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10.3389/fgene.2019.00306

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

10.7554/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: almost 8 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 5 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 6 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 6 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: 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: almost 15 years ago

10.7554/eLife.61965

Sustained TNF-α stimulation leads to transcriptional memory that greatly enhances signal sensitivity and robustness
Cited by: 15
Author(s): Zuodong Zhao, Zhuqiang Zhang, Jingjing Li, Qiang Dong, Jun Xiong, Yingfeng Li, Mengying Lan, Gang Li, Bing Zhu
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: almost 11 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 9 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 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: over 8 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: over 12 years ago

10.1371/journal.pone.0094187

ZBED6 Modulates the Transcription of Myogenic Genes in Mouse Myoblast Cells
Cited by: 19
Author(s): Lin Jiang, Ola Wallerman, Shady Younis, Carl-Johan Rubin, Elizabeth R. Gilbert, Elisabeth Sundström, Awaisa Ghazal, Xiaolan Zhang, Li Wang, Tarjei S. Mikkelsen, Gerhard Andersson, Leif Andersson
Software Mentions: 3
Published: over 12 years ago

10.1038/srep12062

Differential and coherent processing patterns from small RNAs
Cited by: 21
Author(s): Sachin Pundhir, Jan Gorodkin
Software Mentions: 3
Published: about 11 years ago

10.15252/embj.201797038

Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands
Cited by: 88
Author(s): Massimiliano Manzo, Joël Wirz, Christina M. Ambrosi, Rodrigo Villaseñor, Bernd Roschitzki, Tuncay Baubec
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0015392

Identification of De Novo Copy Number Variants Associated with Human Disorders of Sexual Development
Cited by: 133
Author(s): Mounia Tannour‐Louet, Shuo Han, Sean T. Corbett, Jean-François Louet, Svetlana A. Yatsenko, Lindsay Meyers, Chad A. Shaw, Sung-Hae L. Kang, Sau Wai Cheung, Dolores J. Lamb
Software Mentions: 3
Published: almost 16 years ago

10.3389/fnagi.2017.00249

DNA Methylation of Synaptic Genes in the Prefrontal Cortex Is Associated with Aging and Age-Related Cognitive Impairment
Cited by: 48
Author(s): Lara Ianov, Alberto Riva, Ashok Kumar, Thomas C. Foster
Software Mentions: 3
Published: about 9 years ago

10.3389/fbioe.2014.00064

Uncovering RNA Editing Sites in Long Non-Coding RNAs
Cited by: 41
Author(s): Ernesto Picardi, Anna Maria D’Erchia, Angela Gallo, Antonio Montalvo, Graziano Pesole
Software Mentions: 3
Published: over 11 years ago

10.3389/fbioe.2014.00088

Discovery of Proteinâ€“lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets
Cited by: 55
Author(s): Junhao Li, Shun Liu, Ling‐Ling Zheng, Jie Wu, Wenju Sun, Zelin Wang, Hui Zhou, Liang‐Hu Qu, Jianhua Yang
Software Mentions: 3
Published: over 11 years ago

10.3389/fcvm.2018.00159

Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells
Cited by: 22
Author(s): Pierre R. Moreau, Tiit Örd, Nicholas Downes, Henri Niskanen, Maria Bouvy-Liivrand, Einari Aavik, Seppo Ylä‐Herttuala, Minna U. Kaikkonen
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13072-020-00350-y

Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver
Cited by: 15
Author(s): Bryan J. Matthews, David J. Waxman
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0020042

A Locus on Chromosome 5 Is Associated with Dilated Cardiomyopathy in Doberman Pinschers
Cited by: 44
Author(s): Theresa-Bernadette Mausberg, Gerhard Wess, Julia Simak, Lena Keller, Michaela Drögemüller, Cord Drögemüller, Matthew T. Webster, Hannah Stephenson, J. Dukes‐McEwan, Tosso Leeb
Software Mentions: 3
Published: over 15 years ago

10.1038/srep19615

Overlapping signatures of chronic pain in the DNA methylation landscape of prefrontal cortex and peripheral T cells
Cited by: 67
Author(s): Renaud Massart, Sergiy Dymov, Magali Millecamps, Matthew Suderman, Stéphanie Grégoire, Kevin Koenigs, Sebastian Alvarado, Maral Tajerian, Laura S. Stone, Moshe Szyf
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0085648

RNA Polymerase III Transcriptomes in Human Embryonic Stem Cells and Induced Pluripotent Stem Cells, and Relationships with Pluripotency Transcription Factors
Cited by: 32
Author(s): Ravi Alla, Bradley R. Cairns
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.ppat.1007875

Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells
Cited by: 20
Author(s): William J. Neidermyer, Sean P. J. Whelan
Software Mentions: 3
Published: about 7 years ago

10.3389/fcell.2021.666303

Lgr4 Regulates Oviductal Epithelial Secretion Through the WNT Signaling Pathway
Cited by: 3
Author(s): Xue Tan, Lingling Zhang, Tianqi Li, Jia Zhan, Kun Qiao, Haili Wu, Shenfei Sun, Meina Huang, Fangxi Zhang, Meixing Zhang, Changwei Li, Li R, Hongjie Pan
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms19030738

The Coordinated Activities of nAChR and Wnt Signaling Regulate Intestinal Stem Cell Function in Mice
Cited by: 25
Author(s): Toshio Takahashi, Akira Shiraishi, Jun Murata
Software Mentions: 3
Published: over 8 years ago

10.1038/srep22851

An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder
Cited by: 17
Author(s): Leandro Lima, Ana Cecília Feio-dos-Santos, Síntia Belangero, Ary Gadelha, Rodrigo A. Bressan, Giovanni Abrahão Salum, Pedro Mário Pan, Tais Moriyama, Ana Soledade Graeff‐Martins, Ana Carina Tamanaha, Pedro Gomes de Alvarenga, Fernanda Valle Krieger, Bacy Fleitlich-Bilyk, Andrea Parolin Jackowski, Elisa Brietzke, João Ricardo Sato, Guilherme Polanczyk, Jair de Jesus Mari, Gisele Gus Manfro, Maria Conceição do Rosário, Eurípedes Constantino Miguel, Renato Puga, Ana Carolina Tahira, Viviane Neri Souza, Thais Chile, Gisele Rodrigues Gouveia, Sérgio Nery Simões, Xiao Chang, Renata Pellegrino, Lifeng Tian, Joseph T. Glessner, Ronaldo Fumio Hashimoto, Luís Augusto Rohde, Patrick Sleiman, Hákon Hákonarson, Helena Brentani
Software Mentions: 3
Published: over 10 years ago

10.3390/ijms19113607

Methylation-Based Classification of Cervical Squamous Cell Carcinoma into Two New Subclasses Differing in Immune-Related Gene Expression
Cited by: 4
Author(s): Xia Li, Yunpeng Cai
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0105685

Analysis of Papaya Cell Wall-Related Genes during Fruit Ripening Indicates a Central Role of Polygalacturonases during Pulp Softening
Cited by: 56
Author(s): João Paulo Fabi, Sabrina Garcia Broetto, Sarah Lígia Garcia Leme da Silva, Silin Zhong, Franco Maria Lajolo, João Roberto Oliveira do Nascimento
Software Mentions: 3
Published: about 12 years ago

10.3389/fcell.2021.727183

A Novel Pyroptosis-Associated Long Non-coding RNA Signature Predicts Prognosis and Tumor Immune Microenvironment of Patients With Breast Cancer
Cited by: 29
Author(s): Liqin Ping, Kaiming Zhang, Xueqi Ou, Xingsheng Qiu, Xia Xiao
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.ppat.1007948

The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid
Cited by: 19
Author(s): Rocı́o Canals, Roy R. Chaudhuri, Rebecca E. Steiner, Siân V. Owen, Natalia Quinones-Olvera, Michael A. Gordon, Michael Baym, Michael Ibba, Jay C. D. Hinton
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms21124378

Discovery of Isoplumbagin as a Novel NQO1 Substrate and Anti-Cancer Quinone
Cited by: 19
Author(s): Yen-Chi Tsao, Yu‐Jung Chang, Chun-Hsien Wang, Linyi Chen
Software Mentions: 3
Published: about 6 years ago

10.1038/srep28396

Identification of long non-coding RNAs involved in neuronal development and intellectual disability
Cited by: 42
Author(s): Eva D’haene, Eva Jacobs, Pieter-Jan Volders, Tim De Meyer, Björn Menten, Sarah Vergult
Software Mentions: 3
Published: about 10 years ago

10.3390/ijms21165743

Premature Activation of Immune Transcription Programs in Autoimmune-Predisposed Mouse Embryonic Stem Cells and Blastocysts
Cited by: 0
Author(s): Oktay Kirak, Eugene Ke, Kevin Yi Yang, Anna Schwarz, Lars Plate, Amy Nham, Justin R. Abadejos, Anna Valencia, R. Luke Wiseman, Kathy O. Lui, Manching Ku
Software Mentions: 3
Published: about 6 years ago

10.15252/emmm.201606711

Gene signature driving invasive mucinous adenocarcinoma of the lung
Cited by: 72
Author(s): Minzhe Guo, Koichi Tomoshige, Michael Meister, Thomas Muley, Takuya Fukazawa, Tomoshi Tsuchiya, Rebekah Karns, Arne Warth, Iris M. Fink-Baldauf, Takeshi Nagayasu, Yoshio Naomoto, Yan Xu, Marcus Mall, Yutaka Maeda
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms21218383

Trans-Ancestral Fine-Mapping and Epigenetic Annotation as Tools to Delineate Functionally Relevant Risk Alleles at IKZF1 and IKZF3 in Systemic Lupus Erythematosus
Cited by: 6
Author(s): Timothy J. Vyse, Deborah S. Cunninghame Graham
Software Mentions: 3
Published: almost 6 years ago

10.1111/jcmm.15568

A functional genomics approach to investigate the differentiation of iPSCs into lung epithelium at air‐liquid interface
Cited by: 10
Author(s): Jenny L. Kerschner, Alekh Paranjapye, Shiyi Yin, Dannielle L. Skander, Gürkan Bebek, Shih Hsing Leir, Ann Harris
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0247402

DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis
Cited by: 0
Author(s): Davide Noto, Antonina Giammanco, Rossella Spina, Francesca Fayer, Angelo B. Cefalù, Maurizio Averna
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22105335

INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison
Cited by: 11
Author(s): Monika Chanu Chongtham, Tamer Butto, Kanak Mungikar, Susanne Gerber, Jennifer Winter
Software Mentions: 3
Published: over 5 years ago

10.1186/s13072-018-0216-y

The genome-wide transcriptional regulatory landscape of ecdysone in the silkworm
Cited by: 11
Author(s): Dong Cheng, Tingcai Cheng, Xi Yang, Quan Zhang, Jianfeng Fu, Tieshan Feng, Jiao Gong, Qingyou Xia
Software Mentions: 3
Published: about 8 years ago

10.1038/srep37622

HMGA1P7-pseudogene regulates H19 and Igf2 expression by a competitive endogenous RNA mechanism
Cited by: 33
Author(s): Marco De Martino, Floriana Forzati, Marianna Marfella, Simona Pellecchia, Claudio Arra, Luigi Terracciano, Alfredo Fusco, Francesco Esposito
Software Mentions: 3
Published: almost 10 years ago

10.3389/fendo.2015.00021

Promoter Methylation Status of Ras-Association Domain Family Member in Pheochromocytoma
Cited by: 17
Author(s): Antje Richter, Tobias Zimmermann, Tanja Haag, Sara K. Walesch, Reinhard Dammann
Software Mentions: 3
Published: over 11 years ago

10.1186/1756-8935-7-35

High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes
Cited by: 12
Author(s): Raghunath Chatterjee, Ximiao He, Di Huang, Peter Fitzgerald, Andrew D. Smith, Charles Vinson
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13072-019-0325-2

Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans
Cited by: 10
Author(s): Alexis V. Stutzman, April S. Liang, Vera Beilinson, Kohta Ikegami
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2019.00007

A New Panel-Based Next-Generation Sequencing Method for ADME Genes Reveals Novel Associations of Common and Rare Variants With Expression in a Human Liver Cohort
Cited by: 35
Author(s): Kathrin Klein, Roman Tremmel, Stefan Winter, Sarah Fehr, Florian Battke, Tim Scheurenbrand, Elke Schaeffeler, Saskia Biskup, Matthias Schwab, Ulrich M. Zanger
Software Mentions: 3
Published: over 7 years ago

10.1186/s13072-021-00386-8

Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing
Cited by: 20
Author(s): Bradley P. Balaton, Oriol Fornés, Wyeth W. Wasserman, Carolyn J. Brown
Software Mentions: 3
Published: over 5 years ago

10.15252/embr.201745000

<scp>KAP</scp> 1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control
Cited by: 83
Author(s): Christopher H.C. Tie, Liane Fernandes, Lucía Conde, Luisa Robbez‐Masson, Rebecca P. Sumner, Thomas P. Peacock, Maria T. Rodriguez-Plata, Greta Mickute, Robert J. Gifford, Greg J. Towers, Javier Herrero, Helen M. Rowe
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0094101

Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter
Cited by: 52
Author(s): Florian Maumus, Hadi Quesneville
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0102968

Role of Polycomb Group Proteins in the DNA Damage Response – A Reassessment
Cited by: 12
Author(s): Hollie Chandler, Harshil Patel, Richard D. Palermo, Sharon Brookes, Nik Matthews, Gordon Peters
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0193614

A common copy-number variant within SIRPB1 correlates with human Out-of-Africa migration after genetic drift correction
Cited by: 5
Author(s): José Luis Royo, Joan Valls, Rafael D. Acemel, Carlos Gómez-Marín, Mariona Pascual-Pons, Arantxa Lupiañez, José Luis Gómez-Skármeta, Joan Fibla
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2019.00508

F8 Inversions at Xq28 Causing Hemophilia A Are Associated With Specific Methylation Changes: Implication for Molecular Epigenetic Diagnosis
Cited by: 14
Author(s): Muhammad Ahmer Jamil, Amit Sharma, Nicole Nuesgen, Behnaz Pezeshkpoor, André Heimbach, A. Pavlova, Johannes Oldenburg, Osman El‐Maarri
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-00176-x

Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
Cited by: 28
Author(s): Feinan Wu, Jie Yao
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2020.00003

BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets
Cited by: 13
Author(s): Gyan Prakash Mishra, Arup Ghosh, Atimukta Jha, Sunil K. Raghav
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.597943

The Intergenerational Impacts of Paternal Diet on DNA Methylation and Offspring Phenotypes in Sheep
Cited by: 14
Author(s): Nicole Groß, Todd D. Taylor, Thomas D. Crenshaw, Hasan Khatib
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2018.00132

Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs
Cited by: 10
Author(s): Luis DaSilva, Felipe Beckedorff, Ana C. Ayupe, Murilo Sena Amaral, Vinícius C. Mesel, Alexandre Videira, Eduardo M. Reis, João Carlos Setúbal, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: over 8 years ago

10.1530/REP-18-0270

Dynamic changes in gene expression and signalling during trophoblast development in the horse
Cited by: 10
Author(s): Jordan E. Read, Victoria Cabrera-Sharp, Victoria Offord, Samantha Mirczuk, Steve Allen, Robert C. Fowkes, Amanda M. de Mestre
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0079402

Linear Decay of Retrotransposon Antisense Bias across Genes Is Contingent upon Tissue Specificity
Cited by: 1
Author(s): Sara B. Linker, Dale J. Hedges
Software Mentions: 3
Published: almost 13 years ago

10.7554/eLife.26129

FXR1 regulates transcription and is required for growth of human cancer cells with TP53/FXR2 homozygous deletion
Cited by: 25
Author(s): Yichao Fan, Yue Jiao, Mengtao Xiao, Han Han‐Zhang, Yao Vickie Wang, Chun Ma, Zhilin Deng, Yingxiang Li, Yanyan Yu, Xinghao Wang, Shen Niu, Youjia Hua, Zhiping Weng, Peter Atadja, En Li, Bin Xiang
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0018880

Arabidopsis Plasmodesmal Proteome
Cited by: 222
Author(s): Lourdes Fernández‐Calvino, Christine Faulkner, John Walshaw, Gerhard Saalbach, Emmanuelle Bayer, Yoselin Benitez‐Alfonso, Andrew J. Maule
Software Mentions: 3
Published: over 15 years ago

10.3389/fgene.2019.01409

LncRNA LUCRC Regulates Colorectal Cancer Cell Growth and Tumorigenesis by Targeting Endoplasmic Reticulum Stress Response
Cited by: 13
Author(s): G.H. Tang, Xue Chen, Jian Ding, Jie Du, Xun Lin, Lu Xia, Jiabian Lian, Yang Feng, Xiu‐Sheng He, Wen Li
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giy095

Draft genome assembly of the invasive cane toad, Rhinella marina
Cited by: 56
Author(s): Richard J. Edwards, Daniel Enosi Tuipulotu, Timothy G. Amos, Denis O’Meally, Mark F. Richardson, Tonia Russell, Marcelo Vallinoto, Miguel Carneiro, Nuno Ferrand, Marc R. Wilkins, Fernando Sequeira, Lee A. Rollins, Edward C. Holmes, Richard Shine
Software Mentions: 3
Published: about 8 years ago

10.1093/gigascience/giz073

A large interactive visual database of copy number variants discovered in taurine cattle
Cited by: 21
Author(s): Arun Kommadath, Jason R. Grant, Kirill Krivushin, Adrien M. Butty, C.F. Baes, Tara R. Carthy, D.P. Berry, Paul Stothard
Software Mentions: 3
Published: over 7 years ago

10.1093/gigascience/giaa001

A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)
Cited by: 8
Author(s): Martin Pippel, David Jebb, Franziska Patzold, Sylke Winkler, Heiko Vogel, Gene Myers, Michael Hiller, Anna K. Hundsdoerfer
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0133751

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes
Cited by: 43
Author(s): Moon Young Lee, Chanjae Park, Robyn M. Berent, Paul J. Park, Robert Fuchs, Syn Hannah, Chin Albert, Jared Townsend, Craig C. Benson, Doug Redelman, Tong Shen, Sang-Youel Park, Joseph M. Miano, Kenton M. Sanders, Seungil Ro
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0078032

Fine-Mapping an Association of FSHR with Preterm Birth in a Finnish Population
Cited by: 16
Author(s): Sung Chun, Jevon Plunkett, Kari Teramo, Louis J. Muglia, Justin C. Fay
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0222432

The intermediate proteasome is constitutively expressed in pancreatic beta cells and upregulated by stimulatory, low concentrations of interleukin 1 β
Cited by: 13
Author(s): Muhammad Saad Khilji, Danielle Verstappen, Tina Dahlby, Michala Prause, Celina Pihl, Sophie Emilie Bresson, Tenna Holgersen Bryde, Phillip Alexander Keller Andersen, Kristian Klindt, Dušan Živković, Marie‐Pierre Bousquet, Björn Tyrberg, Thomas Mandrup‐Poulsen, Michał Marzec
Software Mentions: 3
Published: over 6 years ago

10.1002/ece3.484

Cis‐regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch ( Carpodacus mexicanus )
Cited by: 11
Author(s): Niclas Backström, Daria Shipilina, Mozes P. K. Blom, Scott V. Edwards
Software Mentions: 3
Published: over 13 years ago

10.7554/eLife.40364

PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells
Cited by: 27
Author(s): Shuchi Agrawal-Singh, Mads Lerdrup, Ana-Luisa R Gomes, Harmen J.G. van de Werken, Jens Vilstrup Johansen, Robin Andersson, Albin Sandelin, Kristian Helin, Klaus Hansen
Software Mentions: 3
Published: over 7 years ago

10.1038/s41438-020-00347-4

Major-effect candidate genes identified in cultivated strawberry (Fragaria × ananassa Duch.) for ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside biosynthesis, key polyphenolic compounds
Cited by: 17
Author(s): Jahn Davik, Kjersti Aaby, Matteo Buti, Muath Alsheikh, Nada Šurbanovski, Stefan Martens, D. Røen, Daniel J. Sargent
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.11469

An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability
Cited by: 55
Author(s): Judith Schütte, Huange Wang, Stella Antoniou, Andrew Jarratt, Nicola K. Wilson, Joey Riepsaame, Fernando J. Calero-Nieto, Victoria Moignard, Silvia Basilico, Sarah Kinston, Rebecca Hannah, Mun Chiang Chan, Sylvia Nürnberg, Willem H. Ouwehand, Nicola Bonzanni, Marella Ftr de Bruijn, Berthold Göttgens
Software Mentions: 3
Published: over 10 years ago

10.1007/978-3-030-58948-6_4

Cross Reality (XR): Challenges and Opportunities Across the Spectrum
Cited by: 25
Author(s): Cindy Ziker, Barbara Truman, Heather Dodds
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0047216

A Hybrid Distance Measure for Clustering Expressed Sequence Tags Originating from the Same Gene Family
Cited by: 5
Author(s): Keng-Hoong Ng, Chin-Kuan Ho, Somnuk Phon-Amnuaisuk
Software Mentions: 3
Published: almost 14 years ago

10.1186/s40537-015-0018-z

SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information
Cited by: 23
Author(s): Syed Sameed Husain, Alexandr A. Kalinin, Anh Truong, Ivo D. Dinov
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0015688

High-Definition Mapping of Retroviral Integration Sites Defines the Fate of Allogeneic T Cells After Donor Lymphocyte Infusion
Cited by: 40
Author(s): Claudia Cattoglio, Giulietta Maruggi, Cynthia C. Bartholomae, Nirav Malani, Danilo Pellin, Fabienne Cocchiarella, Zulma Magnani, Fabio Ciceri, Alessandro Ambrosi, Christof von Kalle, Frederic D. Bushman, Chiara Bonini, Manfred Schmidt, Fulvio Mavilio, Alessandra Recchia
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0239627

Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel
Cited by: 5
Author(s): Gabriel Schneebauer, Constantin Lindemann, Victoria Drechsel, Lasse Marohn, Klaus Wysujack, Elena Santidrian, Ron P. Dirks, Reinhold Hanel, Bernd Pelster
Software Mentions: 3
Published: almost 6 years ago

10.1080/15592294.2018.1429857

Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta
Cited by: 34
Author(s): Sungsam Gong, Michelle D. Johnson, Justyna Dopierała, Francesca Gaccioli, Ulla Sovio, Miguel Constância, Gordon C. S. Smith, D. Stephen Charnock-Jones
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.08954

The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development
Cited by: 110
Author(s): Thomas W. Bebee, Juw Won Park, Katherine I Sheridan, Claude C. Warzecha, Benjamin Cieply, Alex M Rohacek, Yi Xing, Russ P. Carstens
Software Mentions: 3
Published: almost 11 years ago

10.7554/eLife.35989

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation
Cited by: 129
Author(s): Daniel Fuentes, Tomek Swigut, Joanna Wysocka
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.19272

Combinatorial bZIP dimers display complex DNA-binding specificity landscapes
Cited by: 101
Author(s): José A. Rodríguez‐Martínez, Aaron W. Reinke, Devesh Bhimsaria, Amy E. Keating, Aseem Z. Ansari
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.07860

Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain
Cited by: 71
Author(s): Julio Pérez, Nimrod D. Rubinstein, Daniel E. Fernandez, Stephen Santoro, Leigh A. Needleman, Olivia Ho-Shing, John J Choi, Mariela Zirlinger, Shau-Kwaun Chen, Jun S. Liu, Catherine Dulac
Software Mentions: 3
Published: about 11 years ago

10.7554/eLife.20851

Age-dependent diastolic heart failure in an in vivo Drosophila model
Cited by: 32
Author(s): Matthew P. Klassen, Christian J. Peters, Shiwei Zhou, Hannah H Williams, Yuh Nung Jan
Software Mentions: 3
Published: over 9 years ago

10.1016/j.jbc.2021.100784

Generation of an isoform-level transcriptome atlas of macrophage activation
Cited by: 14
Author(s): Apple Cortez Vollmers, Honey Mekonen, Sophia Campos, Susan Carpenter, Christopher Vollmers
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.ppat.1004183

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis
Cited by: 116
Author(s): Luis Solans, Jesús Gonzalo-Asensio, Claudia Sala, Andrej Benjak, Swapna Uplekar, Jacques Rougemont, Christophe Guilhot, Wladimir Malaga, Carlos Martı́n, Stewart T. Cole
Software Mentions: 3
Published: over 12 years ago

10.7554/eLife.15635

Sox9 and Sox8 protect the adult testis from male-to-female genetic reprogramming and complete degeneration
Cited by: 65
Author(s): Francisco Barrionuevo, Alicia Hurtado, Gwang-Jin Kim, Francisca M. Real, Mohammed Bakkali, Janel L. Kopp, Maike Sander, Gerd Scherer, Miguel Burgos, Rafael Jiménez
Software Mentions: 3
Published: about 10 years ago

10.1186/s13072-020-00338-8

The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure
Cited by: 6
Author(s): Dana M. Freeman, Dan Lou, Yanqiang Li, Suzanne N. Martos, Zhibin Wang
Software Mentions: 3
Published: over 6 years ago

10.1038/sdata.2018.240

Meta-mining of copy number profiles of high-risk neuroblastoma tumors
Cited by: 26
Author(s): Pauline Depuydt, Jan Koster, Valentina Boeva, Toby Dylan Hocking, Frank Speleman, Gudrun Schleiermacher, Katleen De Preter
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.ppat.1005166

Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Cited by: 12
Author(s): Seth B. Garren, Yuvabharath Kondaveeti, Michael O. Duff, Gordon G. Carmichael
Software Mentions: 3
Published: almost 11 years ago

10.7554/eLife.44642

Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila
Cited by: 51
Author(s): Ane Martín Anduaga, Naveh Evantal, Inés Lucía Patop, Osnat Bartok, Ron Weiss, Sebastián Kadener
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.25787

Repression by PRDM13 is critical for generating precision in neuronal identity
Cited by: 34
Author(s): Bishakha Mona, Ana Uruena, Rahul K. Kollipara, Zhenzhong Ma, Mark D. Borromeo, Joshua C. Chang, Jane E. Johnson
Software Mentions: 3
Published: about 9 years ago

10.12688/f1000research.11352.2

New chimeric RNAs in acute myeloid leukemia
Cited by: 8
Author(s): Florence Rufflé, Jérôme Audoux, Anthony Boureux, Sacha Beaumeunier, Jean‐Baptiste Gaillard, Elias Bou Samra, André Mégarbané, Bruno Cassinat, Christine Chomienne, Ronnie Alves, Sébastien Riquier, Nicolas Gilbert, Jean-Marc Lemaı̂tre, Delphine Bacq‐Daian, Anne Laure Bougé, Philippe Naveilhan, Thérèse Commes
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0233044

Runx3 prevents spontaneous colitis by directing the differentiation of anti-inflammatory mononuclear phagocytes
Cited by: 13
Author(s): Shay Hantisteanu, Yosef Dicken, Varda Negreanu, Dalia Goldenberg, Ori Brenner, Dena Leshkowitz, Joseph Lotem, Ditsa Levanon, Yoram Groner
Software Mentions: 3
Published: over 6 years ago

10.1038/srep02962

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Cited by: 17
Author(s): Jianliang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher M. Adams, Shaojie Zhang, John S. Mattick, Animesh Ray, Ranjan J. Perera
Software Mentions: 3
Published: almost 13 years ago

10.1186/s13072-017-0123-7

Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA
Cited by: 64
Author(s): Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M. Gould, Shalima S. Nair, Susan J. Clark, Clare Stirzaker
Software Mentions: 3
Published: over 9 years ago

10.1186/1756-8722-6-25

Structurally differentiated cis-elements that interact with PU.1 are functionally distinguishable in acute promyelocytic leukemia
Cited by: 12
Author(s): Maoxiang Qian, Ji Wen, Xuehua Zhu, Xiaohong Jia, Xian‐Wen Yang, Yanzhi Du, Kankan Wang, Ji Zhang
Software Mentions: 3
Published: over 13 years ago

10.18632/aging.101485

Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence
Cited by: 13
Author(s): Qiongye Dong, Lei Wei, Michael Q. Zhang, Xiaowo Wang
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pgen.1000404

Selection at a Single Locus Leads to Widespread Expansion of Toxoplasma gondii Lineages That Are Virulent in Mice
Cited by: 116
Author(s): Asis Khan, Sonya Taylor, James W. Ajioka, Benjamin M. Rosenthal, L. David Sibley
Software Mentions: 3
Published: over 17 years ago

10.1101/2021.07.09.21260221

Genetic regulation ofOAS1nonsense-mediated decay underlies association with risk of severe COVID-19
Cited by: 8
Author(s): Abdul Rouf Banday, Megan L. Stanifer, Óscar Flórez-Vargas, Olusegun O. Onabajo, Muhammad Atif Zahoor, Brenen W. Papenberg, Timothy J. Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G. Biesecker, David L. Boyle, Andrea N. Burnett‐Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton L. Dalgard, Jeff Edberg, Nathan Erdmann, Heather Spencer Feigelson, Gary S. Firestein, Adam J. Gehring, Michelle Ho, Steven M. Holland, Amy Hutchinson, Hogune Im, Michael G. Ison, Hong Bin Kim, Robert J. Kreitman, Bruce R. Korf, Lisa Mirabello, Jennifer A. Pacheco, Michael J. Peluso, Daniel J. Rader, David T. Redden, Marylyn D. Ritchie, Brooke Rosenbloom, Hanaisa P. Sant Anna, Sharon A. Savage, E. Siouti, Vasiliki Triantafyllia, Joselin M. Vargas, Anurag Verma, Vibha Vij, Duane R. Wesemann, Meredith Yeager, Xu G. Yu, Yu Zhang, Steeve Boulant, Stephen J. Chanock, Jordan J. Feld, Ludmila Prokunina–Olsson
Software Mentions: 3
Published: about 5 years ago

10.2196/resprot.9639

A Web-Based Telemanagement System for Patients With Complex Inflammatory Bowel Disease: Protocol for a Randomized Controlled Clinical Trial
Cited by: 9
Author(s): Mariam Aguas, Javier del Hoyo, Raquel Faubel, Diana Muñoz, Dana A. Dominguez, Guillermo Bastida, Belén Navarro, Alejandra Barrios, Bernardo Valdivieso, Marisa Correcher, Pilar Nos
Software Mentions: 3
Published: over 7 years ago

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