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/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

10.3390/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: almost 12 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

10.7554/eLife.27159

Development of Bag-1L as a therapeutic target in androgen receptor-dependent prostate cancer
Cited by: 29
Author(s): Laura Cato, Antje Neeb, Adam Sharp, Víctor Buzón, Scott B. Ficarro, Linxiao Yang, Claudia Muhle‐Goll, Nane C. Kuznik, Ruth Riisnaes, Daniel Nava Rodrigues, Olivier Armant, Victor Gourain, Guillaume Adelmant, Emmanuel Amankwah Ntim, Thomas Westerling, David Dolling, Pasquale Rescigno, Ines Figueiredo, Friedrich Fauser, Jiansheng Wu, Jaice T. Rottenberg, L. Shatkina, Claudia Ester, Burkhard Luy, Holger Puchta, Jakob Troppmair, Nicole Jung, Stefan Bräse, Uwe Strähle, Jarrod A. Marto, G. Ulrich Nienhaus, Bissan Al‐Lazikani, Xavier Salvatella, Johann S. de Bono, Andrew C. B. Cato, Myles Brown
Software Mentions: 5
Published: about 9 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

10.1534/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: about 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

10.1371/journal.pone.0159093

Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal Cortex
Cited by: 57
Author(s): Ke Ma, Li Guo, Aiping Xu, Shan Cui, Jinhui Wang
Software Mentions: 5
Published: about 10 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/s12864-016-3118-z

Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species
Cited by: 10
Author(s): Weizhong Li, René Richter, Yunsup Jung, Quanyin Zhu, Robert W. Li
Software Mentions: 5
Published: almost 10 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

10.3389/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

10.1128/AEM.00338-19

Wood Modification by Furfuryl Alcohol Resulted in a Delayed Decomposition Response in <i>Rhodonia</i> ( <i>Postia</i> ) <i>placenta</i>
Cited by: 13
Author(s): Inger Skrede, Monica Hongrø Solbakken, Jaqueline Hess, Carl Gunnar Fossdal, Olav A. Hegnar, Gry Alfredsen
Software Mentions: 5
Published: about 7 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

10.3389/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

10.18632/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

10.1186/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

10.3389/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

10.15252/emmm.202012105

Neuron type‐specific increase in lamin B1 contributes to nuclear dysfunction in Huntington’s disease
Cited by: 23
Author(s): Rafael Alcalá-Vida, Marta Garcia‐Forn, Carla Castany‐Pladevall, Jordi Creus-Muncunill, Yoko Itō, Enrique Blanco, Arantxa Golbano, Kilian Crespí-Vázquez, Aled Parry, Guy Slater, Shamith A. Samarajiwa, Sandra Peiró, Luciano Di Croce, Masashi Narita, Esther Pérez‐Navarro
Software Mentions: 5
Published: over 5 years ago

10.1016/j.devcel.2021.07.019

Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition
Cited by: 25
Author(s): Christopher J. Price, Dylan Stavish, Paul J. Gokhale, Ben A. Stevenson, Samantha Sargeant, Joanne Lacey, Tristan A. Rodríguez, Ivana Barbaric
Software Mentions: 5
Published: about 5 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/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/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.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

10.1186/s12864-019-6426-2

Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis
Cited by: 17
Author(s): Karen Cristine Gonçalves dos Santos, Isabel Desgagné‐Penix, Hugo Germain
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2164-14-550

Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies
Cited by: 13
Author(s): Lucas Swanson, Gordon Robertson, Andrew J. Mungall, Yaron S.N. Butterfield, Readman Chiu, Richard Corbett, T. Roderick Docking, Donna E. Hogge, Shaun D. Jackman, Richard A. Moore, Ka Ming Nip, Jeremy Parker, Jenny Q. Qian, Anthony Raymond, Sandy S. Sung, Angela Tam, Nina Thiessen, Richard Varhol, Sherry Wang, Deniz Yörükoğlu, Yongjun Zhao, Pamela A. Hoodless, S. Cenk Şahinalp, Aly Karsan, İnanç Birol
Software Mentions: 5
Published: about 13 years ago

10.1038/s42003-020-01620-x

RNA editing enzyme APOBEC3A promotes pro-inflammatory M1 macrophage polarization
Cited by: 20
Author(s): Emad Alqassim, Shraddha Sharma, Aalia Khan, Tiffany R. Emmons, Eduardo Cortes Gomez, Abdulrahman A. Alahmari, Kelly L. Singel, Jaron Mark, Bruce A. Davidson, AJ Robert McGray, Qian Liu, Brian D. Lichty, Kirsten B. Moysich, Jianmin Wang, Kunle Odunsi, Brahm H. Segal, Bora E. Baysal
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-018-0094-7

Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis
Cited by: 53
Author(s): Taro Maeda, Yuuki Kobayashi, Hiromu Kameoka, Nao Okuma, Nobuo Takeda, Katsushi Yamaguchi, Takahiro Bino, Shuji Shigenobu, Masayoshi Kawaguchi
Software Mentions: 5
Published: about 8 years ago

10.1186/s12864-016-2745-8

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq
Cited by: 17
Author(s): Yongxian Yuan, Huaiqian Xu, Rufina Leung
Software Mentions: 5
Published: over 10 years ago

10.1016/j.ccell.2019.02.009

Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets
Cited by: 533
Author(s): Luca Cassetta, Stamatina Fragkogianni, Andrew H. Sims, Agnieszka Swierczak, Lesley M. Forrester, Hui Zhang, Daniel Soong, Tiziana Cotechini, Pavana Anur, Elaine Y. Lin, A Fidanza, Martha Lopez‐Yrigoyen, Michael Millar, Alexandra Urman, Zhichao Ai, Paul T. Spellman, E. Shelley Hwang, JM Dixon, Lisa Wiechmann, Lisa M. Coussens, Harriet O. Smith, Jeffrey W. Pollard
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-017-4351-9

Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat
Cited by: 3
Author(s): David Martín‐Gálvez, Denis Dunoyer de Segonzac, Man Chun John, Anne E. Kwitek, David Thybert, Paul Flicek
Software Mentions: 5
Published: almost 9 years ago

10.1038/s42003-018-0037-3

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization
Cited by: 18
Author(s): Lisa Lindström, Tongbin Li, Darina Malycheva, Arun Kancharla, Helén Nilsson, Neelanjan Vishnu, Hindrik Mulder, Martin Johansson, Catalina Ana Rosselló, María Alvarado-Kristensson
Software Mentions: 5
Published: over 8 years ago

10.1093/database/bax079

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species
Cited by: 9
Author(s): Leandro Costa do Nascimento, Marcela Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas S. Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-020-06795-5

Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality
Cited by: 27
Author(s): Alessandra Zombardo, Cristina Crosatti, Paolo Bagnaresi, Laura Bassolino, Noam Reshef, Sergio Puccioni, Primetta Faccioli, Alessio Tafuri, Massimo Delledonne, Aaron Fait, Paolo Storchi, Luigi Cattivelli, Erica Mica
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0151917

Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns
Cited by: 9
Author(s): Yayoi Natsume-Kitatani, Hiroshi Mamitsuka
Software Mentions: 5
Published: over 10 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

10.1186/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/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

10.1371/journal.pone.0225180

Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation
Cited by: 10
Author(s): Aisling M. Redmond, Soleilmane Omarjee, Igor Chernukhin, Muriel Le Romancer, Jason S. Carroll
Software Mentions: 5
Published: almost 7 years ago

10.1186/1471-2164-15-917

Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut
Cited by: 37
Author(s): Matan Shelomi, W. Cameron Jasper, Joel Atallah, Lynn S. Kimsey, Brian R. Johnson
Software Mentions: 5
Published: over 12 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/s13075-015-0544-2

Transcriptome analysis of ageing in uninjured human Achilles tendon
Cited by: 61
Author(s): Mandy J. Peffers, Yongxiang Fang, Kathleen Cheung, Tim Koh Jia Wei, Peter Clegg, Helen L. Birch
Software Mentions: 5
Published: over 11 years ago

10.18632/oncotarget.21031

Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation window
Cited by: 22
Author(s): Qi Wang, Nan Wang, Rui Cai, Fan Zhao, Yi Xiong, Xiao Li, Aihua Wang, Peng Lin, Yaping Jin
Software Mentions: 5
Published: about 9 years ago

10.18632/oncotarget.8192

Integrated analysis of long non-coding RNAs in human colorectal cancer
Cited by: 32
Author(s): Xiaohua Chen, Binjian Liu, Rui Yang, Yong Guo, Feng Li, Lin Wang, Hanyang Hu
Software Mentions: 5
Published: over 10 years ago

10.18632/oncotarget.16493

ERK signalling modulates epigenome to drive epithelial to mesenchymal transition
Cited by: 20
Author(s): Mohit Navandar, Angela Garding, Sanjeeb Kumar Sahu, Abhijeet Pataskar, Sandra Schick, Vijay Tiwari
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0153932

Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis
Cited by: 24
Author(s): Randy J. Hempel, John P. Bannantine, Judith R. Stabel
Software Mentions: 5
Published: over 10 years ago

10.1186/s12974-021-02154-7

Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder
Cited by: 11
Author(s): Fumie Horiuchi, Yuta Yoshino, Hiroshi Kumon, Rie Hosokawa, Kiwamu Nakachi, Kentaro Kawabe, Jun‐ichi Iga, Shu‐ichi Ueno
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0109715

Genome-Wide Identification and Tissue-Specific Expression Analysis of UDP-Glycosyltransferases Genes Confirm Their Abundance in Cicer arietinum (Chickpea) Genome
Cited by: 33
Author(s): Ranu Sharma, Vimal Rawat, C.G. Suresh
Software Mentions: 5
Published: almost 12 years ago

10.7554/eLife.07103

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
Cited by: 103
Author(s): Irene Gallego Romero, Bryan J. Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C. Ward, Nicholas E. Banovich, Courtney L Kagan, Jonathan E. Burnett, Constance H Huang, Amy Mitrano, Claudia Chavarria, Inbar Friedrich Ben-Nun, Yingchun Li, Karen Sabatini, Trevor R. Leonardo, Mana M. Parast, Tomàs Marquès‐Bonet, Louise C. Laurent, Jeanne F. Loring, Yoav Gilad
Software Mentions: 5
Published: about 11 years ago

10.7554/eLife.37184

An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer
Cited by: 68
Author(s): Ji Li, Peter S. Choi, Christine L. Chaffer, Katherine Labella, Justin Hwang, Andrew O. Giacomelli, Jong Wook Kim, Nina Ilić, John G. Doench, Seav Huong Ly, Chao Dai, Kimberly R. Hagel, Andrew L. Hong, Ole Gjoerup, Shom Goel, Jennifer Y Ge, David E. Root, Jean J. Zhao, Angela N. Brooks, Robert A. Weinberg, William C. Hahn
Software Mentions: 5
Published: about 8 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: about 6 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.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

10.7554/eLife.21049

Proliferation-independent regulation of organ size by Fgf/Notch signaling
Cited by: 36
Author(s): Agnė Kozlovskaja-Gumbrienė, Yi Ren, Alexander Richard, Andy Aman, Ryan Jiskra, Danielle Nagelberg, Holger Knaut, Melainia McClain, Tatjana Piotrowski
Software Mentions: 5
Published: over 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: almost 9 years ago

10.7554/eLife.64317

Evolutionary shifts in taste coding in the fruit pest Drosophila suzukii
Cited by: 33
Author(s): Hany K.M. Dweck, Gaëlle J.S. Talross, Wanyue Wang, John R. Carlson
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.44161

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition
Cited by: 30
Author(s): Andrew L. Hong, Yuen-Yi Tseng, Jeremiah A. Wala, Won-Jun Kim, Bryan D. Kynnap, Mihir B. Doshi, Guillaume Kugener, Gabriel J. Sandoval, Thomas P. Howard, Ji Li, Xiaoping Yang, Michelle Tillgren, Mahmhoud Ghandi, Abeer Sayeed, Rebecca Deasy, Abigail Ward, Brian McSteen, Katherine Labella, Paula Keskula, Adam Tracy, Cora Connor, Catherine Clinton, Alanna J. Church, Brian D. Crompton, Katherine A. Janeway, Barbara Van Hare, David Sandak, Ole Gjoerup, Pratiti Bandopadhayay, Paul A. Clemons, Stuart L. Schreiber, David E. Root, Prafulla C. Gokhale, N. Susan, Elizabeth Mullen, Charles W.M. Roberts, Cigall Kadoch, Rameen Beroukhim, Keith L. Ligon, Jesse S. Boehm, William C. Hahn
Software Mentions: 5
Published: over 7 years ago

10.1002/advs.201901672

Comparison of <i>Arachis monticola</i> with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut
Cited by: 38
Author(s): Dongmei Yin, Changmian Ji, Qingxin Song, Wan–Ke Zhang, Xingguo Zhang, Kunkun Zhao, Charles Y. Chen, Chuan Tang Wang, He Guo, Zhe Liang, Xingli Ma, Zhongfeng Li, Yueyi Tang, Yuejun Wang, Ké Li, Longlong Ning, Hui Zhang, Kai Zhao, Xuming Li, Haiyan Yu, Lei Yan, Mingcheng Wang, Liming Ma, Hongkun Zheng, Yijing Zhang, Jinsong Zhang, Wei Hu, Z Jeffrey Chen
Software Mentions: 5
Published: almost 7 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

10.3390/ijms22179146

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses
Cited by: 5
Author(s): Mirosław Tyrka, Beata Bakera, Magdalena Szeliga, Magdalena Święcicka, Paweł Krajewski, Monika Mokrzycka, Monika Rakoczy-Trojanowska
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.07295

Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100
Cited by: 179
Author(s): Shouan Liu, Barbara Kracher, J. Ziegler, Rainer P. Birkenbihl, Imre E. Somssich
Software Mentions: 5
Published: over 11 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

10.7554/eLife.15657

An integrative transcriptomic atlas of organogenesis in human embryos
Cited by: 55
Author(s): Dave T. Gerrard, Andrew Berry, Rachel Jennings, Karen Piper Hanley, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 5
Published: about 10 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

10.7554/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

10.7554/eLife.51373

PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cells
Cited by: 18
Author(s): Payal Jain, Cecilia Ballaré, Enrique Blanco, Pedro Vizán, Luciano Di Croce
Software Mentions: 5
Published: over 6 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: about 5 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

10.7554/eLife.49044

NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress
Cited by: 22
Author(s): Dongdong Han, Lars Schomacher, Katrin M. Schüle, Medhavi Mallick, Michael U. Musheev, Emil Karaulanov, Laura Krebs, Annika von Seggern, Christof Niehrs
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-018-33718-y

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat
Cited by: 40
Author(s): Yongpeng Li, Xing Fu, Meicheng Zhao, Wei Zhang, Bo Li, Diaoguo An, Junming Li, Aimin Zhang, Renyi Liu, Xigang Liu
Software Mentions: 5
Published: almost 8 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

10.1371/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

10.1371/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: over 9 years ago

10.1038/s41598-018-20262-y

Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes
Cited by: 15
Author(s): Austin Alleman, Barbara Feldmeyer, Susanne Foitzik
Software Mentions: 5
Published: over 8 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

10.1038/s41598-017-11036-z

SRSF1 suppresses selection of intron-distal 5′ splice site of DOK7 intron 4 to generate functional full-length Dok-7 protein
Cited by: 3
Author(s): Khalid Ahsan, Akio Matsubara, Mohammad Alinoor Rahman, Jun‐ichi Takeda, Mohammad Nazim, Bisei Ohkawara, Mikako Ito, Kinji Ohno
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.ppat.1002567

Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy
Cited by: 197
Author(s): Adam J. Reid, Sarah J. Vermont, James A. Cotton, David J. Harris, Grant A. Hill-Cawthorne, Stephanie Könen‐Waisman, Sophia M. Latham, Tobias Mourier, Rebecca Norton, Michael A. Quail, Mandy Sanders, Dhanasekaran Shanmugam, Amandeep Sohal, James D. Wasmuth, Brian P. Brunk, Michael E. Grigg, Jonathan C. Howard, John Parkinson, David S. Roos, A. J. Trees, Matthew Berriman, Arnab Pain, Jonathan M. Wastling
Software Mentions: 5
Published: over 14 years ago

10.3390/jcm9092730

Metastatic Burden Defines Clinically and Biologically Distinct Subgroups of Stage 4 High-Risk Neuroblastoma
Cited by: 2
Author(s): Eun Seop Seo, Eun-Jin Lee, Boram Lee, Min Jae Shin, Young-Seok Cho, Hee Young Ju, Hee Won Cho, Hee Young Ju, Keon Hee Yoo, Hong Hoe Koo, Ji Won Lee, Ki Woong Sung
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.ppat.1008221

PDGFRA defines the mesenchymal stem cell Kaposi’s sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment
Cited by: 23
Author(s): Julián Naipauer, Santas Rosario, Sachin Gupta, Courtney Premer, Omayra Méndez-Solís, Mariana Schlesinger, Virginia Ponzinibbio, Vaibhav Jain, Rolf Renne, Ho Lam Chan, Lluís Morey, Daria Salyakina, Martı́n C. Abba, Siôn L. Williams, Joshua M. Hare, Pascal J. Goldschmidt‐Clermont, Enrique A. Mesri
Software Mentions: 5
Published: over 6 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

10.7554/eLife.14997

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons
Cited by: 326
Author(s): Mark S. Cembrowski, Lihua Wang, Ken Sugino, Brenda C. Shields, Nelson Spruston
Software Mentions: 5
Published: over 10 years ago

10.1111/tpj.14299

Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat
Cited by: 46
Author(s): Xiaoming Wang, Siyuan Chen, Song Xue, Danni Liu, Peng Zhao, Yunze Lu, Yanbing Cheng, Zhenshan Liu, Xiaojun Nie, Weining Song, Qixin Sun, Shengbao Xu, Chuang Ma
Software Mentions: 4
Published: over 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

10.1007/s11105-017-1032-4

Drought-Tolerant Brassica rapa Shows Rapid Expression of Gene Networks for General Stress Responses and Programmed Cell Death Under Simulated Drought Stress
Cited by: 25
Author(s): Yi Guo, Birgit Samans, Sheng Chen, Kidist B. Kibret, Sarah Hatzig, Neil C. Turner, Matthew N. Nelson, Wallace Cowling, Rod J. Snowdon
Software Mentions: 4
Published: over 9 years ago

10.1186/s13742-015-0046-9

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing
Cited by: 118
Author(s): Vikas Gupta, April D Estrada, Ivory C. Blakley, Robert W. Reid, Ketan Patel, Mason D. Meyer, Stig Uggerhøj Andersen, Allan Brown, Mary Ann Lila, Ann E. Loraine
Software Mentions: 4
Published: over 11 years ago

10.1186/s13073-014-0059-5

A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD
Cited by: 21
Author(s): Peter K. Davidsen, John Herbert, Philipp Antczak, Kim Clarke, Elisabet Ferrer, Víctor I. Peinado, C. González, Josep Roca, Stuart Egginton, Joan Albert Barberà, Francesco Falciani
Software Mentions: 4
Published: about 12 years ago

10.3390/plants10040669

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Cited by: 4
Author(s): Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela J. Green, Senthil Subramanian, Anne Fennell
Software Mentions: 4
Published: over 5 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

10.1093/gigascience/gix109

Genome sequence of the small brown planthopper, Laodelphax striatellus
Cited by: 90
Author(s): Jiachen Zhu, Feng Jiang, Xianhui Wang, Pengcheng Yang, Yan-Yuan Bao, Wan Zhao, Wei Wang, Hong Liang, Qianshuo Wang, Na Cui, Jing Li, Xiaofang Chen, Luo Li, Jianping Yu, Le Kang, Feng Cui
Software Mentions: 4
Published: almost 9 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

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: over 10 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

10.1186/s13059-021-02444-6

Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network
Cited by: 12
Author(s): Zhonghua Du, Wei Xue, Yichen Wang, Lin Jia, Shilin Zhang, Yudi Liu, Lei Zhou, Hui Li, Yang Wang, Cong Wang, Jingcheng Chen, Yajing Hao, Daniela Salgado Figueroa, Huiling Chen, Dan Li, Naifei Chen, Ilkay Celik, Yanbo Zhu, Zi Yan, Changhao Fu, Shanshan Liu, Benzheng Jiao, Zhuo Wang, Hui Zhang, Günhan Gülsoy, Jianjun Luo, Baoming Qin, Sujun Gao, Philipp Kapranov, Miguel A. Esteban, Songling Zhang, Wei Li, Ferhat Ay, Runsheng Chen, Andrew R. Hoffman, Jiuwei Cui, Ji-Fan Hu
Software Mentions: 4
Published: about 5 years ago

10.1093/gbe/evy188

Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence
Cited by: 17
Author(s): Larissa Calarco, Joel Barratt, John Ellis
Software Mentions: 4
Published: about 8 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/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