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10.1371/journal.pone.0140829

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud
Cited by: 99
Author(s): Enis Afgan, Clare Sloggett, Nuwan Goonasekera, Igor V. Makunin, Derek Benson, Mark L. Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-019-40403-1

A multimodal approach to cardiovascular risk stratification in patients with type 2 diabetes incorporating retinal, genomic and clinical features
Cited by: 19
Author(s): Ahmed E. Fetit, Alex S.F. Doney, Stephen Hogg, Ruixuan Wang, Tom MacGillivray, Joanna M. Wardlaw, Fergus Doubal, Gareth J. McKay, Stephen J. McKenna, Emanuele Trucco
Software Mentions: 4
Published: over 7 years ago

10.1186/s13072-019-0286-5

BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity
Cited by: 20
Author(s): Pierre Khoueiry, Aoife Ward Gahlawat, Massimo Petretich, Anne-Marie Michon, Daniel F. Simola, Enid Y.N. Lam, Eileen E. M. Furlong, Vladimı́r Beneš, Mark A. Dawson, Rab K. Prinjha, Gerard Drewes, Paola Grandi
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0021495

MicroRNA Expression Profiling Reveals MiRNA Families Regulating Specific Biological Pathways in Mouse Frontal Cortex and Hippocampus
Cited by: 70
Author(s): Juuso Juhila, Tessa Sipilä, Katherine Icay, Daniel Nicorici, Pekka Ellonen, Aleksi Kallio, Eija Korpelainen, Dario Greco, Iiris Hovatta
Software Mentions: 4
Published: about 15 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

10.1084/jem.20181276

Contrasting requirements during disease evolution identify EZH2 as a therapeutic target in AML
Cited by: 78
Author(s): Faisal Basheer, George Giotopoulos, Eshwar Meduri, Haiyang Yun, Milena Mazan, Daniel Sasca, Paolo Gallipoli, Ludovica Marando, Malgorzata Gozdecka, Ryan Asby, Olivia Sheppard, Monika Dudek, Lars Bullinger, Hartmut Döhner, Richard Dillon, Sylvie Freeman, Oliver G. Ottmann, Alan Kenneth Burnett, Nigel H. Russell, Elli Papaemmanuil, Robert Kerrin Hills, Peter J. Campbell, George S. Vassiliou, Brian J. P. Huntly
Software Mentions: 4
Published: over 7 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: over 7 years ago

10.3389/fendo.2021.679756

Pre-Menopausal Women With Breast Cancers Having High AR/ER Ratios in the Context of Higher Circulating Testosterone Tend to Have Poorer Outcomes
Cited by: 5
Author(s): Savitha Rajarajan, Aruna Korlimarla, A. Alexander, C E Anupama, Rakesh Ramesh, B S Srinath, T.S. Sridhar, Jyothi S Prabhu
Software Mentions: 4
Published: about 5 years ago

10.3390/ijerph17207671

Significant Associations between AXIN1 rs1805105, rs12921862, rs370681 Haplotypes and Variant Genotypes of AXIN2 rs2240308 with Risk of Congenital Heart Defects
Cited by: 0
Author(s): George Andrei Crauciuc, Mihaela Iancu, Peter Olah, Florin Tripon, Mădălina Anciuc, Liliana Gozar, Rodica Togănel, Claudia Bănescu
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41388-019-1005-1

Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines
Cited by: 12
Author(s): Li Wang, Hongying Zhao, Jing Li, Yingqi Xu, Yujia Lan, Wenkang Yin, Xiaoqin Liu, Lei Yu, Shan Lin, Michael Yifei Du, Xia Li, Yun Xiao, Yunpeng Zhang
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0098122

A Bayesian Method to Incorporate Hundreds of Functional Characteristics with Association Evidence to Improve Variant Prioritization
Cited by: 30
Author(s): Sarah A. Gagliano, Michael R. Barnes, Michael E. Weale, Jo Knight
Software Mentions: 4
Published: over 12 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: almost 11 years ago

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 5 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

10.15252/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

10.3389/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/s13072-018-0216-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/s41598-020-78555-0

Evolutionary divergence of novel open reading frames in cichlids speciation
Cited by: 5
Author(s): Shraddha Puntambekar, Rachel Newhouse, Jaime San-Miguel, Ruchi Chauhan, Grégoire Vernaz, Thomas W. Willis, Matthew T. Wayland, Yagnesh Umrania, Eric A. Miska, Sudhakaran Prabakaran
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-42686-w

Enhanced early-life nutrition upregulates cholesterol biosynthetic gene expression and Sertoli cell maturation in testes of pre-pubertal Holstein bulls
Cited by: 12
Author(s): Chinju Johnson, Alysha Dance, Igor Kovalchuk, John P. Kastelic, Jacob C. Thundathil
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0022046

Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs
Cited by: 18
Author(s): Abhishek Kumar, Anita Bhandari, Rahul Sinha, Pankaj Goyal, Alessandro Grapputo
Software Mentions: 3
Published: about 15 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

10.15252/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

10.1186/1756-8935-7-35

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

10.1371/journal.pone.0233191

Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene
Cited by: 3
Author(s): Jaafar Alomairi, Anne Molitor, Nori Sadouni, Saadat Hussain, Magali Torres, Wiam Saadi, Lan T M Dao, Guillaume Charbonnier, David Santiago-Algarra, Jean-Christophe Andrau, Denis Puthier, Tom Sexton, Salvatore Spicuglia
Software Mentions: 3
Published: over 6 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

10.1186/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

10.1371/journal.pone.0043652

Pitfalls of Establishing DNA Barcoding Systems in Protists: The Cryptophyceae as a Test Case
Cited by: 26
Author(s): Kerstin Hoef‐Emden
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0185678

A tissue-specific promoter derived from a SINE retrotransposon drives biallelic expression of PLAGL1 in human lymphocytes
Cited by: 5
Author(s): Claire E. L. Smith, Alexia Alexandraki, Sarah F. Cordery, Rekha Parmar, David T. Bonthron, Elizabeth M. A. Valleley
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0073953

Human Melanoma Cells Over-Express Extracellular Matrix 1 (ECM1) Which Is Regulated by TFAP2C
Cited by: 18
Author(s): Geeta Lal, Piedad Gómez Contreras, Mikhail V. Kulak, George W. Woodfield, Thomas B. Bair, Frederick E. Domann, Ronald J. Weigel
Software Mentions: 3
Published: about 13 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: almost 12 years ago

10.1371/journal.pone.0254444

Using Assessment Design Decision Framework in understanding the impact of rapid transition to remote education on student assessment in health-related colleges: A qualitative study
Cited by: 8
Author(s): Myriam Jaam, Zachariah Nazar, Daniel Rainkie, Diana Alsayed Hassan, Farhat Hussain, Salah Kassab, Abdelali Agouni
Software Mentions: 3
Published: about 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

10.1186/1756-8722-6-25

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

10.1080/15592294.2018.1429857

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

10.1038/s41598-018-22284-y

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis
Cited by: 19
Author(s): Li Jin, Peng Yu
Software Mentions: 3
Published: over 8 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

10.1371/journal.pone.0190992

HAfTs are novel lncRNA transcripts from aflatoxin exposure
Cited by: 9
Author(s): B. Alex Merrick, Justin Chang, Dhiral Phadke, Meredith A. Bostrom, Ruchir Shah, Xinguo Wang, Oksana Gordon, Garron M. Wright
Software Mentions: 3
Published: over 8 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

10.2196/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

10.1016/j.stemcr.2020.01.004

Activin A and BMP4 Signaling Expands Potency of Mouse Embryonic Stem Cells in Serum-Free Media
Cited by: 13
Author(s): Baojiang Wu, Lin Li, Bojiang Li, Junpeng Gao, Yanglin Chen, Mengyi Wei, Zhiqing Yang, Baojing Zhang, Shudong Li, Kexin Li, Changshan Wang, M. Azim Surani, Xihe Li, Fuchou Tang, Siqin Bao
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0031915

3T3 Cell Lines Stably Expressing Pax6 or Pax6(5a) – A New Tool Used for Identification of Common and Isoform Specific Target Genes
Cited by: 32
Author(s): Yury Kiselev, Tonje Engevik Eriksen, Siri Forsdahl, Lan Huong Nguyen, Ingvild Mikkola
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0013020

Genome-Wide DNA Methylation Maps in Follicular Lymphoma Cells Determined by Methylation-Enriched Bisulfite Sequencing
Cited by: 36
Author(s): Jeong-Hyeon Choi, Yajun Li, Jiangtao Guo, Lirong Pei, Tibor A. Rauch, Robin Kramer, Simone Macmil, Graham B. Wiley, Lynda Bennett, Jennifer Schnabel, Kristen H. Taylor, Sun Il Kim, Dong Xu, Arun Sreekumar, Gerd P. Pfeifer, Bruce A. Roe, Charles W. Caldwell, Kapil N. Bhalla, Huidong Shi
Software Mentions: 3
Published: almost 16 years ago

10.1038/s41388-018-0659-4

Histoepigenetic analysis of HPV- and tobacco-associated head and neck cancer identifies both subtype-specific and common therapeutic targets despite divergent microenvironments
Cited by: 20
Author(s): Ivenise Carrero, Hsuan-Chen Liu, Andrew G. Sikora, Aleksandar Milosavljevic
Software Mentions: 3
Published: over 7 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

10.1371/journal.pone.0159024

Functional Characterization of the Osteoarthritis Susceptibility Mapping to CHST11—A Bioinformatics and Molecular Study
Cited by: 10
Author(s): Louise N. Reynard, Madhushika Ratnayake, Mauro Santibanez‐Koref, John Loughlin
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-021-89798-w

Genomic selection signatures in autism spectrum disorder identifies cognitive genomic tradeoff and its relevance in paradoxical phenotypes of deficits versus potentialities
Cited by: 3
Author(s): Anil Prakash, Moinak Banerjee
Software Mentions: 3
Published: over 5 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

10.1002/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

10.1038/s41389-020-00285-9

Triptolide targets super-enhancer networks in pancreatic cancer cells and cancer-associated fibroblasts
Cited by: 32
Author(s): Pawan Noel, Shaimaa Hussein, Serina Ng, Corina E. Antal, Wei Lin, Emily Rodela, Priscilla Delgado, Sanna Naveed, Michael Downes, Yin Lin, Ronald M. Evans, Daniel D. Von Hoff, Haiyong Han
Software Mentions: 3
Published: almost 6 years ago

10.1186/1751-0473-6-2

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format
Cited by: 55
Author(s): Guiyin Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik K. Flemington, Dongxiao Zhu
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

10.1038/s41398-021-01360-4

Genome wide association study identifies four loci for early onset schizophrenia
Cited by: 12
Author(s): Shuxia Guo, Jiewei Liu, Wenqiang Li, Yongfeng Yang, Luxian Lv, Xiao Xiao, Ming Li, Fanglin Guan, Xiong‐Jian Luo
Software Mentions: 3
Published: over 5 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

10.1371/journal.pone.0165395

TCGA Expedition: A Data Acquisition and Management System for TCGA Data
Cited by: 56
Author(s): Uma Chandran, Olga Medvedeva, M. Michael Barmada, Philip D. Blood, Anish Chakka, Soumya Luthra, Antonio M. Ferreira, Kim F. Wong, Adrian V. Lee, Zhihui Zhang, Robert Budden, James R. Scott, Annerose Berndt, Jeremy M. Berg, Rebecca S. Jacobson
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0193790

Ribosome profiling uncovers selective mRNA translation associated with eIF2 phosphorylation in erythroid progenitors
Cited by: 13
Author(s): Nahuel A. Paolini, Kat Moore, Franca M. di Summa, Ivo F.A.C. Fokkema, Peter A.C. ’t Hoen, Marieke von Lindern
Software Mentions: 3
Published: over 8 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

10.1128/mBio.00768-21

Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans
Cited by: 7
Author(s): Joel T Steyer, Damien J. Downes, Cameron C. Hunter, Pierre Migeon, Richard B. Todd
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-98708-z

AGO CLIP-based imputation of potent siRNA sequences targeting SARS-CoV-2 with antifibrotic miRNA-like activity
Cited by: 6
Author(s): Seung Hyun Ahn, Dowoon Gu, Yongjun Koh, Hye-Sook Lee, Sung Wook
Software Mentions: 3
Published: almost 5 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

10.1186/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

10.1038/s41598-021-97350-z

Genetic predisposition to tinnitus in the UK Biobank population
Cited by: 1
Author(s): Madeleine E Urbanek, Jian Zuo
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-91503-w

Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Cited by: 12
Author(s): Jessica Gray, P. Scott Chandry, Mandeep Kaur, Chawalit Kocharunchitt, Séamus Fanning, John P. Bowman, Edward M. Fox
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-34864-z

Interactome determination of a Long Noncoding RNA implicated in Embryonic Stem Cell Self-Renewal
Cited by: 14
Author(s): Keriayn N. Smith, Joshua Starmer, Terry Magnuson
Software Mentions: 3
Published: almost 8 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

10.3389/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

10.1038/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

10.1186/s12915-019-0679-8

Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response
Cited by: 13
Author(s): Xiaoman Xie, Casey Hanson, Saurabh Sinha
Software Mentions: 3
Published: about 7 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

10.18632/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

10.1038/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

10.1038/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

10.1038/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

10.1186/1741-7007-10-107

Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes
Cited by: 106
Author(s): Christine E. Schnitzler, Kevin Pang, Meghan L. Powers, Adam M. Reitzel, Joseph F. Ryan, David Simmons, Takeshi Tada, Morgan Park, Jyoti Gupta, Shelise Brooks, Robert W. Blakesley, Shozo Yokoyama, Steven H. D. Haddock, Mark Q. Martindale, Andreas D. Baxevanis
Software Mentions: 3
Published: almost 14 years ago

10.1038/s41598-017-12335-1

Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts
Cited by: 23
Author(s): Nathan Lawlor, Ahrim Youn, Romy Kursawe, Duygu Ucar, Michael L. Stitzel
Software Mentions: 3
Published: almost 9 years ago

10.1186/1741-7007-5-37

The DNA binding parvulin Par17 is targeted to the mitochondrial matrix by a recently evolved prepeptide uniquely present in Hominidae
Cited by: 31
Author(s): Daniel S. Kessler, Panagiotis Papatheodorou, Tina Stratmann, Elke A. Dian, Cristina Hartmann-Fatu, Joachim Rassow, Peter Bayer, Jonathan Wolf Mueller
Software Mentions: 3
Published: almost 19 years ago

10.1186/s12915-019-0674-0

RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting
Cited by: 24
Author(s): Bharati Jadhav, Ramin Monajemi, Kristina K. Gagalova, Daniel J. Ho, Harmen H.M. Draisma, Mark A. van de Wiel, Lude Franke, Bastiaan T. Heijmans, Joyce B. J. van Meurs, Rick Jansen, Peter A.C. ’t Hoen, Andrew J. Sharp, Szymon M. Kiełbasa
Software Mentions: 3
Published: about 7 years ago

10.18632/aging.202353

Cell lineage-specific methylome and genome alterations in gout
Cited by: 6
Author(s): Chia‐Chun Tseng, Wei‐Ting Liao, Man-Chun Wong, Chung‐Jen Chen, Su-Chen Lee, Jeng-Hsien Yen, Shun‐Jen Chang
Software Mentions: 3
Published: over 5 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

10.1038/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

10.1111/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

10.18632/aging.102652

Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson’s disease
Cited by: 8
Author(s): Chunlei Han, Yunpeng Liu, Yun‐Peng Sui, Ning Chen, Tingting Du, Ying Jiang, Chenjia Guo, Kailiang Wang, Qiao Wang, Shiying Fan, Michio Shimabukuro, Fangang Meng, Yuan Fang, Jianguo Zhang
Software Mentions: 3
Published: over 6 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

10.1016/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.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

10.1186/s12915-018-0580-x

Identification of cell types in a mouse brain single-cell atlas using low sampling coverage
Cited by: 15
Author(s): Aparna Bhaduri, Tomasz J. Nowakowski, Alex A. Pollen, Arnold R. Kriegstein
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1007156

Regulation of circadian clock transcriptional output by CLOCK:BMAL1
Cited by: 112
Author(s): Alexandra J. Trott, Jérôme S. Menet
Software Mentions: 3
Published: over 8 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.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

10.1186/1471-2105-13-85

DIPSBC - data integration platform for systems biology collaborations
Cited by: 13
Author(s): Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, K. Schellander, Hans Lehrach, Bodo Lange, Ralf Herwig
Software Mentions: 3
Published: over 14 years ago

10.1186/s12864-016-2457-0

Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster
Cited by: 18
Author(s): Mei-Ju May Chen, Li-Kai Chen, Yu-Shing Lai, Yu-Yu Lin, Dung-Chi Wu, Yi-Chung Tung, Kwei-Yan Liu, Hsueh‐Tzu Shih, Yi-Jyun Chen, Yen‐Ting Lin, Li‐Ting Ma, Jun Huang, Po-Chun Wu, Hong Mei, Fang-Hua Chu, June‐Tai Wu, Wen-Hsiung Li, Chien‐Yu Chen
Software Mentions: 3
Published: over 10 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

10.1186/s12864-021-07478-5

Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs
Cited by: 13
Author(s): Christine N Goldfarb, David J. Waxman
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1005154

Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in Arabidopsis
Cited by: 49
Author(s): Tasuku Ito, Yoshiaki Tarutani, Taiko Kim To, Mohamed Kassam, Evelyne Duvernois-Berthet, Sandra Cortijo, Kazuya Takashima, Hidetoshi Saze, Atsushi Toyoda, Asao Fujiyama, Vincent Colot, Tetsuji Kakutani
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-016-1139-x

CerealsDB 3.0: expansion of resources and data integration
Cited by: 38
Author(s): Paul Wilkinson, Mark Winfield, Gary Barker, Simon Tyrrell, Xingdong Bian, Alexandra M. Allen, Amanda Burridge, Jane A. Coghill, Christy Waterfall, Mario Cáccamo, Robert P. Davey, Keith J. Edwards
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pgen.1005652

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals
Cited by: 69
Author(s): Gung Wei Chirn, Reazur Rahman, Yuliya A. Sytnikova, Jessica Matts, Mei Zeng, Daniel Gerlach, Michael Yu, Bonnie Berger, Mayumi Naramura, Benjamin T. Kile, Nelson C. Lau
Software Mentions: 3
Published: almost 11 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

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