10.7554/eLife.31683

Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm
Cited by: 36
Author(s): Xinan Yang, Rangarajan D. Nadadur, Catharina R.E. Hilvering, Valerio Bianchi, Michael S. Werner, Stefan R. Mazurek, Margaret Gadek, Karen Shen, Joseph D. Goldman, Leonid Tyan, Jenna C. Bekeny, Johnathon M Hall, Nutishia Lee, Carlos Perez-Cervantes, Ozanna Burnicka-Turek, Kenneth D. Poss, Christopher R. Weber, Wouter de Laat, Alexander J. Ruthenburg, Ivan P. Moskowitz
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0235218

Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualities
Cited by: 17
Author(s): Yan Li, Meimei Wang, Qiufeng Li, Yanxia Gao, Qian Li, Jianguo Li, Yong Cao
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0085568

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines
Cited by: 58
Author(s): Oliver Rupp, J. Ole Becker, Karina Brinkrolf, Christina Timmermann, Nicole Borth, Alfred Pühler, Thomas Noll, Alexander Goesmann
Software Mentions: 5
Published: over 12 years ago

10.1186/s12864-019-5511-x

RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions
Cited by: 35
Author(s): Kirti Shekhawat, Hugh-G. Patterton, Florian F. Bauer, Mathabatha Evodia Setati
Software Mentions: 5
Published: over 7 years ago

10.18632/aging.102822

Transcriptomic and metabolomic profiling of long-lived growth hormone releasing hormone knock-out mice: evidence for altered mitochondrial function and amino acid metabolism
Cited by: 13
Author(s): Jessica M. Hoffman, Aliza Poonawalla, Mert Icyuz, William R. Swindell, Landon Wilson, Stephen Barnes, Liou Y. Sun
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.39054

New insights into the cellular temporal response to proteostatic stress
Cited by: 40
Author(s): Justin Rendleman, Zhe Cheng, Shuvadeep Maity, Nicolai Kastelic, Mathias Munschauer, Kristina Allgoewer, Guoshou Teo, Yun Bin Matteo Zhang, Amy Lei, Brian J. Parker, Markus Landthaler, Lindsay Freeberg, Scott Kuersten, Hyungwon Choi, Christine Vogel
Software Mentions: 5
Published: almost 8 years ago

10.3390/ijms21031067

Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress
Cited by: 32
Author(s): Zhaoyang Hu, Yufei Zhang, Yue Ping He, Qingqing Cao, Ting Zhang, Laiqing Lou, Qingqing Cai
Software Mentions: 5
Published: over 6 years ago

10.1155/2017/6218353

Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers
Cited by: 105
Author(s): Luka Bolha, Metka Ravnik‐Glavač, Damjan Glavač
Software Mentions: 5
Published: over 9 years ago

10.1038/onc.2016.382

Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer
Cited by: 125
Author(s): Alison Harrod, Janet S. Fulton, Van Nguyen, Manikandan Periyasamy, L Ramos-Garcia, C-F Lai, Gergana Metodieva, Alex de Giorgio, Richard Williams, Delfran Batista dos Santos, Pablo Gómez, M-L Lin, Metodi V. Metodiev, Justin Stebbing, Leandro Castellano, Luca Magnani, R. Charles Coombes, Laki Buluwela, Simak Ali
Software Mentions: 5
Published: almost 10 years ago

10.1155/2013/481545

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies
Cited by: 13
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith
Software Mentions: 5
Published: about 13 years ago

10.1128/mBio.01496-21

The Interspecific Fungal Hybrid <i>Verticillium longisporum</i> Displays Subgenome-Specific Gene Expression
Cited by: 6
Author(s): Jasper R L Depotter, Fabian van Beveren, Luis Rodríguez‐Moreno, Holger Kramer, Edgar A. Chavarro Carrero, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Thomas A. Wood, Bart P.H.J. Thomma, Michael Seidl
Software Mentions: 5
Published: about 5 years ago

10.1084/jem.20191257

Combined deletion of <i>Bap1</i>, <i>Nf2</i>, and <i>Cdkn2ab</i> causes rapid onset of malignant mesothelioma in mice
Cited by: 28
Author(s): Jitendra Badhai, Gaurav Kumar Pandey, Ji‐Ying Song, Oscar Krijgsman, Rajith Bhaskaran, G. Chandrasekaran, Min-Chul Kwon, Lorenzo Bombardelli, Kim Monkhorst, Cristoforo Grasso, John Zevenhoven, Jan van der Vliet, Miranda Cozijnsen, Paul Krimpenfort, Daniel S. Peeper, Maarten van Lohuizen, Anton Berns
Software Mentions: 5
Published: over 6 years ago

10.3892/or.2015.4023

Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome
Cited by: 20
Author(s): Jie Du, Lin Zhang
Software Mentions: 5
Published: over 11 years ago

10.1038/s41598-021-92610-4

Identification of biological pathway and process regulators using sparse partial least squares and triple-gene mutual interaction
Cited by: 2
Author(s): Jun-Yan Hong, T.D.C.P. Gunasekara, Cheng He, Sanzhen Liu, Jianqin Huang, Hairong Wei
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0167488

Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial
Cited by: 46
Author(s): Leigh M. Howard, Kristen L. Hoek, Johannes Goll, Parimal Samir, Allison C. Galassie, Tara M. Allos, Xinnan Niu, Laura E. Gordy, C. Buddy Creech, Nripesh Prasad, Travis L. Jensen, Heather Hill, Shawn Levy, Sebastian Joyce, Andrew J. Link, Kathryn M. Edwards
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-021-86544-0

An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
Cited by: 5
Author(s): Gabriel Jiménez-Domínguez, Patrice Ravel, Stéphan Jalaguier, Vincent Cavaillès, Jacques Colinge
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-76404-8

Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy
Cited by: 67
Author(s): Abul B.M.M.K. Islam, A. A. Khan
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0197162

A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells
Cited by: 15
Author(s): Alexander Wolff, Michaela Bayerlová, Jochen Gaedcke, Dieter Kube, Tim Beißbarth
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0101374

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads
Cited by: 21
Author(s): Shanrong Zhao
Software Mentions: 5
Published: about 12 years ago

10.7554/eLife.25762

Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution
Cited by: 102
Author(s): Yuh Chwen G Lee, Gary H. Karpen
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0185376

Cellular heterogeneity contributes to subtype-specific expression of ZEB1 in human glioblastoma
Cited by: 10
Author(s): Philipp Euskirchen, Josefine Radke, Marc Soeren Schmidt, Eva Schulze Heuling, Eric Kadikowski, Meron Maricos, Felix Knab, Ulrike Grittner, Norman Zerbe, Marcus Czabanka, Christoph Dieterich, Hrvoje Miletić, Sverre Mørk, Arend Koch, Matthias Endres, Christoph Harms
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0252457

Lack of parent-of-origin effects in Nasonia jewel wasp: A replication and extension study
Cited by: 1
Author(s): Kimberly C. Olney, Joshua D. Gibson, Heini M. Natri, Avery Underwood, Juergen Gadau, Melissa A. Wilson
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0143128

RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize
Cited by: 30
Author(s): Liu Ya, Miaoyi Zhou, Zhaoxu Gao, Wen Ren, Fan Yang, Hang He, Jiuran Zhao
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pone.0016266

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease
Cited by: 257
Author(s): Natalie A. Twine, Karolina Janitz, Marc R. Wilkins, Michał Janitz
Software Mentions: 5
Published: over 15 years ago

10.1371/journal.pntd.0003853

The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection
Cited by: 46
Author(s): David Roquis, Julie M. J. Lepesant, Marion Picard, Michael Freitag, Hugues Parrinello, Marco Groth, Rémi Emans, Céline Cosseau, Christoph Grunau
Software Mentions: 5
Published: about 11 years ago

10.1093/gbe/evz280

Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae)
Cited by: 2
Author(s): Laramie L. Lindsey, Roy N. Platt, C. Douglas Phillips, David A. Ray, Robert D. Bradley
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0182270

Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans
Cited by: 4
Author(s): Kapil Dev Singh, Xue Zheng, Stuart Milstein, Martin Keller, Bernd Roschitzki, Jonas Grossmann, Michael O. Hengartner
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-018-36840-z

Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas
Cited by: 28
Author(s): Susan K. Rathe, Flavia E. Popescu, James E. Johnson, Adrienne L. Watson, Tracy A. Marko, Branden S. Moriarity, John R. Ohlfest, David A. Largaespada
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.50541

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
Cited by: 62
Author(s): Rita A Batista, Jordi Moreno‐Romero, Yue Qiu, Joram van Boven, Juan Santos‐González, Duarte D. Figueiredo, Claudia Köhler
Software Mentions: 5
Published: almost 7 years ago

10.3390/ijms21051630

Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines
Cited by: 1
Author(s): Dóra Bojcsuk, Gergely Nagy, Bálint László Bálint
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1004648

Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements
Cited by: 36
Author(s): Robin P. Smith, Walter L. Eckalbar, Kari M. Morrissey, Marcelo R. Luizon, Thomas J. Hoffmann, Xinwei Sun, Stacy L. Jones, Shelley Force Aldred, Anuradha Ramamoorthy, Zeruesenay Desta, Yunlong Liu, Todd C. Skaar, Nathan D. Trinklein, Kathleen M. Giacomini, Nadav Ahituv
Software Mentions: 5
Published: almost 12 years ago

10.1186/s13059-017-1281-4

Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid
Cited by: 77
Author(s): Weiren Zhu, Bo Hu, Claude Becker, Ezgi Sueheyla Dogan, Kenneth W. Berendzen, Detlef Weigel, Chang Liu
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-017-1304-1

Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis
Cited by: 16
Author(s): Maria Ninova, Sam Griffiths-Jones, Matthew Ronshaugen
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-016-1057-2

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis
Cited by: 52
Author(s): Nina Koenecke, Jeff Johnston, Bjoern Gaertner, Malini Natarajan, Julia Zeitlinger
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pgen.1005698

Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans
Cited by: 43
Author(s): Maxwell Kramer, Anna Lena Kranz, Amanda Su, Lara Winterkorn, Sarah Elizabeth Albritton, Sevinç Ercan
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12859-018-2013-9

TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association
Cited by: 8
Author(s): Seo Won Choi, Jin Wu Nam
Software Mentions: 5
Published: over 8 years ago

10.1186/s13059-015-0734-x

Errors in RNA-Seq quantification affect genes of relevance to human disease
Cited by: 128
Author(s): Christelle Robert, Michael Watson
Software Mentions: 5
Published: about 11 years ago

10.1186/s13059-015-0856-1

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation
Cited by: 85
Author(s): Stephan Busche, Xiaojian Shao, Maxime Caron, Tony Kwan, Fiona Allum, Warren A. Cheung, Bing Ge, Susan Westfall, Simon Maguire, Amy Barrett, Jordana T. Bell, Mark I. McCarthy, Panos Deloukas, Mathieu Blanchette, Guillaume Bourque, Timothy D. Spector, Mark Lathrop, Tomi Pastinen, Elin Grundberg
Software Mentions: 5
Published: almost 11 years ago

10.1186/gb-2014-15-8-r70

DNA copy number evolution in Drosophila cell lines
Cited by: 94
Author(s): Hangnoh Lee, C. Joel McManus, Dong-Yeon Cho, Matthew L. Eaton, Fioranna Renda, Maria Patrizia Somma, Lucy Cherbas, Gemma E. May, Sara Powell, Dayu Zhang, Lijun Zhan, Alissa Resch, Justen Andrews, S Celniker, Peter Cherbas, Teresa M. Przytycka, Maurizio Gatti, Brian Oliver, Brenton R. Graveley, David M. MacAlpine
Software Mentions: 5
Published: about 12 years ago

10.1186/s13059-014-0429-8

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer
Cited by: 177
Author(s): Nicole M. White, Christopher R. Cabanski, Jessica Silva-Fisher, Ha X. Dang, Ramaswamy Govindan, Christopher A. Maher
Software Mentions: 5
Published: about 12 years ago

10.1186/s13059-015-0840-9

A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63
Cited by: 126
Author(s): Xiaomin Bao, Adam J. Rubin, Kun Qu, Jiajing Zhang, Paul G. Giresi, Howard Y. Chang, Paul A. Khavari
Software Mentions: 5
Published: almost 11 years ago

10.1186/s13059-018-1403-7

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues
Cited by: 37
Author(s): Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Hagit T. Porath, Kevin Hsieh, Linus Chen, Timothy Daley, S. Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernández, Roel A. Ophoff, Jose Rodriguez Santana, Erez Y. Levanon, Prescott G. Woodruff, Esteban G. Burchard, Max A. Seibold, Sagiv Shifman, Eleazar Eskin, Noah Zaitlen
Software Mentions: 5
Published: over 8 years ago

10.3390/genes10070552

Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation
Cited by: 14
Author(s): Xitong Zhao, Shaokang Chen, Zhen Tan, Yuan Wang, Fengxia Zhang, Ting Yang, Yibing Liu, Ai Hong, Kai Xing, Chuduan Wang
Software Mentions: 5
Published: about 7 years ago

10.3390/genes5040957

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
Cited by: 57
Author(s): Vahan Simonyan, Raja Mazumder
Software Mentions: 5
Published: about 12 years ago

10.1534/g3.116.030783

ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress
Cited by: 47
Author(s): Benoît Castandet, Amber M. Hotto, Susan R. Strickler, David B. Stern
Software Mentions: 5
Published: about 10 years ago

10.1186/s12859-018-2019-3

Closha: bioinformatics workflow system for the analysis of massive sequencing data
Cited by: 15
Author(s): Gun Hwan Ko, Pan Gyu Kim, Jong-Cheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byung-Wook Lee
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1008566

The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants
Cited by: 54
Author(s): Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle Henry
Software Mentions: 5
Published: over 6 years ago

10.1186/s12879-018-3127-4

“Tuberculosis in advanced HIV infection is associated with increased expression of IFNγ and its downstream targets”
Cited by: 18
Author(s): Sheetal Verma, Peicheng Du, Damalie Nakanjako, Sabine Hermans, Jessica Briggs, Lydia Nakiyingi, Jerrold J. Ellner, Yukari C. Manabe, Padmini Salgame
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-018-4763-1

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea
Cited by: 36
Author(s): Jérémy Berthelier, Nathalie Casse, Nicolas Daccord, Véronique Jamilloux, Bruno Saint‐Jean, Grégory Carrier
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1005385

MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis
Cited by: 66
Author(s): Kieu T.M. Pham, Yushi Inoue, Vu Van Ba, Hanh Hieu Nguyen, Toru Nakayashiki, Kenichi Ikeda, Hitoshi Nakayashiki
Software Mentions: 5
Published: about 11 years ago

10.1186/s13059-014-0527-7

The importance of study design for detecting differentially abundant features in high-throughput experiments
Cited by: 12
Author(s): Huaien Luo, Juntao Li, Burton Kuan Hui Chia, Paul Robson, Niranjan Nagarajan
Software Mentions: 5
Published: almost 12 years ago

10.1186/s13059-014-0511-2

A genomic and evolutionary approach reveals non-genetic drug resistance in malaria
Cited by: 34
Author(s): Jonathan D. Herman, Daniel P. Rice, Ulf Ribacke, Jacob Silterra, Amy Deik, Eli L. Moss, Kate M Broadbent, Daniel E. Neafsey, Michael M. Desai, Clary B. Clish, Ralph Mazitschek, Dyann F. Wirth
Software Mentions: 5
Published: almost 12 years ago

10.1371/journal.pntd.0004992

Meta-transcriptome Profiling of the Human-Leishmania braziliensis Cutaneous Lesion
Cited by: 54
Author(s): Stephen M Christensen, Laura A. L. Dillon, Lucas P. Carvalho, Sara Passos, Fernanda O. Novais, V. K. Hughitt, Daniel P. Beiting, Edgar M. Carvalho, Phillip Scott, Najib M. El-Sayed, David M. Mosser
Software Mentions: 5
Published: about 10 years ago

10.1186/s12983-015-0109-x

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex
Cited by: 33
Author(s): Andrey Rozenberg, Mrutyunjaya Parida, Florian Leese, Linda C. Weiss, Ralph Tollrian, J. Robert Manak
Software Mentions: 5
Published: about 11 years ago

10.1534/g3.115.019166

Genome-Wide Analysis of<i>Drosophila</i>RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis
Cited by: 15
Author(s): Yiliang Wei, Shamba S. Mondal, Rima Mouawad, Bartek Wilczyński, R. William Henry, David N. Arnosti
Software Mentions: 5
Published: over 11 years ago

10.1186/gb-2014-15-4-r56

Hypermethylation in the ZBTB20 gene is associated with major depressive disorder
Cited by: 84
Author(s): Matthew N. Davies, Lutz Krause, Jordana T. Bell, Fei Gao, Kirsten Ward, Honglong Wu, Hanlin Lu, Yuan Liu, Pei-Chien Tsai, David A. Collier, Therese M. Murphy, Emma Dempster, Jonathan Mill, Alexis Battle, Sara Mostafavi, Xiaowei Zhu, Anjali K. Henders, Enda M. Byrne, Naomi R. Wray, Nicholas G. Martin, Tim D. Spector, Jun Wang
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pcbi.1005274

Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs
Cited by: 61
Author(s): Nadezda Kryuchkova-Mostacci, Marc Robinson‐Rechavi
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pbio.3000719

Discovery of genes required for body axis and limb formation by global identification of retinoic acid–regulated epigenetic marks
Cited by: 22
Author(s): Marie Berenguer, Karolin F Meyer, Jun Yin, Gregg Duester
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-020-07002-1

Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking
Cited by: 13
Author(s): Clemens Falker‐Gieske, Andrea Mott, Siegfried Preuß, Sören Franzenburg, W. Bessei, Jörn Bennewitz, Jens Tetens
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pbio.1001229

Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution
Cited by: 91
Author(s): Robert K. Bradley, Jason J. Merkin, Nicole Lambert, Christopher B. Burge
Software Mentions: 5
Published: over 14 years ago

10.1186/s12870-020-02702-y

Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development
Cited by: 3
Author(s): Xiaobo Zhao, Chunjuan Li, Hao Zhang, Yan Cheng, Quanxi Sun, Juan Wang, Cuiling Yuan, Shiguang Shan
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-021-07451-2

Multi-species transcriptome meta-analysis of the response to retinoic acid in vertebrates and comparative analysis of the effects of retinol and retinoic acid on gene expression in LMH cells
Cited by: 5
Author(s): Clemens Falker‐Gieske, Andrea Mott, Sören Franzenburg, Jens Tetens
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pbio.1002585

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process
Cited by: 192
Author(s): Richard Angélique, Boullu Loïs, Ulysse Herbach, Bonnafoux Arnaud, Valérie Morin, Elodie Vallin, Anissa Guillemin, Nan Gao, Gunawan Rudiyanto, Jérémie Cosette, Ophélie Arnaud, Jean-Jacques Kupiec, Thibault Espinasse, Sandrine Gonin-Giraud, Olivier Gandrillon
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pgen.1005819

Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Cited by: 21
Author(s): Н. А. Иванов, Ran Tao, Joshua G. Chenoweth, Anna C. Brandtjen, Michelle I. Mighdoll, John D. Genova, Ronald D.G. McKay, Yankai Jia, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde, Andrew E. Jaffe
Software Mentions: 5
Published: over 10 years ago

10.3389/fphys.2021.585089

Characterization of Chicken Skin Yellowness and Exploration of Genes Involved in Skin Yellowness Deposition in Chicken
Cited by: 9
Author(s): Jingwen Wu, Zetong Lin, Chen Geng-Hua, Qianyi Luo, Qinghua Nie, Xiquan Zhang, Wen Luo
Software Mentions: 5
Published: over 5 years ago

10.1111/pbi.12615

A comprehensive draft genome sequence for lupin (<i>Lupinus angustifolius</i>), an emerging health food: insights into plant–microbe interactions and legume evolution
Cited by: 149
Author(s): James K. Hane, Ming Yao, Lars G. Kamphuis, Matthew N. Nelson, Gagan Garg, Craig A. Atkins, Philipp E. Bayer, Armando Bravo, Scott Bringans, Steven B. Cannon, David Edwards, Rhonda C. Foley, Ling Gao, Maria J. Harrison, Wei Huang, Bhavna Hurgobin, Sean Li, Cheng-Wu Liu, Annette McGrath, Grant Morahan, Jeremy D. Murray, James L. Weller, Jianbo Jian, Karam B. Singh
Software Mentions: 5
Published: about 10 years ago

10.1002/pld3.239

N⁶‐methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis
Cited by: 35
Author(s): Marianne C. Kramer, Kevin A. Janssen, Kyle Palos, Andrew D. L. Nelson, Lee E. Vandivier, Benjamin A. García, Eric Lyons, Mark A. Beilstein, Brian D. Gregory
Software Mentions: 5
Published: over 6 years ago

10.3389/fonc.2019.01206

Exploration of the Transcriptional Landscape of ALPPS Reveals the Pathways of Accelerated Liver Regeneration
Cited by: 11
Author(s): Pieter Borger, Marcel Schneider, Lukas Frick, Magda Langiewicz, Maksim Sorokin, Anton Buzdin, Ekaterina Kachaylo, Rolf Graf, Bostjan Humar, Pierre‐Alain Clavien
Software Mentions: 5
Published: almost 7 years ago

10.1111/pbi.12852

The transcriptome, extracellular proteome and active secretome of agroinfiltrated<i>Nicotiana benthamiana</i>uncover a large, diverse protease repertoire
Cited by: 52
Author(s): Friederike Grosse‐Holz, Steven L. Kelly, Svenja Blaskowski, Farnusch Kaschani, Markus Kaiser, Renier A. L. van der Hoorn
Software Mentions: 5
Published: almost 9 years ago

10.3389/fmicb.2018.02212

A Class 1 Histone Deacetylase as Major Regulator of Secondary Metabolite Production in Aspergillus nidulans
Cited by: 29
Author(s): Angelo Pidroni, Birgit Faber, Gerald Brosch, Ingo Bauer, Stefan Graessle
Software Mentions: 5
Published: about 8 years ago

10.3389/fphys.2019.01305

The Regulation of Ruminal Short-Chain Fatty Acids on the Functions of Rumen Barriers
Cited by: 28
Author(s): Hong Shen, Zhihui Xu, Zanming Shen, Zhongyan Lu
Software Mentions: 5
Published: almost 7 years ago

10.3389/fimmu.2020.00425

Interleukin-17A/F1 Deficiency Reduces Antimicrobial Gene Expression and Contributes to Microbiome Alterations in Intestines of Japanese medaka (Oryzias latipes)
Cited by: 18
Author(s): Yo Okamura, Natsuki Morimoto, Daisuke Ikeda, Naoki Mizusawa, Shugo Watabe, Hiroshi Miyanishi, Yuichi Saeki, Haruko Takeyama, Takashi Aoki, Masato Kinoshita, Tomoya Kono, Masahiro Sakai, Jun ichi Hikima
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.3091

Effect of method of deduplication on estimation of differential gene expression using RNA-seq
Cited by: 20
Author(s): Anna V. Klepikova, Artem S. Kasianov, Mikhail S. Chesnokov, Н. Л. Лазаревич, Aleksey A. Penin, Maria D. Logacheva
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-019-5801-3

Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum
Cited by: 15
Author(s): Zehui Wei, Pengcheng Li, Sijia Huang, Purevsuren Lkhagvagarav, Mengqi Zhu, C. Liang, Caixia Jia
Software Mentions: 5
Published: over 7 years ago

10.3389/fimmu.2020.584116

Rheumatoid Arthritis Synovial Fluid Neutrophils Drive Inflammation Through Production of Chemokines, Reactive Oxygen Species, and Neutrophil Extracellular Traps
Cited by: 62
Author(s): Helen L. Wright, Max Lyon, Elinor A Chapman, Robert J. Moots, Steven W. Edwards
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2016.01335

Visual Comparative Omics of Fungi for Plant Biomass Deconstruction
Cited by: 31
Author(s): Shingo Miyauchi, David Navarro, Igor V. Grigoriev, Anna Lipzen, Robert Riley, Didier Chevret, Sacha Grisel, Jean‐Guy Berrin, Bernard Henrissat, Marie‐Noëlle Rosso
Software Mentions: 5
Published: about 10 years ago

10.1186/1471-2164-14-230

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
Cited by: 39
Author(s): Nicolas C. Nalpas, Stephen D. E. Park, David A. Magee, Maria Taraktsoglou, John A. Browne, Kevin M. Conlon, Kévin Rue-Albrecht, Kate E. Killick, Karsten Hokamp, Amanda J. Lohan, Brendan J. Loftus, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 5
Published: over 13 years ago

10.3389/fgene.2016.00080

Recursive Indirect-Paths Modularity (RIP-M) for Detecting Community Structure in RNA-Seq Co-expression Networks
Cited by: 12
Author(s): Bahareh Rahmani, Michael T. Zimmermann, Diane E. Grill, Richard B. Kennedy, Ann L. Oberg, Bill C. White, Gregory A. Poland, Brett A. McKinney
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2018.00491

Dynamic Changes in the Global MicroRNAome and Transcriptome Identify Key Nodes Associated With Ovarian Development in Chickens
Cited by: 12
Author(s): Wenwen Wang, Keliang Wu, Meiting Jia, Siyuan Sun, Kang Li, Qin Zhang, Hui Tang
Software Mentions: 5
Published: almost 8 years ago

10.3389/fgene.2020.591806

Genome-Wide Identification of Circular RNAs in Response to Low-Temperature Stress in Tomato Leaves
Cited by: 11
Author(s): Xuedong Yang, Yahui Liu, Hui Zhang, Jinyu Wang, Gaurav Zinta, Shangbo Xie, Weimin Zhu, Wen-Feng Nie
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2019.01347

Emerging Roles of Heat-Induced circRNAs Related to Lactogenesis in Lactating Sows
Cited by: 11
Author(s): Jiajie Sun, Haojie Zhang, Bao-Yu Hu, Yueqin Xie, Dongyang Wang, Jinzhi Zhang, Ting Chen, Junyi Luo, Songbo Wang, Qinyan Jiang, Qianyun Xi, Zujing Chen, Yongliang Zhang
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pntd.0002905

Dual RNA-seq of Parasite and Host Reveals Gene Expression Dynamics during Filarial Worm–Mosquito Interactions
Cited by: 59
Author(s): Young Jun Choi, Matthew T. Aliota, George F. Mayhew, Sara M. Erickson, Bruce M. Christensen
Software Mentions: 5
Published: over 12 years ago

10.3389/fgene.2018.00441

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle
Cited by: 30
Author(s): Tassia M. Goncalves, Luciana Correia de Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sónia Cristina da Silva Andrade, Gérson Barreto Mourão, G. Gasparin, Gabriel Costa Monteiro Moreira, Eric R. Fritz-Waters, James M. Reecy
Software Mentions: 5
Published: almost 8 years ago

10.3389/fgene.2019.00766

Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data
Cited by: 30
Author(s): Sharmin Akter, Dong Xu, Susan C. Nagel, John J. Bromfield, Katherine E. Pelch, Gilbert B Wilshire, Trupti Joshi
Software Mentions: 5
Published: about 7 years ago

10.1186/1471-2105-12-323

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Cited by: 14,016
Author(s): Bo Li, Colin N. Dewey
Software Mentions: 4
Published: about 15 years ago

10.1186/s13071-019-3534-4

Eimeria maxima-induced transcriptional changes in the cecal mucosa of broiler chickens
Cited by: 15
Author(s): Charles Li, Xianghe Yan, Hyun S. Lillehoj, Seong-Hwan Oh, Liheng Liu, Zhifeng Sun, Changqin Gu, Youngsub Lee, Zhezi Xianyu, Hongyan Zhao
Software Mentions: 4
Published: over 7 years ago

10.3390/v12080817

Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain
Cited by: 6
Author(s): Jayeshbhai Chaudhari, Chia-Sin Liew, Aspen M. Workman, Jean-Jack M. Riethoven, David Steffen, Sarah Sillman, Hiep L.X. Vu
Software Mentions: 4
Published: about 6 years ago

10.1186/s12859-017-1816-4

mmquant: how to count multi-mapping reads?
Cited by: 29
Author(s): Matthias Zytnicki
Software Mentions: 4
Published: about 9 years ago

10.1242/dmm.042713

Leptin and fractalkine: Novel subcutaneous cytokines in burn injury
Cited by: 4
Author(s): Dominic Friston, Sini Junttila, Júlia Borges Paes Lemes, Helen Laycock, Jose Vicente Torres-Pérez, Elizabeth J. Want, Attila Gyenesei, I. Nagy
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2019.00306

Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark Stress
Cited by: 13
Author(s): Hengyu Yan, Yue Liu, Kang Zhang, Jakyoung Song, Wenying Xu, Zhen Su
Software Mentions: 4
Published: over 7 years ago

10.1186/s12863-018-0608-9

RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat &amp; rat
Cited by: 21
Author(s): Xiaoxiao Gao, Jing Ye, Chen Yang, Lei Luo, Ya Liu, Jianping Ding, Yunhai Zhang, Yinghui Ling, Weiping Huang, Xiaorong Zhang, Kaifa Zhang, Xiumei Li, Jie Zhou, Fugui Fang, Zubing Cao
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-015-0795-6

TOGGLE: toolbox for generic NGS analyses
Cited by: 20
Author(s): Cécile Monat, Christine Tranchant‐Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela, Marilyne Summo, François Sabot
Software Mentions: 4
Published: almost 11 years ago

10.1093/database/bav047

GraP: platform for functional genomics analysis of Gossypium raimondii
Cited by: 12
Author(s): Liwei Zhang, Jinyan Guo, Qi You, Xin Yi, Yi Ling, Wenying Xu, Jinping Hua, Zhen Su
Software Mentions: 4
Published: over 11 years ago

10.1016/j.ydbio.2016.06.016

Developmentally regulated long non-coding RNAs in Xenopus tropicalis
Cited by: 17
Author(s): Elmira Forouzmand, Nick Owens, Ira L. Blitz, Kitt D. Paraiso, Mustafa K. Khokha, Michael J. Gilchrist, Xiaohui Xie, Ken W.Y. Cho
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-021-07699-8

Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome
Cited by: 8
Author(s): Stefania Bertazzoni, Darcy A. B. Jones, H. Phan, Kar‐Chun Tan, James K. Hane
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-017-1897-0

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
Cited by: 6
Author(s): Ethan Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12985-016-0659-3

Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection
Cited by: 7
Author(s): Leonardo Susta, Ying He, Jessica M. Hutcheson, Yangqing Lu, Franklin D. West, Steven L. Stice, Ping Yu, Zaid Abdo, Claudio L. Afonso
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12864-020-6613-1

Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals
Cited by: 11
Author(s): Yali Hou, Furong Qi, Xue Bai, Tong Ren, Xu Shen, Qing Chu, Xiquan Zhang, Xuemei Lu
Software Mentions: 4
Published: over 6 years ago

10.1080/21505594.2021.1958057

Transcriptional response of <i>Aspergillus fumigatus</i> to copper and the role of the Cu chaperones
Cited by: 6
Author(s): Duaa Anabosi, Zohar Meir, Yana Shadkchan, Mariana Handelman, Ammar Abou-Kandil, Annie Yap, Daniel Urlings, Morgan Gold, Sven Krappmann, Hubertus Haas, Nir Osherov
Software Mentions: 4
Published: about 5 years ago

10.1186/s12989-018-0244-6

Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition
Cited by: 53
Author(s): Deniz Öner, Manosij Ghosh, Hannelore Bové, Matthieu Moisse, Bram Boeckx, Radu Corneliu Duca, Katrien Poels, Katrien Luyts, Eveline Putzeys, Kirsten Van Landuydt, Jeroen Vanoirbeek, Marcel Ameloot, Diether Lambrechts, Lode Godderis, Peter Hoet
Software Mentions: 4
Published: over 8 years ago