): Murilo Delgobo, Daniel A G B Mendes, Edgar Kozlova, Edroaldo Lummertz da Rocha, Gabriela F. Rodrigues-Luiz, Lucas Mascarin, Greicy Brisa Malaquias Dias, Daniel de Oliveira Patricio, Tim Dierckx, Maíra A. Bicca, G Bretton, Yonne Karoline Tenório de Menezes, Márick R Starick, Darcita Büerger Rovaris, Joanita Del Moral, Daniel Santos Mansur, Johan Van Weyenbergh, André Báfica
Software Mentions: 4
Published: about 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/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: about 11 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

10.7554/eLife.47835

Epigenetic silencing of a multifunctional plant stress regulator
Cited by: 25
Author(s): Mark Zander, Björn C. Willige, Yiping He, Thu Anh Nguyen, Amber E. Langford, Ramlah Nehring, Elizabeth D. Howell, Robert B. McGrath, Anna Bartlett, Rosa Castanon, Joseph R. Nery, Huaming Chen, Zhuzhu Zhang, Florian Jupe, Anna N. Stepanova, Robert J. Schmitz, Mathew G. Lewsey, Joanne Chory, Joseph R. Ecker
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.67615

Local adaptation and archaic introgression shape global diversity at human structural variant loci
Cited by: 27
Author(s): Shouqing Yan, Rachel M. Sherman, Dylan J. Taylor, Divya R. Nair, Andrew N Bortvin, Michael C. Schatz, Rajiv C. McCoy
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2020.577718

Augmenting E Protein Activity Impairs cDC2 Differentiation at the Pre-cDC Stage
Cited by: 0
Author(s): Sandra Bajaña, Kevin L. Thomas, Constantin Georgescu, Ying Zhao, Jonathan D. Wren, Susan Kovats, Xiaohong Sun
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2020.590618

A TP53-Associated Immune Prognostic Signature for the Prediction of Overall Survival and Therapeutic Responses in Muscle-Invasive Bladder Cancer
Cited by: 32
Author(s): Xiangkun Wu, Daojun Lv, Chao Cai, Zhijian Zhao, Ming Wang, Wenzhe Chen, Yongda Liu
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2021.631472

An Inflammatory Loop Between Spleen-Derived Myeloid Cells and CD4+ T Cells Leads to Accumulation of Long-Lived Plasma Cells That Exacerbates Lupus Autoimmunity
Cited by: 4
Author(s): Eunkyeong Jang, Somi Cho, Sung-Jin Pyo, Jin Wu Nam, Jeehee Youn
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.60562

Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra
Cited by: 20
Author(s): Jack Cazet, Adrienne Cho, Celina E. Juliano
Software Mentions: 4
Published: over 5 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

10.1371/journal.pone.0115740

Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression
Cited by: 10
Author(s): Carol Soderlund, William M. Nelson, Stephen A. Goff
Software Mentions: 4
Published: almost 12 years ago

10.3389/fimmu.2021.644350

Analysis of Bulk RNA Sequencing Data Reveals Novel Transcription Factors Associated With Immune Infiltration Among Multiple Cancers
Cited by: 5
Author(s): Lei Liu, Qiuchen Zhao, Chao Cheng, Jingwen Yi, Hongyan Sun, Qi Wang, Weili Quan, Yaqiang Xue, Luguo Sun, Xianling Cong, Yi Zhang
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.29156

Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria
Cited by: 33
Author(s): Jaclyn Quin, Ioana Bujila, Mariama Chérif, Guillaume S. Sanou, Ying Qu, Manijeh Vafa Homann, Anna Rolicka, Sodiomon B. Sirima, Mary A. O’Connell, Andreas Lennartsson, Marita Troye‐Blomberg, Issa Nébié, Ann‐Kristin Östlund Farrants
Software Mentions: 4
Published: about 9 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/fgene.2018.00265

Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis
Cited by: 119
Author(s): Xinkui Liu, Jiarui Wu, Dan Zhang, Zhitong Bing, Jinhui Tian, Mengwei Ni, Xiaomeng Zhang, Ziqi Meng, Shuyu Liu
Software Mentions: 4
Published: over 8 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

10.7554/eLife.55911

Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
Cited by: 4
Author(s): Marina Kovalenko, Serkan Erdin, Marissa A Andrew, Jason St. Claire, Melissa Shaughnessey, Leroy Hubert, João Luís Neto, Alexei Stortchevoi, Daniel M. Fass, Ricardo Mouro Pinto, Stephen J. Haggarty, John H. Wilson, Michael E. Talkowski, Vanessa C. Wheeler
Software Mentions: 4
Published: about 6 years ago

10.1093/molbev/msv016

The Avian Transcriptome Response to Malaria Infection
Cited by: 71
Author(s): Elin Videvall, Charlie K. Cornwallis, Vaidas Palinauskas, Gediminas Valkiūnas, Olof Hellgren
Software Mentions: 4
Published: almost 12 years ago

10.1093/molbev/msab197

Functional Characterization of the Cnidarian Antiviral Immune Response Reveals Ancestral Complexity
Cited by: 13
Author(s): Magda Lewandowska, Ton Sharoni, Yael Admoni, Reuven Aharoni, Yehu Moran
Software Mentions: 4
Published: over 5 years ago

10.1093/molbev/msaa172

Gene Loss Predictably Drives Evolutionary Adaptation
Cited by: 49
Author(s): Jana Helsen, Karin Voordeckers, Laura Vanderwaeren, Toon Santermans, Maria Tsontaki, Kevin J. Verstrepen, Rob Jelier
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

10.7554/eLife.53704

Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones
Cited by: 41
Author(s): Anastasia A. Minervina, Mikhail V. Pogorelyy, Ekaterina A. Komech, В. К. Карнаухов, Petra Bächer, Elisa Rosati, André Franke, Dmitriy M. Chudakov, Ilgar Z. Mamedov, Yuri B Lebedev, Thierry Mora, Aleksandra M. Walczak
Software Mentions: 4
Published: over 6 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/s13229-021-00432-y

Neuroanatomy and behavior in mice with a haploinsufficiency of AT-rich interactive domain 1B (ARID1B) throughout development
Cited by: 17
Author(s): Jacob Ellegood, Stela P. Petkova, Adrienne Kinman, Lily R. Qiu, Anna Adhikari, A. Ayanna Wade, Darren Fernandes, Zsuzsa Lindenmaier, Amie Creighton, Lauryl M. J. Nutter, Alexander Nord, Jill L. Silverman, Jason P. Lerch
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.24414

Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria
Cited by: 38
Author(s): M. Sabrina Pankey, Randi L Foxall, Ian M Ster, Lauren A Perry, Brian G. Schuster, Rachel A Donner, Matthew Coyle, Vaughn S. Cooper, Cheryl A. Whistler
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2021.628136

Breast Cancer Case Identification Based on Deep Learning and Bioinformatics Analysis
Cited by: 8
Author(s): Dongfang Jia, Cheng Chen, Fangfang Chen, Ningrui Zhang, Ziwei Yan
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.36828

Hypoxia-inducible factor cell non-autonomously regulates C. elegans stress responses and behavior via a nuclear receptor
Cited by: 12
Author(s): Corinne L Pender, H. Robert Horvitz
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2018.00330

Across-Experiment Transcriptomics of Sheep Rumen Identifies Expression of Lipid/Oxo-Acid Metabolism and Muscle Cell Junction Genes Associated With Variation in Methane-Related Phenotypes
Cited by: 7
Author(s): Ruidong Xiang, Jody McNally, J. J. Bond, David J. Tucker, Cameron McCarthy, A. J. Donaldson, K. L. Austin, Suzanne Rowe, Arjan Jonker, C. S. Pinares-Patiño, John C. McEwan, Phil Vercoe, V. H. Oddy, Brian P. Dalrymple
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.64204

Single-PanIN-seq unveils that ARID1A deficiency promotes pancreatic tumorigenesis by attenuating KRAS-induced senescence
Cited by: 5
Author(s): Shou Liu, Wenjian Cao, Yichi Niu, Jiayi Luo, Yanhua Zhao, Zheng Hu, Chenghang Zong
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/fgene.2021.563051

Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis
Cited by: 7
Author(s): Chunhong Hong, Shaohua Yang, Qiaojin Wang, Shiqiang Zhang, Wenhui Wu, Jinyao Chen, Danhui Zhong, Mingzhe Li, Liang Li, Jianfeng Li, Hong Yu, Hong Chen, Qianlin Zeng, Changhua Zhang
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.67740

Bacterial–fungal interactions in the neonatal gut influence asthma outcomes later in life
Cited by: 16
Author(s): Rozlyn C.T. Boutin, Charisse Petersen, Sarah E. Woodward, Antonio Serapio-Palacios, Tahereh Bozorgmehr, Rachelle Loo, Alina Chalanuchpong, Mihai Cirstea, Bernard C. Lo, Kelsey E. Huus, Weronika Barcik, Meghan B. Azad, Allan B. Becker, Piush J. Mandhane, Theo J. Moraes, Malcolm R. Sears, Padmaja Subbarao, Kelly M. McNagny, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.55775

Homeostatic plasticity fails at the intersection of autism-gene mutations and a novel class of common genetic modifiers
Cited by: 13
Author(s): Özgür Genç, Joon Yong An, Richard D. Fetter, Yelena Kulik, Giulia Zunino, Stephan J. Sanders, Graeme W. Davis
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2021.636419

Five Circular RNAs in Metabolism Pathways Related to Prostate Cancer
Cited by: 6
Author(s): Lili Zhang, Wei Zhang, Hexin Li, Xiaokun Tang, Siyuan Xu, Meng Wu, Li Wan, Fei Su, Yaqun Zhang
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2019.01018

Transcriptome Analysis Identifies Piwi-Interacting RNAs as Prognostic Markers for Recurrence of Prostate Cancer
Cited by: 12
Author(s): Yuanli Zuo, Liang Yu, Jiting Zhang, You-Zeng Hao, Menglong Li, Zhining Wen, Yun Zhao
Software Mentions: 4
Published: about 7 years ago

10.3390/microorganisms7010017

Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study
Cited by: 84
Author(s): Ruth C E Bowyer, Matthew A. Jackson, Caroline I. Le Roy, Mary Ní Lochlainn, Timothy D. Spector, Jennifer Beam Dowd, Claire J. Steves
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2019.00210

Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle
Cited by: 23
Author(s): Wellison J. S. Diniz, Gianluca Mazzoni, Luiz Lehmann Coutinho, Priyanka Banerjee, Ludwig Geistlinger, Francesca Bertolini, Juliana Afonso, P. S. N. Oliveira, P. C. Tizioto, Haja N. Kadarmideen, Luciana Correia de Almeida Regitano
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0207952

RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns
Cited by: 8
Author(s): Gary P. Brennan, Dimitrios Vitsios, Sophie Casey, Ann-Marie Looney, Boubou Hallberg, David C. Henshall, Geraldine B. Boylan, Deirdre M. Murray, Catherine Mooney
Software Mentions: 4
Published: almost 8 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/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

10.1371/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

10.7554/eLife.41641

IFNγ induces epigenetic programming of human T-bethi B cells and promotes TLR7/8 and IL-21 induced differentiation
Cited by: 104
Author(s): Esther Zumaquero, Sara L Stone, Christopher D. Scharer, Scott A. Jenks, Anoma Nellore, Betty Mousseau, Antonio Rosal-Vela, Davide Botta, John E. Bradley, Wojciech Wojciechowski, Travis Ptacek, Maria I. Danila, Jeffrey C. Edberg, S. Louis Bridges, Robert P. Kimberly, W. Winn Chatham, Trenton R. Schoeb, Alexander F. Rosenberg, Jeremy M. Boss, Igñacio Sanz, Frances E. Lund
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.53127

Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity
Cited by: 23
Author(s): Nairita Maitra, Chi He, Heidi M. Blank, Mitsuhiro Tsuchiya, Birgit Schilling, Matt Kaeberlein, Rodolfo Aramayo, Brian K. Kennedy, Michael Polymenis
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms9010149

Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species
Cited by: 21
Author(s): Niranjan P. Sahu, Zsolt Merényi, Balázs Bálint, Brigitta Kiss, György Sipos, Rebecca A. Owens, László G. Nagy
Software Mentions: 4
Published: almost 6 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

10.1186/s12864-016-2403-1

RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations
Cited by: 20
Author(s): Edin Hamzić, Rikke Brødsgaard Kjærup, Núria Mach, Guilietta Minozzi, Francesco Strozzi, V. Gualdi, J. L. Williams, Jun Chen, Eva Wattrang, Bart Buitenhuis, Helle R. Juul‐Madsen, Tina Sørensen Dalgaard
Software Mentions: 4
Published: almost 11 years ago

10.7554/eLife.45310

A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development
Cited by: 45
Author(s): Christopher I. Cazzonelli, Xin Hou, Yağiz Alagöz, John Rivers, Namraj Dhami, Jiwon Lee, Shashikanth Marri, Barry J. Pogson
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2020.599292

Hybrid Incompatibilities and Transgressive Gene Expression Between Two Closely Related Subspecies of Drosophila
Cited by: 10
Author(s): Alwyn C. Go, Alberto Civetta
Software Mentions: 4
Published: almost 6 years ago

10.3390/ani11082241

Transcriptomic Response under Heat Stress in Chickens Revealed the Regulation of Genes and Alteration of Metabolism to Maintain Homeostasis
Cited by: 8
Author(s): Hana Kim, Hye‐Ran Kim, Pil‐Nam Seong, D. K. Arora, Donghyun Shin, Woncheoul Park, Jong-Eun Park
Software Mentions: 4
Published: over 5 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

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2020.563954

Identification of Critical Genes and Proteins for Stent Restenosis Induced by Esophageal Benign Hyperplasia in Esophageal Cancer
Cited by: 4
Author(s): Li Weng, Shanshan Shen, Shaoqiu Wu, Xiaoxing Yin, Bingyan Liu, Ming Shang, Xiaoping Zou, Aiwu Mao
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-015-2114-z

Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis
Cited by: 9
Author(s): Gareth D. Weedall, Helen Irving, Margaret Hughes, Charles S. Wondji
Software Mentions: 4
Published: almost 11 years ago

10.3389/fgene.2017.00052

Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs
Cited by: 25
Author(s): Andrew D. L. Nelson, Upendra Kumar Devisetty, Kyle Palos, Asher Haug-Baltzell, Eric Lyons, Mark A. Beilstein
Software Mentions: 4
Published: over 9 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

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568