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10.1038/s41598-020-79781-2

Novel circRNA discovery in sheep shows evidence of high backsplice junction conservation
Cited by: 7
Author(s): Endika Varela-Martínez, Giulia I. Corsi, Christian Anthon, Jan Gorodkin, Begoña M. Jugo
Software Mentions: 4
Published: over 3 years ago

10.1016/j.jmb.2019.04.043

PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants
Cited by: 19
Author(s): Tochukwu C. Ofoegbu, Alessia David, Lawrence A. Kelley, Stefans Mezulis, Suhail A. Islam, Sophia F. Mersmann, Léonie Strömich, Ilya A. Vakser, Richard S. Houlston, Michael J.E. Sternberg
Software Mentions: 4
Published: almost 5 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 6 years ago

10.1128/mBio.01650-17

De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae , the Causal Agent of Oat Crown Rust
Cited by: 45
Author(s): Marisa E. Miller, Ying Zhang, Vahid Omidvar, Jana Sperschneider, Benjamin Schwessinger, Castle Raley, Jonathan M. Palmer, Diana Garnica, Narayana M. Upadhyaya, John P. Rathjen, Jennifer Taylor, Robert Park, Peter N. Dodds, Cory D. Hirsch, Shahryar F. Kianian, Melania Figueroa
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2020.01707

Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803
Cited by: 16
Author(s): Ulysse Guyet, Ngoc-An Nguyen, Hugo Doré, Julie Haguait, Justine Pittera, Maël Conan, Morgane Ratin, Erwan Corre, Gildas Le Corguillé, Loraine Brillet-Guéguen, Mark Hoebeke, Christophe Six, Claudia Steglich, Anne Siegel, Damien Eveillard, Frédéric Partensky, Laurence Garczarek
Software Mentions: 4
Published: almost 4 years ago

10.3389/fimmu.2020.01089

IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells
Cited by: 4
Author(s): Darely Y. Gutiérrez-Reyna, Alejandra Cedillo-Baños, Linda A Kempis-Calanis, Oscar Ramírez-Pliego, Lisa Bargier, Denis Puthier, José David Abad Flores, Morgane Thomas‐Chollier, Denis Thieffry, Alejandra Medina-Rivera, Salvatore Spicuglia, María Angélica Santana
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2020.586614

Deciphering Microbial Community Dynamics and Biochemical Changes During Nyons Black Olive Natural Fermentations
Cited by: 18
Author(s): Marine Penland, Stéphanie-Marie Deutsch, Hélène Falentin, Audrey Pawtowski, Elisabeth Poirier, Giorgia Visenti, Christophe Le Meur, Marie-Bernadette Maillard, Anne Thierry, Jérôme Mounier, Monika Coton
Software Mentions: 4
Published: over 3 years ago

10.1093/database/bau076

APADB: a database for alternative polyadenylation and microRNA regulation events
Cited by: 88
Author(s): Sören Müller, Lukas Rycak, Fabian Afonso-Grunz, Peter Winter, Adam M. Zawada, Ewa Damrath, Jessica Scheider, Juliane Schmäh, Ina Koch, Günter Kahl, Björn Rotter
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2164-11-50

Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data
Cited by: 17
Author(s): Jun Yin, Sarah McLoughlin, Ian B. Jeffery, Antonino Glaviano, Breandán N. Kennedy, Desmond G. Higgins
Software Mentions: 4
Published: over 14 years ago

10.7717/peerj.2056

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals
Cited by: 9
Author(s): Yevgeny Nikolaichik, Aliaksandr U. Damienikan
Software Mentions: 4
Published: almost 8 years ago

10.1093/database/baw063

PGD: a pangolin genome hub for the research community
Cited by: 4
Author(s): Tze King Tan, Ka Yun Tan, Riitta Hari, Aini Mohamed Yusoff, George T.F. Wong, Cheuk Chuen Siow, Naresh V.R. Mutha, Mikhail Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Ian C. Paterson, Wesley C. Warren, Warren E. Johnson, Stephen J. O’Brien, Siew Woh Choo
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2105-12-447

OmniMapFree: A unified tool to visualise and explore sequenced genomes
Cited by: 12
Author(s): J. F. Antoniw, Andrew M Beacham, Tyler Baldwin, Martin Urban, J. J. Rudd, K. E. Hammond‐Kosack
Software Mentions: 4
Published: over 12 years ago

10.1093/database/bax039

GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species
Cited by: 14
Author(s): Richard Challis, Sujai Kumar, Lewis Stevens, Mark Blaxter
Software Mentions: 4
Published: over 7 years ago

10.1007/s00294-020-01096-6

Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality
Cited by: 11
Author(s): Anton Levitan, Andrew N. Gale, Emma Dallon, Darby W. Kozan, Kyle W. Cunningham, Roded Sharan, Judith Berman
Software Mentions: 4
Published: almost 4 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: about 5 years ago

10.1186/s12864-020-6687-9

Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct properties
Cited by: 2
Author(s): Jing Jin, Ximiao He, Elena M. Silva
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pbio.2003648

A direct link between MITF, innate immunity, and hair graying
Cited by: 37
Author(s): Melissa L. Harris, Temesgen Fufa, Joseph W. Palmer, Sandeep S. Joshi, Denise M. Larson, Arturo Incao, Derek Gildea, Niraj Trivedi, Autumne N Lee, Chi-Ping Day, Helen Michael, Thomas J. Hornyak, Glenn Merlino, Nisc Comparative Sequencing Program, William J. Pavan
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2164-12-S3-S9

UASIS: Universal Automatic SNP Identification System
Cited by: 5
Author(s): Danny Chiang Choon Poo, Shaojiang Cai, James T. L. Mah
Software Mentions: 4
Published: over 13 years ago

10.1186/s12915-015-0119-3

Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish
Cited by: 87
Author(s): Masato Yoshizawa, Beatriz G. Robinson, Erik R. Duboué, Pavel Mašek, James B. Jaggard, Kelly E. O’Quin, Richard Borowsky, William R. Jeffery, Alex C. Keene
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-015-1374-y

Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals
Cited by: 29
Author(s): Vincent A. Streva, Vallmer E Jordan, Sara B. Linker, Dale J. Hedges, Prescott L. Deininger
Software Mentions: 4
Published: about 9 years ago

10.1186/1471-2164-14-S8-S3

QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions
Cited by: 28
Author(s): Bin Liu, Jimmy Yi, Aishwarya Sv, Xun Lan, Yiyi Ma, Tim H.M. Huang, Gustavo Leone, Victor X. Jin
Software Mentions: 4
Published: over 10 years ago

10.1186/1471-2105-8-456

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
Cited by: 33
Author(s): J. Christopher Bare, Paul Shannon, Amy K. Schmid, Nitin S. Baliga
Software Mentions: 4
Published: over 16 years ago

10.1002/mgg3.1346

Dysregulated expression of androgen metabolism genes and genetic analysis in hypospadias
Cited by: 7
Author(s): Zhongzhong Chen, Xiaoling Lin, Yaping Wang, Hua Xie, Fang Chen
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2164-15-539

ChIPseek, a web-based analysis tool for ChIP data
Cited by: 59
Author(s): Ting-Wen Chen, Hsin Pai Li, Chi-Ching Lee, Ruei Chi Gan, Po-Jung Huang, Timothy Wu, Cheng Yang Lee, Ian Yi‐Feng Chang, Petrus Tang
Software Mentions: 4
Published: almost 10 years ago

10.1242/dev.175265

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs
Cited by: 21
Author(s): Alexandra L. McCorkindale, Philipp Wahle, Irwin Jungreis, Peter Menzel, Chinmay Shukla, Rúben Lopes Pereira Abreu, Rafael A. Irizarry, Irmtraud M. Meyer, M Kellis, Robert P. Zinzen
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-020-07100-0

Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus
Cited by: 16
Author(s): Marina Athanasouli, Hanh Witte, Christian Weiler, Tobias Loschko, Gabi Eberhardt, Ralf J. Sommer, Christian Rödelsperger
Software Mentions: 4
Published: over 3 years ago

10.1186/s12943-019-1115-y

LINC02273 drives breast cancer metastasis by epigenetically increasing AGR2 transcription
Cited by: 118
Author(s): Bingqiu Xiu, Yayun Chi, Lei Liu, Weiru Chi, Qi Zhang, Jiajian Chen, Rong Guo, Jingjing Si, Lun Li, Jian Xue, Zhi‐Ming Shao, Zhao-Hui Wu, Shenglin Huang, Jiong Wu
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms21020440

Anisotropic Platinum Nanoparticle-Induced Cytotoxicity, Apoptosis, Inflammatory Response, and Transcriptomic and Molecular Pathways in Human Acute Monocytic Leukemia Cells
Cited by: 24
Author(s): Sangiliyandi Gurunathan, M. Jeyaraj, Hyeonwoo La, Hyunjin Yoo, Youngsok Choi, Jeong Tae, Chankyu Park, Jin‐Hoi Kim, Kwonho Hong
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.9535

Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer
Cited by: 35
Author(s): Jingwen Zhao, Yu Zhao, Liguo Wang, Jun Zhang, Jeffrey Karnes, Manish Kohli, Guixia Wang, Haojie Huang
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41422-020-0281-1

Refined spatial temporal epigenomic profiling reveals intrinsic connection between PRDM9-mediated H3K4me3 and the fate of double-stranded breaks
Cited by: 34
Author(s): Yao Chen, Ruitu Lyu, Bowen Rong, Yuxuan Zheng, Zhen Lin, Ruofei Dai, Xi Zhang, Nannan Xie, Siqing Wang, Fuchou Tang, Fei Lan, Ming-Han Tong
Software Mentions: 4
Published: over 4 years ago

10.18632/aging.202365

Transcriptomic characterization reveals prognostic molecular signatures of sorafenib resistance in hepatocellular carcinoma
Cited by: 7
Author(s): Wei Yuan, Ran Tao, Da Huang, Weiming Yan, Shen Gao, Qin Ning
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms20061370

Transcriptomic Impact of IMA-08401, a Novel AHR Agonist Resembling Laquinimod, on Rat Liver
Cited by: 3
Author(s): Stephenie D. Prokopec, Raimo Pohjanvirta, Selma Mahiout, Lars Pettersson, Paul C. Boutros
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-11-74

Automated design of genomic Southern blot probes
Cited by: 6
Author(s): Mike D. R. Croning, David Fricker, Noboru H. Komiyama, Seth G. N. Grant
Software Mentions: 4
Published: over 14 years ago

10.7554/eLife.04235

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-020-3386-0

GsmPlot: a web server to visualize epigenome data in NCBI
Cited by: 2
Author(s): Jia Li, Yue Yin, Mutian Zhang, Jie Cui, Zhenhai Zhang, Zhiyong Zhang, Deqiang Sun
Software Mentions: 4
Published: over 4 years ago

10.1186/s13100-021-00235-1

Genomic properties of variably methylated retrotransposons in mouse
Cited by: 13
Author(s): Jessica L. Elmer, Amir D. Hay, Noah J. Kessler, Tessa M. Bertozzi, Eve Ainscough, Anne C. Ferguson-Smith
Software Mentions: 4
Published: about 3 years ago

10.1186/s12859-020-03565-8

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
Cited by: 22
Author(s): Tiziana Castrignanò, Silvia Gioiosa, Tiziano Flati, Mirko Cestari, Ernesto Picardi, Matteo Chiara, Maddalena Fratelli, Stefano Amente, Marco Cirilli, M. A. Tangaro, Giovanni Chillemi, Graziano Pesole, Federico Zambelli
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.celrep.2013.08.012

In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency
Cited by: 95
Author(s): George E. Gentsch, Nick Owens, Stephen R. Martin, Paul Piccinelli, Tiago Faial, Matthew Trotter, Michael J. Gilchrist, James C. Smith
Software Mentions: 4
Published: over 10 years ago

10.1038/s41421-020-00218-1

3D landscape of Hepatitis B virus interactions with human chromatins
Cited by: 20
Author(s): Bo Yang, Boyuan Li, Lingfei Jia, Yongpeng Jiang, Xin Wang, Shaodong Jiang, Shunda Du, Ji Xiong, Pengyuan Yang
Software Mentions: 4
Published: over 3 years ago

10.1186/s13075-015-0677-3

Use of RNA sequencing to evaluate rheumatic disease patients
Cited by: 23
Author(s): Ευγενία Γιαννοπούλου, Olivier Elemento, Lionel B. Ivashkiv
Software Mentions: 4
Published: almost 9 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: almost 6 years ago

10.7554/eLife.08904

Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals
Cited by: 57
Author(s): Alex de Mendoza, Hiroshi Suga, Joan Permanyer, Manuel Irimia, Iñaki Ruiz‐Trillo
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.47835

Epigenetic silencing of a multifunctional plant stress regulator
Cited by: 25
Author(s): Mark Zander, Björn C. Willige, Yiping He, Thu Anh Nguyen, Amber E. Langford, Ramlah Nehring, Elizabeth D. Howell, Robert B. McGrath, Anna Bartlett, Rosa Castanon, Joseph R. Nery, Huaming Chen, Zhuzhu Zhang, Florian Jupe, Anna N. Stepanova, Robert J. Schmitz, Mathew G. Lewsey, Joanne Chory, Joseph R. Ecker
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41419-018-0841-1

The detrimental effects of glucocorticoids exposure during pregnancy on offspring’s cardiac functions mediated by hypermethylation of bone morphogenetic protein-4
Cited by: 13
Author(s): Jun Peng, Yuhao Zhou, Zhiyu Zhang, Zhiming Wang, Ling-Tong Gao, Xiao Zhang, Fang Zhou, Guangyao Li, Huaiyan Chen, Hongxing Yang, Lu Gao
Software Mentions: 4
Published: almost 6 years ago

10.26508/lsa.202000944

In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord blood
Cited by: 6
Author(s): Louis Legoff, Shereen Cynthia D’Cruz, Katia Bouchekhchoukha, Christine Monfort, Christian Jaulin, Luc Multigner, Fátima Smagulova
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-017-06200-4

Associating transcription factors and conserved RNA structures with gene regulation in the human brain
Cited by: 12
Author(s): Nikolai Hecker, Stefan E. Seemann, Asli Silahtaroglu, Walter L. Ruzzo, Jan Gorodkin
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13148-021-01127-0

DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies
Cited by: 7
Author(s): Julien Morival, Halida P. Widyastuti, Christopher Nguyen, Michael V. Zaragoza, Timothy L. Downing
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12864-019-5605-5

Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens
Cited by: 20
Author(s): Andrei A. Kudinov, Natalia V. Dementieva, О.В. Митрофанова, Olga I. Stanishevskaya, Е.С. Федорова, Tatiana A. Larkina, Arina I Mishina, Kirill Plemyashov, Darren K. Griffin, Michael N Romanov
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.62438

Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
Cited by: 52
Author(s): Philip P. Adams, Gabriele Baniulyte, Caroline Esnault, Kavya Chegireddy, Navjot Singh, Molly Monge, Ryan Dale, Gisela Storz, Joseph T. Wade
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-8-265

Inference of transcriptional regulation using gene expression data from the bovine and human genomes
Cited by: 8
Author(s): Amonida Zadissa, John C. McEwan, Chris M. Brown
Software Mentions: 4
Published: almost 17 years ago

10.1186/1471-2156-13-24

Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap software system
Cited by: 4
Author(s): Ross E. Curtis, Anuj Goyal, Eric P. Xing
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0024542

Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing
Cited by: 62
Author(s): Dale N. Richardson, Mark F. Rogers, Adam Labadorf, Asa Ben-Hur, Hui Guo, Andrew H. Paterson, Anireddy S. N. Reddy
Software Mentions: 4
Published: over 12 years ago

10.1155/2017/8932583

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos
Cited by: 9
Author(s): Wenqing Jean Lee, Satadal Chatterjee, Sook Peng Yap, Siew Lan Lim, Xing Xing, Petra Kraus, Wenjie Sun, Xiaoming Hu, V. Sivakamasundari, Hsiao Yun Chan, Prasanna R. Kolatkar, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.39658

Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome
Cited by: 33
Author(s): Srivarsha Rajshekar, Jun Yao, Paige K. Arnold, Sara G. Payne, Yinwen Zhang, Teresa V. Bowman, Robert J. Schmitz, John Edwards, Mary Goll
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.29005

Conserved noncoding transcription and core promoter regulatory code in early Drosophila development
Cited by: 10
Author(s): Philippe Batut, T Gingeras
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.50895

Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation
Cited by: 23
Author(s): Callison E Alcott, Hari Krishna Yalamanchili, Ping Ji, Meike E van der Heijden, Alexander B. Saltzman, Nathan D. Elrod, Lin Ai, Mei Leng, Bhoomi Bhatt, Shuang Hao, Qi Wang, Afaf Saliba, Jianrong Tang, Anna Malovannaya, Eric J. Wagner, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 4
Published: about 4 years ago

10.1007/s00401-019-02109-6

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases
Cited by: 37
Author(s): Elena Perenthaler, Anita Nikoncuk, Soheil Yousefi, Woutje M. Berdowski, Maysoon Alsagob, Ivan Čapo, Herma C. van der Linde, Paul van den Berg, Edwin H. Jacobs, Darija Putar, Mehrnaz Ghazvini, Eleonora Aronica, Wilfred F. J. van IJcken, Walter G. de Valk, Evita Medici-van den Herik, Marjon van Slegtenhorst, Lauren Brick, Mariya Kozenko, Jennefer N. Kohler, Jonathan A. Bernstein, Kristin G. Monaghan, Amber Begtrup, Rebecca Torene, Amna Al Futaisi, Fathiya Al Murshedi, Renjith Mani, Faisal Al Azri, Erik‐Jan Kamsteeg, Majid Mojarrad, Atieh Eslahi, Zaynab Khazaei, Fateme Massinaei Darmiyan, Mohammad Doosti, Ehsan Ghayoor Karimiani, Jana Vandrovcová, Faisal Zafar, Nuzhat Rana, Krishna Kumar Kandaswamy, Jozef Hertecant, Péter Bauer, Mohammed A. AlMuhaizea, Mustafa A. Salih, Mazhor Aldosary, Rawan Almass, Laila AlQuait, Wafa Qubbaj, Serdar Coşkun, Khaled O. Alahmadi, Muddathir H. Hamad, Salem Alwadaee, Khalid Awartani, Anas Dababo, Futwan Al‐Mohanna, Dilek Çolak, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Murat Günel, A. Gülhan Ercan-Şençiçek, Gouri Rao Passi, Huma Arshad Cheema, Stéphanie Efthymiou, Henry Houlden, Aida M. Bertoli‐Avella, Alice S. Brooks, Kyle Retterer, Reza Maroofian, Namik Kaya, Tjakko J. van Ham, Tahsin Stefan Barakat
Software Mentions: 4
Published: over 4 years ago

10.1155/2018/2906292

A Simple Guideline to Assess the Characteristics of RNA-Seq Data
Cited by: 21
Author(s): Keun Hong Son, Sungryul Yu, Wonseok Shin, Kyudong Han, Keunsoo Kang
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.43922

Dynamic repression by BCL6 controls the genome-wide liver response to fasting and steatosis
Cited by: 38
Author(s): Meredith A Sommars, Krithika Ramachandran, Madhavi D. Senagolage, Christopher R. Futtner, Derrik M Germain, Amanda L. Allred, Yasuhiro Omura, Ilya Bederman, Grant D. Barish
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.36435

Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters
Cited by: 8
Author(s): Ryo Nabeshima, Osamu Nishimura, Takako Maeda, Nobujiro Shimizu, Takahiro Ide, Kenta Yashiro, Yasuo Sakai, Chikara Meno, Mitsutaka Kadota, Hidetaka Shiratori, Shigehiro Kuraku, Hiroshi Hamada
Software Mentions: 4
Published: almost 6 years ago

10.1186/1745-6150-3-24

In silico regulatory analysis for exploring human disease progression
Cited by: 8
Author(s): Dustin T. Holloway, Mark A. Kon, Charles DeLisi
Software Mentions: 4
Published: almost 16 years ago

10.1371/journal.pone.0238546

MITF and TFEB cross-regulation in melanoma cells
Cited by: 12
Author(s): Josué Ballesteros‐Álvarez, Ramile Dilshat, Valerie Fock, Katrín Möller, Ludwig Karl, Lionel Larue, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-017-17996-6

Identification of long non-coding RNAs in the immature and mature rat anterior pituitary
Cited by: 19
Author(s): Dong-Xu Han, Xiaolong Sun, Yao Fu, Changjiang Wang, Jianbo Li, Hao Jiang, Yan Gao, Chengzhen Chen, Bao Yuan, Jiabao Zhang
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.02104

Mof-associated complexes have overlapping and unique roles in regulating pluripotency in embryonic stem cells and during differentiation
Cited by: 41
Author(s): Sarina Ravens, Marjorie Fournier, Tao Ye, Matthieu Stierlé, Doulaye Dembelé, Virginie Chavant, László Tora
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.38340

The origin of the odorant receptor gene family in insects
Cited by: 88
Author(s): Philipp Brand, Hugh M. Robertson, Wei Lin, Ratnasri Pothula, William E. Klingeman, Juan Luís Jurat-Fuentes, Brian R. Johnson
Software Mentions: 4
Published: almost 6 years ago

10.1038/srep20369

Multidisciplinary investigation links backward-speech trait and working memory through genetic mutation
Cited by: 5
Author(s): Stefan Prekovic, Dušica Filipović Đurđević, Gábor Csifcsák, Olivera Šveljo, Oliver Stojković, Milica M. Janković, Katarina Koprivšek, Laura Covill, Miloš Lučić, Thomas Van den Broeck, Christine Helsen, Fabiola Ceroni, Frank Claessens, Dianne F. Newbury
Software Mentions: 4
Published: over 8 years ago

10.1126/sciadv.abe3516

Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor
Cited by: 37
Author(s): Kang Wang, Honghong Wang, Conghui Li, Zhenggang Yin, Ran Xiao, Qiuzi Li, Xiaofang Ying, Wen Wang, Jian Huang, Liang Chen, Pingping Fang, Kaiwei Liang
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0218552

SNP-based mixed model association of growth- and yield-related traits in popcorn
Cited by: 9
Author(s): Gabrielle Sousa Mafra, Antônio Teixeira do Amaral Júnior, Janeo Eustáquio de Almeida Filho, Marcelo Vivas, Pedro Henrique Araújo Diniz Santos, Juliana Saltires Santos, Guilherme Ferreira Pena, Valter Jário de Lima, Samuel Henrique Kamphorst, Fábio Tomaz de Oliveira, Yure Pequeno de Souza, Ismael Albino Schwantes, Talles de Oliveira Santos, Rosimeire Barbosa Bispo, Carlos Maldonado, Freddy Mora
Software Mentions: 4
Published: almost 5 years ago

10.1099/acmi.0.000082

Transcriptome analysis of Brucella abortus S19∆per immunized mouse spleen revealed activation of MHC-I and MHC-II pathways
Cited by: 2
Author(s): K. S. Solanki, Ravikumar Gandham, Prasad Thomas, Pallab Chaudhuri
Software Mentions: 4
Published: over 4 years ago

10.1038/sdata.2014.38

DNA methylation temporal profiling following peripheral versus central nervous system axotomy
Cited by: 14
Author(s): Ricco Lindner, Radhika Puttagunta, Tuan Nguyen, Simone Di Giovanni
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.15614

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes
Cited by: 35
Author(s): Yehudit Hasin-Brumshtein, Khan Ah, Farhad Hormozdiari, Calvin Pan, Brian W. Parks, Vladislav Petyuk, Paul Piehowski, Anneke Brümmer, Matteo Pellegrini, Xinshu Xiao, Eleazar Eskin, Richard Smith, Aldons J. Lusis, Desmond J. Smith
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-018-2086-5

An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data
Cited by: 23
Author(s): W. Garrett Jenkinson, Jordi Abante, Andrew P. Feinberg, John Goutsias
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1006964

rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline
Cited by: 56
Author(s): Devanshi Jain, Cem Meydan, Julian Lange, Corentin Claeys Bouuaert, Nathalie Lailler, Christopher E. Mason, Kathryn V. Anderson, Scott Keeney
Software Mentions: 4
Published: over 6 years ago

10.1186/s12920-018-0430-2

CRlncRNA: a manually curated database of cancer-related long non-coding RNAs with experimental proof of functions on clinicopathological and molecular features
Cited by: 20
Author(s): Jun Wang, Xuan Zhang, Wen Chen, Jing Li, Changning Liu
Software Mentions: 4
Published: over 5 years ago

10.1038/s41438-020-0338-9

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics
Cited by: 43
Author(s): Junyang Yue, Jiacheng Liu, Wei Tang, Ya Qing Wu, Xiaofeng Tang, Wei Li, Ying Yang, Lihuan Wang, Shengxiong Huang, Congbing Fang, Kun Zhao, Zhangjun Fei, Yongsheng Liu, Yi Zheng
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1007819

The complex architecture and epigenomic impact of plant T-DNA insertions
Cited by: 98
Author(s): Florian Jupe, Angeline Rivkin, Todd P. Michael, Mark Zander, S. Timothy Motley, Justin P. Sandoval, R. Keith Slotkin, Huaming Chen, Rosa Castanon, Joseph R. Nery, Joseph R. Ecker
Software Mentions: 4
Published: over 5 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: about 9 years ago

10.1186/s13059-016-0882-7

Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay
Cited by: 50
Author(s): Brandon C. Sos, Ho-Lim Fung, Derek Gao, Trina Osothprarop, Amirali Kia, M.M. He, Kun Zhang
Software Mentions: 4
Published: over 8 years ago

10.1186/gb-2014-15-2-r32

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Cited by: 112
Author(s): Benjamin L. Kidder, Gangqing Hu, Keji Zhao
Software Mentions: 4
Published: over 10 years ago

10.1186/gb-2014-15-4-r57

Evidence for the biogenesis of more than 1,000 novel human microRNAs
Cited by: 214
Author(s): Marc R. Friedländer, Esther Lizano, Anna J.S. Houben, Daniela Bezdan, Mónica Báñez-Coronel, Grzegorz Kudla, Elisabet Mateu-Huertas, Birgit Kagerbauer, Justo González, Kevin C. Chen, Emily LeProust, Eulàlia Martı́, Xavier Estivill
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pgen.1008273

BCDIN3D regulates tRNAHis 3’ fragment processing
Cited by: 21
Author(s): Calder Reinsborough, Hélène Ipas, Nathan S. Abell, Ryan M. Nottingham, Jun Yao, Sravan K. Devanathan, Samantha B. Shelton, Alan M. Lambowitz, Blerta Xhemalçe
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-017-07100-3

Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcription
Cited by: 59
Author(s): Yumiko Oishi, Shinichiro Hayashi, Takayuki Isagawa, Motohiko Oshima, Atsushi Iwama, Shigeki Shimba, Hitoshi Okamura, Ichiro Manabe
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12920-015-0139-4

Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis
Cited by: 27
Author(s): Hongying Zhao, Jiu Hua Xu, Lin Pang, Yunpeng Zhang, Huihui Fan, Ling Liu, Tingting Liu, Fulong Yu, Guanxiong Zhang, Yujia Lan, Jing Bai, Xia Li, Yun Xiao
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 10 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 11 years ago

10.1080/15476286.2020.1777768

Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples
Cited by: 10
Author(s): Fabiola Curion, Adam E. Handel, Moustafa Attar, Giuseppe Gallone, Rory Bowden, M Z Cader, Michael B. Clark
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-015-1954-x

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
Cited by: 8
Author(s): David Wragg, Andrew S. Mason, Lejun Yu, Richard Kuo, Raman Akinyanju Lawal, Takele Taye Desta, Joram M. Mwacharo, Chang-Yeon Cho, Stephen J. Kemp, David W. Burt, Olivier Hanotte
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1002603

An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors
Cited by: 15
Author(s): Idit Kosti, Predrag Radivojac, Yael Mandel-Gutfreund
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12864-021-07731-x

Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of mice
Cited by: 16
Author(s): Haijing Wang, Daoxin Liu, Pengfei Song, Feng Jiang, Xiaowei Chi, Tongzuo Zhang
Software Mentions: 4
Published: almost 3 years ago

10.1371/journal.pcbi.1006937

Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder
Cited by: 9
Author(s): Abrar E. Al‐Shaer, George R. Flentke, Mark E. Berres, Ana Garic, Susan Smith
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2015.00331

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line
Cited by: 12
Author(s): Marina Lizio, Yuri Ishizu, Masayoshi Itoh, Timo Lassmann, Akira Hasegawa, Atsutaka Kubosaki, Jessica Severin, Hideya Kawaji, Yukio Nakamura, Harukazu Suzuki, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2019.01361

Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data
Cited by: 16
Author(s): Sateesh Peri, Susan C. Roberts, Isabella R Kreko, Lauren B McHan, Alexandra Naron, Archana Ram, Rebecca L. Murphy, Eric Lyons, Brian D. Gregory, Upendra Kumar Devisetty, Andrew D. L. Nelson
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2164-13-549

Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes
Cited by: 17
Author(s): Heidrun Sigrid Windisch, Magnus Lucassen, Stephan Frickenhaus
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-020-07200-x

iCLIP analysis of RNA substrates of the archaeal exosome
Cited by: 2
Author(s): Jochen Bathke, A. Susann Gauernack, Oliver Rupp, Lennart Weber, Christian Preußer, Marcus Lechner, Oliver Roßbach, Alexander Goesmann, Elena Evguenieva‐Hackenberg, Gabriele Klug
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.0030087

Whole-Genome Cartography of Estrogen Receptor α Binding Sites
Cited by: 414
Author(s): Chin-Yo Lin, Vinsensius B. Vega, Jane S. Thomsen, Tao Zhang, Say Li Kong, Ming Xie, King-Wah Chiu, Leonard Lipovich, Daniel H. Barnett, Fabio Stossi, A. Yeo, Joshy George, Vladimir A. Kuznetsov, Yew Kok Lee, Tze Howe Charn, Nallasivam Palanisamy, Lance D. Miller, Edwin Cheung, Benita S. Katzenellenbogen, Yijun Ruan, Guillaume Bourque, Chia Lin Wei, Edison T. Liu
Software Mentions: 4
Published: almost 17 years ago

10.1186/s12864-019-6088-0

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Cited by: 10
Author(s): Jonas Ibn-Salem, Miguel A. Andrade‐Navarro
Software Mentions: 4
Published: over 4 years ago

10.1093/database/bav096

Ensembl comparative genomics resources
Cited by: 315
Author(s): Javier Herrero, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo I. Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, M Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha, Andy Yates, Paul Flicek
Software Mentions: 4
Published: over 8 years ago

10.3389/fcell.2018.00020

Improved circRNA Identification by Combining Prediction Algorithms
Cited by: 123
Author(s): Thomas B. Hansen
Software Mentions: 4
Published: about 6 years ago

10.3390/plants10071405

Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil
Cited by: 4
Author(s): Oussama Badad, Naoufal Lakhssassi, Nabil Zaïd, Abdelhalim El Baze, Younes Zaid, Jonas Meksem, David A. Lightfoot, Hüseyin Tombuloğlu, El Houcine Zaid, Turgay Ünver, Khalid Meksem
Software Mentions: 4
Published: almost 3 years ago

10.1111/tpj.15278

An Arabidopsis lipid map reveals differences between tissues and dynamic changes throughout development
Cited by: 17
Author(s): Cheka Kehelpannala, Thusitha Rupasinghe, Asher Pasha, Eddi Esteban, Thomas Hennessy, David Bradley, Berit Ebert, Nicholas J. Provart, Ute Roessner
Software Mentions: 4
Published: almost 3 years ago

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