Ecosyste.ms: Papers

10.1371/journal.pgen.1006563

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing
Cited by: 163
Author(s): Rui Zhang, Patricia Deng, Jacobson Dionna, Jin Billy Li
Software Mentions: 6
Published: over 7 years ago

10.1186/s12920-020-0668-3

AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting
Cited by: 3
Author(s): Christian Wünsch, Henrik Banck, Carsten Müller‐Tidow, Martin Dugas
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.35368

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila
Cited by: 92
Author(s): Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu, Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu, Zhandong Liu, Yaoyang Zhang, Rui Li, Zheng‐Jiang Zhu, Nan Liu
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.cub.2018.09.026

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis
Cited by: 35
Author(s): Ignacio E. Schor, Giovanni Bussotti, Matilda Maleš, Mattia Forneris, Rebecca R. Viales, Anton J. Enright, Eileen E. M. Furlong
Software Mentions: 6
Published: over 5 years ago

10.15252/emmm.202114123

Mitogen‐activated protein kinase activity drives cell trajectories in colorectal cancer
Cited by: 33
Author(s): Florian Uhlitz, Philip Bischoff, Stefan Peidli, Anja Sieber, Alexandra Trinks, Mareen Lüthen, Benedikt Obermayer, Eric Blanc, Yana Ruchiy, Thomas Sell, Soulafa Mamlouk, Roberto Arsiè, Tzu-Ting Wei, Kathleen Klotz-Noack, Roland F. Schwarz, Birgit Sawitzki, Carsten Kamphues, Dieter Beule, Markus Landthaler, Christine Sers, David Horst, Nils Blüthgen, Markus Morkel
Software Mentions: 6
Published: almost 3 years ago

10.1186/1471-2105-13-102

Workflows for microarray data processing in the Kepler environment
Cited by: 14
Author(s): Thomas Stropp, Timothy M. McPhillips, Bertram Ludäscher, Mark Bieda
Software Mentions: 6
Published: about 12 years ago

10.7554/eLife.30860

A high-resolution mRNA expression time course of embryonic development in zebrafish
Cited by: 218
Author(s): Richard White, John Collins, Ian Sealy, Neha Wali, Christopher M. Dooley, Zsofia Digby, Derek L. Stemple, Daniel N. Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J. Enright, Elisabeth M Busch-Nentwich
Software Mentions: 6
Published: over 6 years ago

10.7554/eLife.66321

Channel nuclear pore complex subunits are required for transposon silencing in Drosophila
Cited by: 10
Author(s): Marzia Munafò, Victoria R Lawless, Alessandro Passera, Serena MacMillan, Susanne Bornelöv, Irmgard U. Haussmann, Matthias Soller, Gregory J. Hannon, Benjamin Czech
Software Mentions: 6
Published: about 3 years ago

10.7554/eLife.57189

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma
Cited by: 11
Author(s): Connor Rogerson, Samuel Ogden, Edward Britton, Yeng Ang, Andrew D. Sharrocks
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0123380

Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1)
Cited by: 41
Author(s): Christopher Terranova, Sridhar T. Narla, Yu Wei Lee, Jonathan Bard, Abhirath Parikh, Ewa K. Stachowiak, Emmanuel S. Tzanakakis, Michael Buck, Barbara Birkaya, Michal K. Stachowiak
Software Mentions: 6
Published: about 9 years ago

10.1155/2018/8354350

Systematic Analysis of RNA Regulatory Network in Rat Brain after Ischemic Stroke
Cited by: 11
Author(s): Liu Juan, Kunshan Zhang, Bin Hu, Siguang Li, Qing Li, Yuan Luo, Yang Wang, Zhifeng Deng
Software Mentions: 6
Published: over 6 years ago

10.1186/2045-9769-3-1

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data
Cited by: 52
Author(s): Andrew P. Hutchins, Ralf Jauch, Mateusz Dyla, Diego Miranda‐Saavedra
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pgen.1009338

Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization
Cited by: 15
Author(s): Margarita V. Brovkina, Rachel Duffié, Abbigayl E. C. Burtis, E. Josephine Clowney
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giaa137

Long-read assembly of the <i>Brassica napus</i> reference genome Darmor-bzh
Cited by: 50
Author(s): Mathieu Rousseau‐Gueutin, Caroline Belser, Corinne Da Silva, Gautier Richard, Benjamin Istace, Corinne Cruaud, Cyril Falentin, Franz Boideau, Julien Boutte, Régine Delourme, Gwenaëlle Deniot, Stéfan Engelen, Julie Ferreira de Carvalho, Arnaud Lemainque, Loeiz Maillet, Jérôme Morice, Patrick Wincker, Anne‐Marie Chèvre, Jean‐Marc Aury
Software Mentions: 6
Published: over 3 years ago

10.12688/f1000research.6157.2

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines
Cited by: 21
Author(s): Michael T. Wolfinger, Jörg Fallmann, Florian Eggenhofer, Fabian Amman
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pcbi.1008414

Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex
Cited by: 4
Author(s): Rachael L. Sumner, Meg J. Spriggs, Alexander D Shaw
Software Mentions: 6
Published: over 3 years ago

10.1534/g3.119.400273

DPAC: A Tool for Differential Poly(A)–Cluster Usage from Poly(A)–Targeted RNAseq Data
Cited by: 16
Author(s): Andrew Routh
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.celrep.2020.108545

CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
Cited by: 23
Author(s): Jonathan Martínez-Fábregas, Luopin Wang, Elizabeth Pöhler, Adeline Cozzani, Stephan Wilmes, Majid Kazemian, Suman Mitra, Ignacio Moraga
Software Mentions: 6
Published: over 3 years ago

10.3390/genes9080392

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates
Cited by: 16
Author(s): Bernhard C. Thiel, Roman Ochsenreiter, Veerendra P. Gadekar, Andrea Tanzer, Ivo L. Hofacker
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-017-17407-w

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation
Cited by: 37
Author(s): Mariana Fontes, Ayşegül Güvenek, Riki Kawaguchi, Dinghai Zheng, Alden Huang, Victoria M. Ho, Patrick B. Chen, Xiaochuan Liu, Thomas J. O’Dell, Giovanni Coppola, Bin Tian, Kelsey C. Martin
Software Mentions: 6
Published: over 6 years ago

10.1016/j.stem.2019.03.017

Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency
Cited by: 78
Author(s): Tüzer Kalkan, Susanne Bornelöv, Carla Mulas, Evangelia Diamanti, Tim Lohoff, Markus Ralser, Sjors Middelkamp, Patrick Lombard, Jennifer Nichols, Austin Smith
Software Mentions: 5
Published: about 5 years ago

10.1016/j.stem.2020.09.001

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder
Cited by: 86
Author(s): Hannah K. Long, Marco Osterwalder, Ian Welsh, Karissa Hansen, James O. J. Davies, Yiran E. Liu, Mervenaz Koska, Alexander T. Adams, Robert Aho, Neiha Arora, Kazuya Ikeda, Ruth M. Williams, Tatjana Sauka‐Spengler, Matthew H. Porteus, Tim Mohun, Diane E. Dickel, Tomek Swigut, Jim R. Hughes, Douglas R. Higgs, Axel Visel, Licia Selleri, Joanna Wysocka
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2021.705848

Brg1 Supports B Cell Proliferation and Germinal Center Formation Through Enhancer Activation
Cited by: 6
Author(s): Dominik Schmiedel, Hadas Hezroni, Amit Hamburg, Ziv Shulman
Software Mentions: 5
Published: over 2 years ago

10.1371/journal.pgen.1005385

MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis
Cited by: 66
Author(s): Kieu T.M. Pham, Yushi Inoue, Vu Van Ba, Hanh Hieu Nguyen, Toru Nakayashiki, Kenichi Ikeda, Hitoshi Nakayashiki
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pgen.1007114

ciRS-7 exonic sequence is embedded in a long non-coding RNA locus
Cited by: 62
Author(s): Steven P. Barrett, Kevin R. Parker, Caroline Horn, Miguel A. Mata, Julia Salzman
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2105-14-169

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data
Cited by: 21
Author(s): Yanchun Bao, Veronica Vinciotti, Ernst Wit, Peter A C ‘t Hoen
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pcbi.1006555

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps
Cited by: 53
Author(s): Camden Jansen, Ricardo N. Ramirez, Nicole El-Ali, David Green, Jesper Tegnér, Matthias Merkenschlager, Ana Conesa, A Mortazavi
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-016-0991-z

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains
Cited by: 29
Author(s): Joshua Starmer, Terry Magnuson
Software Mentions: 5
Published: about 8 years ago

10.3390/ani11092606

Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens
Cited by: 2
Author(s): Panpradub Sinpru, Cindy Riou, Shin Kubota, Chotima Poompramun, Wittawat Molee, Amonrat Molee
Software Mentions: 5
Published: over 2 years ago

10.15252/emmm.202012105

Neuron type‐specific increase in lamin B1 contributes to nuclear dysfunction in Huntington’s disease
Cited by: 23
Author(s): Rafael Alcalá-Vida, Marta Garcia‐Forn, Carla Castany‐Pladevall, Jordi Creus-Muncunill, Yoko Itō, Enrique Blanco, Arantxa Golbano, Kilian Crespí-Vázquez, Aled Parry, Guy Slater, Shamith A. Samarajiwa, Sandra Peiró, Luciano Di Croce, Masashi Narita, Esther Pérez‐Navarro
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2021.698033

ACE2 Netlas: In silico Functional Characterization and Drug-Gene Interactions of ACE2 Gene Network to Understand Its Potential Involvement in COVID-19 Susceptibility
Cited by: 4
Author(s): Gita A. Pathak, Frank R. Wendt, Aranyak Goswami, Dóra Koller, Flavio De Angelis, Covid Host Genetics Initiative, Renato Polimanti
Software Mentions: 5
Published: over 2 years ago

10.1093/database/bax079

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species
Cited by: 9
Author(s): Leandro Costa do Nascimento, Marcela Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas S. Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pbio.3000719

Discovery of genes required for body axis and limb formation by global identification of retinoic acid–regulated epigenetic marks
Cited by: 22
Author(s): Marie Berenguer, Karolin F Meyer, Jun Yin, Gregg Duester
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2105-14-S19-S1

MaTSE: the gene expression time-series explorer
Cited by: 46
Author(s): P. Craig, Alan Cannon, Robert Kukla, Jessie Kennedy
Software Mentions: 5
Published: over 10 years ago

10.1186/1471-2164-15-459

Structured RNAs and synteny regions in the pig genome
Cited by: 19
Author(s): Christian Anthon, Hakim Tafer, Jakob Hull Havgaard, Bo Thomsen, Jakob Hedegaard, Stefan E. Seemann, Sachin Pundhir, Stephanie Kehr, Sebastian Bartschat, Marie Konge Nielsen, Rasmus Oestergaard Nielsen, Merete Fredholm, Peter F. Stadler, Jan Gorodkin
Software Mentions: 5
Published: almost 10 years ago

10.7554/eLife.15716

The Arabidopsis thaliana mobilome and its impact at the species level
Cited by: 242
Author(s): Leandro Quadrana, Amanda Bortolini Silveira, George F. Mayhew, Chantal LeBlanc, Robert A. Martienssen, Jeffrey A. Jeddeloh, Vincent Colot
Software Mentions: 5
Published: almost 8 years ago

10.3390/ijms19020593

Luminal lncRNAs Regulation by ERα-Controlled Enhancers in a Ligand-Independent Manner in Breast Cancer Cells
Cited by: 13
Author(s): Valentina Miano, Giulio Ferrero, Valentina Rosti, Eleonora Manitta, Jamal Elhasnaoui, Giulia Basile, Michele De Bortoli
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.11418

An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells
Cited by: 212
Author(s): Marius Walter, Aurélie Teissandier, Raquel Pérez-Palacios, Déborah Bourc’his
Software Mentions: 5
Published: over 8 years ago

10.1186/1471-2164-10-22

BioMart – biological queries made easy
Cited by: 718
Author(s): Damian Smedley, Syed Haider, Benoît Ballester, Richard Holland, Darin London, Guðmundur Á. Þórisson, Arek Kasprzyk
Software Mentions: 5
Published: over 15 years ago

10.1038/s41598-017-08010-0

Small secreted proteins from the necrotrophic conifer pathogen Heterobasidion annosum s.l. (HaSSPs) induce cell death in Nicotiana benthamiana
Cited by: 25
Author(s): Tommaso Raffaello, Fred O. Asiegbu
Software Mentions: 5
Published: almost 7 years ago

10.3390/ijms20194688

SNPs rs11240569, rs708727, and rs823156 in SLC41A1 Do Not Discriminate Between Slovak Patients with Idiopathic Parkinson’s Disease and Healthy Controls: Statistics and Machine-Learning Evidence
Cited by: 7
Author(s): Michal Cibulka, Mária Brodňanová, Marián Grendár, Milan Grofik, Egon Kurča, Ivana Pilchová, Oto Osina, Zuzana Tatarková, Dušan Dobrota, Martin Kolísek
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-018-0122-7

Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish
Cited by: 44
Author(s): Marianna Pauletto, Tereza Manousaki, Serena Ferraresso, Massimiliano Babbucci, Alexandros Tsakogiannis, Bruno Louro, Nicola Vitulo, Viet Ha Quoc, R. Carraro, Daniela Bertotto, Rafaella Franch, Francesco Maroso, Muhammad Aslam, Anna K. Sonesson, Barbara Simionati, G Malacrida, Alessandro Cestaro, Stefano Caberlotto, Elena Sarropoulou, C. C. Mylonas, Deborah M. Power, Tomaso Patarnello, Adelino V.M. Canário, Costas S. Tsigenopoulos, Luca Bargelloni
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13148-020-00970-x

Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming
Cited by: 15
Author(s): Karen L. Leung, Smriti Sanchita, Catherine T. Pham, Brett A. Davis, Mariam Okhovat, Xiangming Ding, Phillip A. Dumesic, Tristan Grogan, Kevin J. Williams, Marco Morselli, Feiyang Ma, Lucia Carbone, Xinmin Li, Matteo Pellegrini, Daniel A. Dumesic, Gregorio D. Chazenbalk
Software Mentions: 5
Published: over 3 years ago

10.1038/s41380-020-0671-2

Inhibition of colony stimulating factor 1 receptor corrects maternal inflammation-induced microglial and synaptic dysfunction and behavioral abnormalities
Cited by: 36
Author(s): Seiko Ikezu, Hana Yeh, Jean-Christophe Delpech, Maya E. Woodbury, Alicia A. Van Enoo, Zhi Ruan, Sudhir Sivakumaran, Yang You, C. A. Holland, Teresa Guillamón-Vivancos, Asuka Yoshii-Kitahara, Mina Botros, Charlotte Madore, Pin-Hao Chao, Ankita Desani, Solaiappan Manimaran, Srinidhi Venkatesan Kalavai, W. Evan Johnson, Oleg Butovsky, Maria Medalla, Jennifer I. Luebke, Tsuneya Ikezu
Software Mentions: 5
Published: over 4 years ago

10.1107/S0907444911007281

Presenting your structures: the<i>CCP</i>4<i>mg</i>molecular-graphics software
Cited by: 1,079
Author(s): Stuart McNicholas, E. A. Potterton, K.S. Wilson, M.E.M. Noble
Software Mentions: 5
Published: about 13 years ago

10.7554/eLife.48216

Cis-regulatory basis of sister cell type divergence in the vertebrate retina
Cited by: 28
Author(s): Daniel P. Murphy, Andrew Hughes, Karen A. Lawrence, Connie A. Myers, Joseph C. Corbo
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.32332

Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex
Cited by: 131
Author(s): Marta Florio, Michael Heide, Anneline Pinson, Holger Brandl, Mareike Albert, Sylke Winkler, Pauline Wimberger, Wieland B. Huttner, Michael Hiller
Software Mentions: 5
Published: about 6 years ago

10.1186/s13148-018-0588-7

Analysis of repeated leukocyte DNA methylation assessments reveals persistent epigenetic alterations after an incident myocardial infarction
Cited by: 18
Author(s): Cavin Ward‐Caviness, Golareh Agha, Brian H. Chen, Liliane Pfeiffer, Rory Wilson, Peter Wolf, Christian Gieger, Joel Schwartz, Pantel Vokonas, Lifang Hou, Allan C. Just, Stefania Bandinelli, Dena G. Hernandez, Andrew B. Singleton, Holger Prokisch, Thomas Meitinger, Gabi Kastenmüller, Luigi Ferrucci, Andrea A. Baccarelli, Mélanie Waldenberger, Annette Peters
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.63088

The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis in mammals
Cited by: 37
Author(s): Lotte Victoria Winther Stagsted, Eoghan Thomas O’Leary, Karoline K Ebbesen, Thomas B. Hansen
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.63093

MITF reprograms the extracellular matrix and focal adhesion in melanoma
Cited by: 42
Author(s): Ramile Dilshat, Valerie Fock, Colin Kenny, Ilse Gerritsen, Romain Lasseur, Jana Trávníčková, Ossia M. Eichhoff, Philipp Cerny, Katrín Möller, Sara Sigurbjörnsdóttir, Kritika Kirty, Berglind O. Einarsdottir, Phil F. Cheng, Mitchell P. Levesque, Robert A. Cornell, E. Elizabeth Patton, Lionel Larue, Marie de Tayrac, Erna Magnúsdóttir, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.13926

Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci
Cited by: 122
Author(s): Claude Philippe, Dulce B Vargas-Landin, Aurélien J. Doucet, Dominic van Essen, Jorge Vera-Otárola, Monika Kuciak, Antoine Corbin, Pilvi Nigumann, Gaël Cristofari
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.64932

Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci
Cited by: 41
Author(s): Victoria J Sugrue, Joseph A. Zoller, Pritika Narayan, Ake T. Lu, Oscar Ortega‐Recalde, Megan Grant, C. Simon Bawden, Skye R. Rudiger, Amin Haghani, Donna M. Bond, Reuben R Hore, Michael Garratt, Karen E. Sears, Nan Wang, Xiangdong Yang, Russell G. Snell, Timothy A Hore, Steve Horvath
Software Mentions: 5
Published: almost 3 years ago

10.1016/j.celrep.2020.107691

Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells
Cited by: 17
Author(s): Monica Nafria, Peter Keane, Elizabeth Ng, Edouard G. Stanley, Andrew G. Elefanty, Constanze Bonifer
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.03549

Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment
Cited by: 21
Author(s): Brenda Y. Han, Shuang Wu, Chuan-Sheng Foo, Robert M. Horton, Craig N. Jenne, Susan R. Watson, Belinda Whittle, Christopher C. Goodnow, Jason G. Cyster
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.62522

Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes
Cited by: 117
Author(s): Allen Wang, Joshua Chiou, Olivier Poirion, Justin Buchanan, Michael J. Valdez, Jamie M. Verheyden, Xiaomeng Hou, Parul Kudtarkar, Sharvari Narendra, Jacklyn Newsome, Minzhe Guo, Dina A. Faddah, Kai Zhang, Randee E. Young, Justinn Barr, Enikö Sajti, Ravi S. Misra, Heidie Huyck, Lisa M. Rogers, Cory Poole, JA Whitsett, Gloria S. Pryhuber, Yan Xu, Kyle J. Gaulton, Sebastian Preißl, Xin Sun
Software Mentions: 5
Published: over 3 years ago

10.1016/j.chom.2018.03.007

Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development
Cited by: 122
Author(s): Christa Geeke Toenhake, Sabine Anne‐Kristin Fraschka, M. Vijayabaskar, David R. Westhead, Simon J. van Heeringen, Richárd Bártfai
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.34077

Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver
Cited by: 51
Author(s): Bryan J. Matthews, David J. Waxman
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.38619

Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain
Cited by: 52
Author(s): Ken Sugino, Erin Clark, Anton Schulmann, Yasuyuki Shima, Lihua Wang, David Hunt, Bryan M. Hooks, Dimitri Tränkner, Jayaram Chandrashekar, Serge Picard, Andrew Lemire, Nelson Spruston, Adam W. Hantman, Sacha B. Nelson
Software Mentions: 5
Published: about 5 years ago

10.1038/s41420-020-0263-6

Temporal transcriptome analysis of neuronal commitment reveals the preeminent role of the divergent lncRNA biotype and a critical candidate gene during differentiation
Cited by: 3
Author(s): Bharat Prajapati, Mahar Fatima, Mena Fatma, Priya Maddhesiya, Himali Arora, Teesta Naskar, Subhashree Devasenapathy, Pankaj Seth, Subrata Sinha
Software Mentions: 5
Published: about 4 years ago

10.3390/cancers11010101

SP1 and STAT3 Functionally Synergize to Induce the RhoU Small GTPase and a Subclass of Non-canonical WNT Responsive Genes Correlating with Poor Prognosis in Breast Cancer
Cited by: 16
Author(s): Emanuele Monteleone, Valeria Orecchia, Paola Corrieri, Davide Schiavone, Lidia Avalle, Enrico Moiso, Aurora Savino, Ivan Molineris, Paolo Provero, Valeria Poli
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-15-1072

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column
Cited by: 18
Author(s): Satadal Chatterjee, V. Sivakamasundari, Sook Peng Yap, Petra Kraus, Vibhor Kumar, Xing Xing, Siew Lan Lim, Joel Sng, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-213X-12-33

Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst
Cited by: 82
Author(s): Manabu Ozawa, Miki Sakatani, Jiqiang Yao, Savita Shanker, Fahong Yu, Rui Yamashita, Shokichi Wakabayashi, Kenta Nakai, Kyle B. Dobbs, Mateus José Sudano, William G. Farmerie, Peter J. Hansen
Software Mentions: 5
Published: over 11 years ago

10.7554/eLife.25125

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression
Cited by: 111
Author(s): Daniel Andergassen, Christoph P. Dotter, D. Wenzel, Verena Sigl, Philipp C. Bammer, Markus Muckenhuber, Daniela Mayer, Tomasz M. Kuliński, Hans-Christian Theussl, Josef Penninger, Christoph Bock, Denise P. Barlow, Florian M. Pauler, Quanah J. Hudson
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.51325

Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18
Cited by: 21
Author(s): Huan Liu, Kaylia Duncan, Annika Helverson, Priyanka Kumari, Camille Mumm, Yuchen Xiao, Jenna C. Carlson, Fabrice Darbellay, Axel Visel, Elizabeth J. Leslie, Patrick Breheny, Albert Erives, Robert A. Cornell
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0016266

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease
Cited by: 257
Author(s): Natalie A. Twine, Karolina Janitz, Marc R. Wilkins, Michał Janitz
Software Mentions: 5
Published: over 13 years ago

10.1371/journal.pgen.1000302

The Chromosomal High-Affinity Binding Sites for the Drosophila Dosage Compensation Complex
Cited by: 171
Author(s): Tobias Straub, Charlotte Grimaud, Gregor D. Gilfillan, Angelika Mitterweger, Peter B. Becker
Software Mentions: 5
Published: over 15 years ago

10.7554/eLife.54508

Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation
Cited by: 24
Author(s): Ava C. Carter, Jin Xu, Meagan Y Nakamoto, Yuning Wei, Brian Zarnegar, Quanming Shi, James P. Broughton, Ryan C. Ransom, Ankit Salhotra, Surya Nagaraja, Rui Li, Diana R. Dou, Kathryn E. Yost, Seung Woo Cho, Anil Mistry, Michael T. Longaker, Paul A. Khavari, Robert T. Batey, Deborah S. Wuttke, Howard Y. Chang
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2229-12-106

Genome-wide analysis of the MYB transcription factor superfamily in soybean
Cited by: 320
Author(s): Hongwu Du, Sisi Yang, Zhe Liang, Bo-Run Feng, Lei Liu, Yubi Huang, Yixiong Tang
Software Mentions: 5
Published: almost 12 years ago

10.1371/journal.pntd.0008671

Novel small RNAs expressed by Bartonella bacilliformis under multiple conditions reveal potential mechanisms for persistence in the sand fly vector and human host
Cited by: 6
Author(s): Shaun Wachter, Linda D. Hicks, Rahul Raghavan, Michael F. Minnick
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1008799

BRM-SWI/SNF chromatin remodeling complex enables functional telomeres by promoting co-expression of TRF2 and TRF1
Cited by: 9
Author(s): Shu Wu, Yuanlong Ge, Xiaocui Li, Yiding Yang, Huan Zhou, Kaixuan Lin, Zepeng Zhang, Yong Zhao
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.xpro.2021.100483

Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer
Cited by: 2
Author(s): A. Gordon Robertson, Christina Yau, Jian Carrot‐Zhang, Jeffrey S. Damrauer, Theo Knijnenburg, Nyasha Chambwe, Katherine A. Hoadley, Anab Kemal, Jean C. Zenklusen, Andrew D. Cherniack, Rameen Beroukhim, Wanding Zhou
Software Mentions: 5
Published: almost 3 years ago

10.1371/journal.pgen.1005693

Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome
Cited by: 24
Author(s): Luke Isbel, Richa Srivastava, Harald Oey, Alex Spurling, Lucia Daxinger, Hamsa Puthalakath, Emma Whitelaw
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-017-4351-9

Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat
Cited by: 3
Author(s): David Martín‐Gálvez, Denis Dunoyer de Segonzac, Man Chun John, Anne E. Kwitek, David Thybert, Paul Flicek
Software Mentions: 5
Published: over 6 years ago

10.1093/gigascience/giaa066

CandiMeth: Powerful yet simple visualization and quantification of DNA methylation at candidate genes
Cited by: 5
Author(s): Sara-Jayne Thursby, Darin K Lobo, Kristina Pentieva, Shudong Zhang, Rachelle E Irwin, Colum P. Walsh
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.60743

Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling
Cited by: 18
Author(s): Jun Yao, Douglas C. Wu, Ryan M. Nottingham, Alan M. Lambowitz
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-11-723

Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications
Cited by: 66
Author(s): José M. Otero, Wanwipa Vongsangnak, Mohammad Ali Asadollahi, Roberto Olivares-Hernandes, Jérôme Maury, Laurent Farinelli, Loïc Barlocher, Magne Østerås, Michel Schalk, Anthony Clark, Jens Nielsen
Software Mentions: 5
Published: over 13 years ago

10.15252/embr.201846960

Nucleosome dynamics of human iPSC during neural differentiation
Cited by: 5
Author(s): Janet Harwood, Nicholas A. Kent, Nicholas Denby Allen, Adrian J. Harwood
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1007233

RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes
Cited by: 43
Author(s): Shannel R. Adams, So Maezawa, Kris G. Alavattam, Hironori Abe, Akihiko Sakashita, Megan Shroder, Tyler J. Broering, Julie Sroga Rios, Michael A. Thomas, Xinhua Lin, Carolyn M. Price, Artem Barski, Paul R. Andreassen, Satoshi H. Namekawa
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-021-02417-9

Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells
Cited by: 10
Author(s): Haifeng Fu, Weiyu Zhang, Niannian Li, Jiao Yang, Xiaoying Ye, Chenglei Tian, Xinyi Lu, Lin Liu
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13059-021-02378-z

GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
Cited by: 14
Author(s): Da-Inn Lee, Sushmita Roy
Software Mentions: 5
Published: almost 3 years ago

10.1038/s41598-020-65119-5

Multi-omic signatures identify pan-cancer classes of tumors beyond tissue of origin
Cited by: 17
Author(s): Agustín González-Reymúndez, Ana I. Vázquez
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-015-0720-3

BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
Cited by: 70
Author(s): Andrey V. Kartashov, Artem Barski
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13059-015-0685-2

Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells
Cited by: 64
Author(s): Chi Kong Li, Hongzheng Dai, Suzanne N. Martos, Beisi Xu, Yang Gao, Li Teng, Guangjing Zhu, Dustin E. Schones, Zhibin Wang
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41598-021-92448-w

Focused CRISPR-Cas9 genetic screening reveals USO1 as a vulnerability in B-cell acute lymphoblastic leukemia
Cited by: 8
Author(s): Amit Jaiswal, Hellen Truong, Tiffany Tran, Tasha Lin, David Casero, Michael O. Alberti, Dinesh S. Rao
Software Mentions: 5
Published: almost 3 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

10.1016/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

10.1186/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

10.1371/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: about 10 years ago

10.1128/mBio.01650-17

<i>De Novo</i> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <i>Puccinia coronata</i> f. sp. <i>avenae</i> , 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

10.3390/s130708060

Context Management Platform for Tourism Applications
Cited by: 14
Author(s): David Buján, David L. Martin, Ortzi Torices, Diego López-de-Ipiña, Carlos Lamsfus, Joseba Abaitua, Aurkene Alzua-Sorzabal
Software Mentions: 4
Published: almost 11 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: over 3 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: about 5 years ago

10.1371/journal.pone.0181902

EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomas
Cited by: 4
Author(s): Karol Nowicki-Osuch, Yaoyong Li, Mairi Challinor, Dave T. Gerrard, Neil A. Hanley, Andrew D. Sharrocks
Software Mentions: 4
Published: almost 7 years ago

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: over 8 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

10.1038/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: over 4 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/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

10.1038/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

10.1038/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: about 5 years ago