10.1186/s12915-020-00945-7

Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles
Cited by: 8
Author(s): Hao‐Sen Li, Xiaowen Tang, Yu‐Hao Huang, Zhennan Xu, Meilan Chen, Xue‐Yong Du, Bo-Yuan Qiu, Pei‐Tao Chen, Wei Zhang, Adam Ślipiński, Hermes E. Escalona, Robert M. Waterhouse, Andreas Zwick
Software Mentions: 4
Published: over 5 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

10.1093/gigascience/giy101

The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation
Cited by: 56
Author(s): Conghui Liu, Yan Zhang, Yingxue Ren, Hengchao Wang, Shuqu Li, Fan Jiang, Lei Yin, Xi Qiao, Guojie Zhang, Wanqiang Qian, Bo Liu, Wei Fan
Software Mentions: 4
Published: about 8 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

10.3390/jcm8081158

Role of MYC-miR-29-B7-H3 in Medulloblastoma Growth and Angiogenesis
Cited by: 29
Author(s): Ian J. Purvis, Avilala Janardhan, Maheedhara R. Guda, Sujatha Venkataraman, Rajeev Vibhakar, Andrew J. Tsung, Kiran Kumar Velpula, Swapna Asuthkar
Software Mentions: 4
Published: about 7 years ago

10.1186/s12915-018-0569-5

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

10.1371/journal.pone.0141910

Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?
Cited by: 25
Author(s): Shanrong Zhao, Li Xi, Baohong Zhang
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-017-00823-3

Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish
Cited by: 11
Author(s): Lei Wang, Xiao Ma, Xiaolei Xu, Yuji Zhang
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1008661

An integrated analysis of cell-type specific gene expression reveals genes regulated by REVOLUTA and KANADI1 in the Arabidopsis shoot apical meristem
Cited by: 15
Author(s): Hasthi Ram, Sudeep Sahadevan, Nittaya Gale, Monica Pia Caggiano, Xiulian Yu, Carolyn Ohno, Marcus G. Heisler
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-14-283

Unscrambling butterfly oogenesis
Cited by: 38
Author(s): Jean-Michel Carter, Susan C. Baker, Ryan C. Pink, David R. F. Carter, Aiden Collins, Jeremie Tomlin, Melanie Gibbs, Casper J. Breuker
Software Mentions: 4
Published: over 13 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

10.1093/aobpla/ply013

Patterns of alternative splicing vary between species during heat stress
Cited by: 25
Author(s): Sumetha Kannan, Gillian Halter, Tanya Renner, Elizabeth R. Waters
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-020-01973-w

Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
Cited by: 27
Author(s): Xin Liu, Yong Chen, Yuannyu Zhang, Nan Liu, Giovanni A. Botten, Hui Cao, Stuart H. Orkin, Michael Q. Zhang, Jian Xu
Software Mentions: 4
Published: over 6 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

10.1371/journal.pone.0147221

Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics
Cited by: 36
Author(s): Robert A. Syme, Kar‐Chun Tan, James K. Hane, Kejal N Dodhia, Thomas Stoll, Marcus L. Hastie, Eiko Furuki, Simon R. Ellwood, Angela H. Williams, Yew‐Foon Tan, Alison C. Testa, Jeffrey J. Gorman, Richard P. Oliver
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-018-1551-9

Alternative polyadenylation factors link cell cycle to migration
Cited by: 21
Author(s): Mithun Mitra, Elizabeth L. Johnson, Vinay Swamy, Lois E Nersesian, David C. Corney, David G. Robinson, Daniel Taylor, Aaron M. Ambrus, David Jelínek, Wei Wang, Sandra Batista, Hilary A. Coller
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-015-1308-8

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
Cited by: 109
Author(s): Shanrong Zhao, Baohong Zhang
Software Mentions: 4
Published: over 11 years ago

10.1186/s12887-019-1564-x

Study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation
Cited by: 22
Author(s): Najeeha Talat Iqbal, Sana Syed, Kamran Sadiq, Marium Khan, Junaid Iqbal, Z. Jennie, Fayaz Umrani, Sheraz Ahmed, Elizabeth A. Maier, Lee A. Denson, Yael Haberman, Monica McNeal, Kenneth D.R. Setchell, Xueheng Zhao, Shahida Qureshi, Lanlan Shen, Christopher A. Moskaluk, Ta‐Chiang Liu, Ömer H. Yılmaz, Donald E. Brown, Michael J. Barratt, Vanderlene L. Kung, Jeffrey I. Gordon, Sean R. Moore, Syed Asad Ali
Software Mentions: 4
Published: about 7 years ago

10.1186/s13059-019-1686-3

Whole genomes and transcriptomes reveal adaptation and domestication of pistachio
Cited by: 71
Author(s): Lin Zeng, Xiaolong Tu, He Dai, Fengming Han, LU Bing-she, Ming-Shan Wang, Hojjat Asadollahpour Nanaei, Ali Tajabadipour, Mehdi Mansouri, Xiaolong Li, Lili Ji, David M. Irwin, Zhou Hong, Min Liu, Hongkun Zheng, Ali Esmailizadeh, Dong‐Dong Wu
Software Mentions: 4
Published: over 7 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

10.1186/1471-2164-15-221

From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism
Cited by: 119
Author(s): Inès Zouari, Alessandra Salvioli, Matteo Chialva, Mara Novero, Laura Miozzi, Gian Carlo Tenore, Paolo Bagnaresi, Paola Bonfante
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pgen.1004261

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
Cited by: 329
Author(s): Guilhem Janbon, Kate L. Ormerod, Damien Paulet, Edmond J. Byrnes, Vikas Yadav, Gautam Chatterjee, Nandita Mullapudi, Chung-Chau Hon, R. Blake Billmyre, François Brunel, Yong-Sun Bahn, Weidong Chen, Yuan Chen, Eve W. L. Chow, Jean Yves Coppée, Anna Floyd-Averette, Claude Gaillardin, Kimberly J. Gerik, Jonathan M. Goldberg, Sara Gonzalez-Hilarion, Sharvari Gujja, Joyce L. Hamlin, Yu-Ting Hsueh, Giuseppe Ianiri, Steven J.M. Jones, Chinnappa D. Kodira, Lukasz Kozubowski, Woei C. Lam, Marco A. Marra, Larry D. Mesner, Piotr A. Mieczkowski, Frédérique Moyrand, Kirsten Nielsen, Caroline Proux, Tristan Rossignol, Jacqueline E. Schein, Sheng Sun, Carolin Wollschlaeger, Ian Wood, Qiandong Zeng, Cécile Neuvéglise, Carol S. Newlon, John R. Perfect, Jennifer K. Lodge, Alexander Idnurm, Jason E. Stajich, James W. Kronstad, Kaustuv Sanyal, Joseph Heitman, James A. Fraser, Christina A. Cuomo, Fred S. Dietrich
Software Mentions: 4
Published: over 12 years ago

10.1186/s13059-018-1416-2

Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
Cited by: 135
Author(s): Ji Dong, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Yunuo Mao, Boqiang Hu, Hongshan Guo, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-017-1290-3

A tandem simulation framework for predicting mapping quality
Cited by: 14
Author(s): Ben Langmead
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pgen.1009512

The actin nucleation factors JMY and WHAMM enable a rapid Arp2/3 complex-mediated intrinsic pathway of apoptosis
Cited by: 11
Author(s): Virginia L King, Nathan K. Leclair, Alyssa Coulter, Kenneth Campellone
Software Mentions: 4
Published: over 5 years ago

10.1093/jxb/erw006

Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis
Cited by: 32
Author(s): Xia Zhang, Candice N. Hirsch, Rajandeep S. Sekhon, Natalia de León, Shawn M. Kaeppler
Software Mentions: 4
Published: over 10 years ago

10.1186/s12870-020-2268-y

Modulation of volatile compound metabolome and transcriptome in grape berries exposed to sunlight under dry-hot climate
Cited by: 24
Author(s): Lei He, Xiaoqing Xu, Yu Wang, Wei-Kai Chen, Ruonan Sun, Guodong Cheng, Bin Liu, Changyong Wu, Chang‐Qing Duan, Jun Wang, Qiu-Hong Pan
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0192613

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples
Cited by: 17
Author(s): Hua Yu, Bingke Jiao, Lu Lu, Pengfei Wang, Shuangcheng Chen, Chengzhi Liang, Wei Liu
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1004890

Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation
Cited by: 41
Author(s): Jacob C. Ulirsch, Jessica Lacy, Xiuli An, Narla Mohandas, Tarjei S. Mikkelsen, Vijay G. Sankaran
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1005184

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans
Cited by: 111
Author(s): Li Zhao, Janneke Wit, Nicolas Svetec, David J. Begun
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-021-88363-9

Transcriptional signatures in prefrontal cortex confer vulnerability versus resilience to food and cocaine addiction-like behavior
Cited by: 11
Author(s): Mohit Navandar, Elena Martín‐García, Rafaël Maldonado, Beat Lutz, Susanne Gerber, Iñigo Ruı́z de Azúa
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1004924

The Genetic Architecture of the Genome-Wide Transcriptional Response to ER Stress in the Mouse
Cited by: 29
Author(s): Clement Y. Chow, Xiaozhu Wang, David D. Riccardi, Mariana F. Wolfner, Andrew G. Clark
Software Mentions: 4
Published: over 11 years ago

10.3390/antiox9050402

Long Non-Coding RNA and mRNA Profiling in Early-Stage Bovine Embryos Treated with Glutathione
Cited by: 1
Author(s): Qihao Guo, Linlin Cui, Weijun Sun, Li Feng, Hao Huang, Xueming Zhao, Huabin Zhu, Weihua Du
Software Mentions: 4
Published: over 6 years ago

10.1186/s12870-021-03057-8

Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper
Cited by: 4
Author(s): Myung-Shin Kim, Geun Young Chae, Soohyun Oh, Jihyun Kim, Hyunggon Mang, Seungill Kim, Doil Choi
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-016-0932-1

Single-cell analysis of long non-coding RNAs in the developing human neocortex
Cited by: 291
Author(s): Siyuan John Liu, Tomasz J. Nowakowski, Alex A. Pollen, Jan H. Lui, Max A. Horlbeck, Frank J. Attenello, Daniel He, Jonathan S. Weissman, Arnold R. Kriegstein, Aaron A. Diaz, Daniel A. Lim
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0175528

The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown
Cited by: 61
Author(s): Shingo Miyauchi, David Navarro, Sacha Grisel, Didier Chevret, Jean‐Guy Berrin, Marie Noelle Rosso
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1006464

Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages
Cited by: 52
Author(s): Lauren Gibilisco, Qi Zhou, Shivani Mahajan, Doris Bachtrog
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13059-016-1088-8

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface
Cited by: 214
Author(s): Duane D. McKenna, Erin D. Scully, Yannick Pauchet, Kelli Hoover, Roy Kirsch, Scott M. Geib, Robert F. Mitchell, Robert M. Waterhouse, Seung‐Joon Ahn, Deanna Arsala, Joshua B. Benoit, Heath Blackmon, Tiffany Bledsoe, Julia H. Bowsher, André Busch, Bernarda Calla, Hsu Chao, Anna K. Childers, Christopher P. Childers, Dave J. Clarke, Lorna Cohen, Jeffery P. Demuth, Huyen Dinh, Harshavardhan Doddapaneni, Amanda Dolan, Jian J. Duan, Shannon Dugan, Markus Friedrich, Karl M. Glastad, Michael A. D. Goodisman, Stéphanie Haddad, Yi Han, Daniel Hughes, Panagiotis Ioannidis, J. Spencer Johnston, Jeffery W. Jones, Leslie A. Kuhn, D. R. Lance, Chien Yueh Lee, Sandra L. Lee, Han Lin, Jeremy A. Lynch, Armin P. Moczek, Shwetha C. Murali, Donna M. Muzny, David R. Nelson, Subba Reddy Palli, Kristen A. Panfilio, Dan Pers, Monica F. Poelchau, Honghu Quan, Jiaxin Qu, Anandasankar Ray, Joseph P. Rinehart, Hugh M. Robertson, Richard L. Roehrdanz, Andrew J. Rosendale, Seunggwan Shin, Christian Silva, Alex S. Torson, Iris M. Vargas Jentzsch, John H. Werren, Kim C. Worley, George D. Yocum, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0191564

Study of formation of green eggshell color in ducks through global gene expression
Cited by: 4
Author(s): Fa Xu, Ang Li, Jing Lan, Yue Ming Wang, Mengmeng Yan, Sen Lian, Xu Wu
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1002658

Dynamic Deposition of Histone Variant H3.3 Accompanies Developmental Remodeling of the Arabidopsis Transcriptome
Cited by: 113
Author(s): Heike Wollmann, Sarah Holec, Keith Alden, Neil D. Clarke, Pierre-Étienne Jacques, Frédéric Berger
Software Mentions: 4
Published: over 14 years ago

10.1186/1471-2164-15-636

In depth annotation of the Anopheles gambiae mosquito midgut transcriptome
Cited by: 30
Author(s): Alejandro Padrón, Alvaro Molina-Cruz, Mariam Quiñones, José M. C. Ribeiro, Urvashi N. Ramphul, Janneth Rodrigues, Kui Shen, Ashley Haile, José L. Ramirez, Carolina Barillas‐Mury
Software Mentions: 4
Published: about 12 years ago

10.1186/s13059-015-0746-6

Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
Cited by: 74
Author(s): Adler R. Dillman, Marissa Macchietto, Camille F. Porter, Alicia K. Rogers, Brian A. Williams, Igor Antoshechkin, Ming Min Lee, Z. Goodwin, Xiaojun Lu, Edwin E. Lewis, Heidi Goodrich-Blair, S. Patricia Stock, Byron J. Adams, Paul W. Sternberg, A Mortazavi
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pgen.1004953

Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling
Cited by: 73
Author(s): Kazunari Nozue, An V. Tat, Upendra Kumar Devisetty, Matthew C. Robinson, Maxwell R. Mumbach, Yasunori Ichihashi, Saradadevi Lekkala, Julin N. Maloof
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1007087

Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases
Cited by: 64
Author(s): Zarko Manojlovic, Austin Christofferson, Winnie S. Liang, Jessica Aldrich, Megan Washington, Shukmei Wong, Daniel C. Rohrer, Scott D. Jewell, Rick A. Kittles, Mary DeRome, Daniel Auclair, David W. Craig, Jonathan J. Keats, John D. Carpten
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13059-015-0671-8

An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
Cited by: 76
Author(s): Alaguraj Veluchamy, Achal Rastogi, Xin Lin, Bérangère Lombard, Omer Murik, Y. Thomas, Florent Dingli, Máximo Rivarola, Sandra Ott, Xinyue Liu, Yan Sun, Pablo D. Rabinowicz, James S. McCarthy, Andrew E. Allen, Damarys Loew, Chris Bowler, Leïla Tirichine
Software Mentions: 4
Published: over 11 years ago

10.1186/1752-0509-7-S5-S1

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer
Cited by: 68
Author(s): Akshata R. Udyavar, Megan D. Hoeksema, Jonathan E. Clark, Yong Zou, Zuojian Tang, Zhiguo Li, Ming Li, Heidi Chen, Alexander Statnikov, Yu Shyr, Daniel C. Liebler, John K. Field, Rosana Eisenberg, Lourdes Estrada, Pierre P. Massion, Vito Quaranta
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pgen.1005869

The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster
Cited by: 44
Author(s): Nicolas Svetec, Julie M. Cridland, Li Zhao, David J. Begun
Software Mentions: 4
Published: over 10 years ago

10.1186/1755-8794-7-32

Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers
Cited by: 45
Author(s): Zhifu Sun, Liang Wang, Bruce W. Eckloff, Bo Deng, Yi Wang, Jason A. Wampfler, Jiseon Jang, Eric D. Wieben, Jin Jen, Ming You, Ping Yang
Software Mentions: 4
Published: over 12 years ago

10.1186/s13059-015-0590-8

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population
Cited by: 175
Author(s): Amelia Hubbard, Clare M. Lewis, Kentaro Yoshida, Ricardo H. Ramírez-González, C. de Vallavieille‐Pope, Jane Thomas, Sophien Kamoun, R. A. Bayles, Cristóbal Uauy, Diane G. O. Saunders
Software Mentions: 4
Published: over 11 years ago

10.1186/s13059-015-0825-8

Loss of function of myosin chaperones triggers Hsf1-mediated transcriptional response in skeletal muscle cells
Cited by: 26
Author(s): Christelle Etard, Olivier Armant, Urmas Roostalu, Victor Gourain, Marco Ferg, Uwe Strähle
Software Mentions: 4
Published: almost 11 years ago

10.1186/s13059-016-1146-2

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
Cited by: 148
Author(s): Jonas Paulsen, Monika Sekelja, Anja R. Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L. Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1006295

Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster
Cited by: 35
Author(s): Hangnoh Lee, Dong-Yeon Cho, Cale Whitworth, Robert C. Eisman, Melissa A. S. Phelps, John Roote, Thomas C. Kaufman, Kevin R. Cook, Steven Russell, Teresa M. Przytycka, Brian Oliver
Software Mentions: 4
Published: about 10 years ago

10.1186/s13059-014-0513-0

TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator
Cited by: 120
Author(s): Ya-Ping Tsai, Hsiao-Fan Chen, Sung-Yuan Chen, Wei‐Chung Cheng, Hsei‐Wei Wang, Zih-Jie Shen, Chun-Xiao Song, Shan-Yuan Teng, Chuan He, Kou-Juey Wu
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pgen.1004824

Microevolution of Candida albicans in Macrophages Restores Filamentation in a Nonfilamentous Mutant
Cited by: 64
Author(s): Anja Wartenberg, Jörg Linde, Ronny Martin, Maria Schreiner, Fabian Horn, Ilse D. Jacobsen, Sabrina Jenull, Thomas Wolf, Karl Kuchler, Reinhard Guthke, Oliver Kurzai, Anja Forche, Christophe d’Enfert, Sascha Brunke, Bernhard Hube
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12864-019-5775-1

Translation of upstream open reading frames in a model of neuronal differentiation
Cited by: 25
Author(s): Caitlin M. Rodriguez, Sang-Young Chun, Ryan E. Mills, Peter K. Todd
Software Mentions: 4
Published: over 7 years ago

10.1186/s13059-014-0536-6

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning
Cited by: 41
Author(s): Sarah D. Diermeier, Petros Kolovos, Leonhard Heizinger, Uwe Schwartz, Theodore Georgomanolis, Anne Zirkel, Gero Wedemann, Frank Grosveld, Tobias Knoch, Rainer Merkl, Peter R. Cook, Gernot Längst, Argyris Papantonis
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pgen.1006828

p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate
Cited by: 34
Author(s): Rose Richardson, Karen S. Mitchell, Nigel L. Hammond, Maria Rosaria Mollo, Evelyn N. Kouwenhoven, Niki Wyatt, Ian J. Donaldson, Leo Zeef, Tim Burgis, Rognvald Blance, Simon J. van Heeringen, Hendrik G. Stunnenberg, Huiqing Zhou, Caterina Missero, Rose Anne Romano, Satrajit Sinha, Michael J. Dixon, Jill Dixon
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-15-899

Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding season
Cited by: 40
Author(s): Ran Di, Jianning He, Shuhui Song, Dongmei Tian, Qiuyue Liu, Xiaojun Liang, Qing Ma, Min Sun, Jiandong Wang, Wenming Zhao, G. L. Cao, Jinxin Wang, Ziyin Yang, Ying Ge, Mingxing Chu
Software Mentions: 4
Published: almost 12 years ago

10.6026/97320630013249

Identification of long non-coding RNA in rice lines resistant to Rice blast pathogen Maganaporthe oryzae
Cited by: 33
Author(s): Priyanka Jain, Vinay Sharma, Himanshu Dubey, Pankaj Kumar Singh, Ritu Kapoor, Mandeeep Kumari, Jaya Singh, Deepak Pawar, Deepak Singh Bisht, Amolkumar U. Solanke, Tapan Kumar Mondal, Tilak Raj Sharma
Software Mentions: 4
Published: about 9 years ago

10.1093/bioinformatics/bty125

AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes
Cited by: 28
Author(s): Wanseon Lee, Katharine Plant, Peter Humburg, Julian C. Knight
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-015-0460-0

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data
Cited by: 20
Author(s): Wuming Gong, Naoko Koyano-Nakagawa, Tongbin Li, Daniel J. Garry
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1008797

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

10.1371/journal.pone.0187625

RNA-Seq analysis reveals insight into enhanced rice Xa7-mediated bacterial blight resistance at high temperature
Cited by: 46
Author(s): Stephen P. Cohen, Hongxia Liu, Cristiana T. Argueso, Andy Pereira, Casiana Vera Cruz, Valérie Verdier, Jan E. Leach
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.08384

Signal transducer and activator of transcription 5 (STAT5) paralog dose governs T cell effector and regulatory functions
Cited by: 69
Author(s): Alejandro V. Villarino, Gertraud W. Robinson, Michael Bonelli, Bárbara Dema, Behdad Afzali, Han-Yu Shih, Hongwei Sun, Stephen R. Brooks, Lothar Hennighausen, Yuka Kanno, John J. O’Shea
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-014-0410-6

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

10.1186/gb-2013-14-3-r28

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
Cited by: 272
Author(s): H. Bradley Shaffer, Patrick Minx, Daniel E. Warren, Andrew M. Shedlock, Robert C. Thomson, Nicole Valenzuela, John Abramyan, Chris T. Amemiya, Daleen Badenhorst, Kyle K. Biggar, Glen M. Borchert, Christopher W. Botka, Rachel M. Bowden, Edward L. Braun, Anne M. Bronikowski, Benoit G. Bruneau, Leslie T. Buck, Blanche Capel, Todd A. Castoe, Michael Czerwinski, Kim D. Delehaunty, Scott V. Edwards, Catrina C. Fronick, Matthew K. Fujita, Lucinda A. Fulton, Tina Graves, Edward Green, Wilfried Haerty, Ramkumar Hariharan, Omar Hernández, LaDeana W. Hillier, Alisha K. Holloway, Daniel E. Janes, Fredric J. Janzen, Cyriac Kandoth, Lesheng Kong, A. P. Jason de Koning, Yang Li, Robert Literman, Suzanne E. McGaugh, Lindsey Mork, Michelle O’Laughlin, Ryan T. Paitz, David D. Pollock, Chris P. Ponting, S. Radhakrishnan, Brian J. Raney, Joy M. Richman, John St. John, Tonia S. Schwartz, Arun Sethuraman, Phillip Q. Spinks, Kenneth B. Storey, Nay Thane, Tomáš Vinař, Laura M. Zimmerman, Wesley C. Warren, Elaine R. Mardis, Richard K. Wilson
Software Mentions: 4
Published: over 13 years ago

10.1186/s12864-018-5115-x

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia
Cited by: 19
Author(s): Bi Jun Li, Dan Jiang, Zhijun Meng, Yong Zhang, Zong Xian Zhu, Haoran Lin, Jun Xia
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-015-2270-1

Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis
Cited by: 66
Author(s): Wenli Li, Amy Turner, Praful Aggarwal, Andrea Matter, Erin Storvick, Donna K. Arnett, Ulrich Broeckel
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pgen.1007498

Cyclin G and the Polycomb Repressive complexes PRC1 and PR-DUB cooperate for developmental stability
Cited by: 7
Author(s): Delphine Dardalhon-Cuménal, Jérôme Deraze, Camille Dupont, Valérie Ribeiro, Anne Coléno-Costes, Juliette Pouch, Stéphane Le Crom, Hélène Thomassin, Vincent Debat, Neel B. Randsholt, Frédérique Peronnet
Software Mentions: 4
Published: about 8 years ago

10.1186/gb-2013-14-4-r31

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
Cited by: 368
Author(s): Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D. Uno, Takeshi Imai, Hiroki R. Ueda
Software Mentions: 4
Published: over 13 years ago

10.1186/s12864-016-2618-1

Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage
Cited by: 107
Author(s): Irene da Cruz, Rosana Rodríguez-Casuriaga, Federico F. Santiñaque, Joaquina Farías, Gianni Curti, Carlos A. Capoano, Gustavo A. Folle, Ricardo Benavente, José Sotelo‐Silveira, Adriana Geisinger
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pgen.1006589

Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression
Cited by: 52
Author(s): Thomas Stricker, Christopher D. Brown, Chaitanya Bandlamudi, Megan E. McNerney, Ralf Kittler, Vanessa Montoya, April Peterson, Robert L. Grossman, Kevin P. White
Software Mentions: 4
Published: over 9 years ago

10.1186/gb-2014-15-2-r34

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Cited by: 230
Author(s): Steve Hoffmann, Christian Otto, Gero Doose, Andrea Tanzer, David Langenberger, Sabina Christ, Manfred Kunz, Lesca M. Holdt, Daniel Teupser, Jörg Hackermüller, Peter F. Stadler
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-016-2950-5

The influence of trematode parasite burden on gene expression in a mammalian host
Cited by: 9
Author(s): Bhagya K. Wijayawardena, Dennis J. Minchella, J. Andrew DeWoody
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pgen.1005619

Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection
Cited by: 18
Author(s): Musa A. Hassan, Kirk D. C. Jensen, Vincent Butty, Kenneth H. Hu, Erwan Boedec, Pjotr Prins, Jeroen P. J. Saeij
Software Mentions: 4
Published: almost 11 years ago

10.1186/gb-2013-14-12-r146

Lsh regulates LTR retrotransposon repression independently of Dnmt3b function
Cited by: 53
Author(s): Donncha S. Dunican, Hazel A Cruickshanks, Masako Suzuki, Colin A. Semple, Tracey Davey, Robert J. Arceci, John M. Greally, Ian R. Adams, Richard R. Meehan
Software Mentions: 4
Published: over 13 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/gb-2013-14-11-r131

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
Cited by: 162
Author(s): Ana C. Marques, Jim R. Hughes, Bryony Graham, Monika S. Kowalczyk, Douglas R. Higgs, Chris P. Ponting
Software Mentions: 4
Published: over 13 years ago

10.1186/gb-2012-13-10-r88

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
Cited by: 72
Author(s): Alok K. Tewari, Galip Gürkan Yardımcı, Yoichiro Shibata, Nathan C. Sheffield, Lingyun Song, Barry S. Taylor, Stoyan Georgiev, Gerhard A. Coetzee, Uwe Ohler, Terrence S. Furey, Gregory E. Crawford, Phillip G. Febbo
Software Mentions: 4
Published: over 14 years ago

10.7554/eLife.36998

Downregulation of ribosome biogenesis during early forebrain development
Cited by: 63
Author(s): Kevin F. Chau, Morgan L. Shannon, Ryann M. Fame, Erin Fonseca, Hillary Mullan, Matthew B. Johnson, Anoop K. Sendamarai, Mark W. Springel, Laurent Beaugerie, Maria K. Lehtinen
Software Mentions: 4
Published: over 8 years ago

10.3390/genes11030345

Arabidopsis thaliana MLK3, a Plant-Specific Casein Kinase 1, Negatively Regulates Flowering and Phosphorylates Histone H3 In Vitro
Cited by: 12
Author(s): Junmei Kang, Huiting Cui, Shangang Jia, Wenwen Liu, Renjie Yu, Zhihai Wu, Zhen Wang
Software Mentions: 4
Published: over 6 years ago

10.3390/genes12020203

Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in Australia
Cited by: 8
Author(s): Marnie J. Hodge, Sara de las Heras‐Saldana, Sally J. Rindfleish, Cyril Stephen, Sameer D. Pant
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms19041140

Aging and Intermittent Fasting Impact on Transcriptional Regulation and Physiological Responses of Adult Drosophila Neuronal and Muscle Tissues
Cited by: 14
Author(s): Sharon Zhang, Eric P. Ratliff, Brandon Molina, Nadja El-Mecharrafie, Jessica Mastroianni, Roxanne W. Kotzebue, Madhulika Achal, Ruth E. Mauntz, Arysa Gonzalez, Ayeh Barekat, William A. Bray, Andrew M Macias, Daniel J. Daugherty, Greg L. Harris, Robert A. Edwards, Kim D. Finley
Software Mentions: 4
Published: over 8 years ago

10.1186/gb-2014-15-2-r21

Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans
Cited by: 46
Author(s): Cristina González-Aguilera, Kohta Ikegami, Cristina de la Cruz Ayuso, Alberto de Luis, María Íñiguez, Juan Cabello, Jason D. Lieb, Peter Askjaer
Software Mentions: 4
Published: over 12 years ago

10.3389/fpls.2020.574982

Metabolic, Enzymatic Activity, and Transcriptomic Analysis Reveals the Mechanism Underlying the Lack of Characteristic Floral Scent in Apricot Mei Varieties
Cited by: 6
Author(s): Fei Bao, Tengxun Zhang, Anqi Ding, Aiqin Ding, Weiru Yang, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpls.2020.00551

Glycosyltransferase-Like RSE1 Negatively Regulates Leaf Senescence Through Salicylic Acid Signaling in Arabidopsis
Cited by: 8
Author(s): Seulbee Lee, Myung‐Hee Kim, Jae Ho Lee, Jieun Jeon, June M. Kwak, Yun Ju Kim
Software Mentions: 4
Published: over 6 years ago

10.3390/genes9120574

A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women
Cited by: 25
Author(s): Kadri Rekker, Signe Altmäe, Marina Suhorutshenko, Maire Peters, Juan F. Martínez-Blanch, Francisco M. Codoñer, Felipe Vilella, Carlos Simón, Andres Salumets, Agne Velthut-Meikas
Software Mentions: 4
Published: almost 8 years ago

10.3389/fpls.2020.589005

Elucidation of the miR164c-Guided Gene/Protein Interaction Network Controlling Seed Vigor in Rice
Cited by: 5
Author(s): Kerui Huang, Shiqi Zhou, Kaimin Shen, Yan Zhou, Feng Wang, Xiaocheng Jiang
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-15-845

Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data
Cited by: 66
Author(s): Kunshan Zhang, Kefei Huang, Yuan Luo, Siguang Li
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pbio.1001126

Sex Chromosome-Specific Regulation in the Drosophila Male Germline But Little Evidence for Chromosomal Dosage Compensation or Meiotic Inactivation
Cited by: 123
Author(s): Colin D. Meiklejohn, Emily L. Landeen, Jodi M. Cook, Sarah B. Kingan, Daven C. Presgraves
Software Mentions: 4
Published: about 15 years ago

10.1016/j.celrep.2018.07.026

Fine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic Reprogramming
Cited by: 16
Author(s): Carl Ward, Giacomo Volpe, Pierre Cauchy, Anetta Ptasińska, Ruba Almaghrabi, Daniel Blakemore, Monica Nafria, Doris Kestner, Jon Frampton, George J. Murphy, Yosef Buganim, Keisuke Kaji, Paloma García
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-016-3442-3

Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening
Cited by: 65
Author(s): Qianglong Zhu, Shi Liu, Zhu Zhang, Sikandar Amanullah, Angela R. Davis, Feishi Luan
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pbio.3000382

LATS1/2 suppress NFκB and aberrant EMT initiation to permit pancreatic progenitor differentiation
Cited by: 19
Author(s): Caitlin M. Braitsch, D. Berfin Azizoglu, Yadanar Htike, Haley R. Barlow, Ulrike Schnell, Christopher Chaney, Thomas J. Carroll, Ben Z. Stanger, Ondine Cleaver
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms22020574

The Resistance of Narrow-Leafed Lupin to Diaporthe toxica Is Based on the Rapid Activation of Defense Response Genes
Cited by: 7
Author(s): Michał Książkiewicz, Sandra Rychel-Bielska, Piotr Plewiński, Maria Nuc, Witold Irzykowski, M. Jędryczka, Paweł Krajewski
Software Mentions: 4
Published: over 5 years ago

10.1155/2018/3028290

Stress-Adaptive Responses Associated with High-Level Carbapenem Resistance in KPC-ProducingKlebsiella pneumoniae
Cited by: 4
Author(s): Sheila Adams‐Sapper, Adam Gayoso, Lee W. Riley
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2018.00005

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching
Cited by: 84
Author(s): Sergei A. Filichkin, Michael Hamilton, Palitha Dharmawardhana, Sunil Kumar Singh, Christopher Sullivan, Asa Ben‐Hur, Anireddy S. N. Reddy, Pankaj Jaiswal
Software Mentions: 4
Published: over 8 years ago

10.1186/gb-2014-15-1-r7

RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins
Cited by: 32
Author(s): Zhipeng Lu, Xiaojun Guan, Casey A. Schmidt, A. Gregory Matera
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2105-16-S17-S10

SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data
Cited by: 3
Author(s): Chong Chu, Li X, Yufeng Wu
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12864-019-5709-y

Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data
Cited by: 53
Author(s): Hamid Beiki, Haibo Li, Jinrong Huang, Nancy Manchanda, D. Nonneman, Timothy P. L. Smith, James M. Reecy, Christopher K. Tuggle
Software Mentions: 4
Published: over 7 years ago