cran: BED | Projects | Ecosyste.ms: Papers

10.12688/f1000research.8759.2

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments
Cited by: 16
Author(s): Aaron T. L. Lun, Malcolm Perry, Elizabeth Ing-Simmons
Software Mentions: 10
Published: over 8 years ago

10.12688/f1000research.13925.3

BED: a Biological Entity Dictionary based on a graph data model
Cited by: 1
Author(s): Patrice Godard, Jonathan van Eyll
Software Mentions: 10
Published: over 6 years ago

10.1186/s13148-019-0795-x

DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis
Cited by: 50
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 10
Published: about 5 years ago

10.1186/s13029-016-0059-5

A bedr way of genomic interval processing
Cited by: 19
Author(s): Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei‐Fei Liu, Paul C. Boutros
Software Mentions: 9
Published: about 8 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: almost 11 years ago

10.1371/journal.pgen.1008516

Ligand dependent gene regulation by transient ERα clustered enhancers
Cited by: 17
Author(s): Bharath Saravanan, Deepanshu Soota, Zubairul Islam, Sudeshna Majumdar, Rajat Mann, Sweety Meel, Umer Farooq, Kaivalya Walavalkar, Srimonta Gayen, Anurag Kumar Singh, Sridhar Hannenhalli, Dimple Notani
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12864-015-1303-0

Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line
Cited by: 34
Author(s): Lauren A. Solomon, Stephen K. H. Li, Jan Piskorz, Li Xu, Rodney P. DeKoter
Software Mentions: 6
Published: almost 10 years ago

10.1534/g3.117.300152

Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (<i>Phylloscopus collybita abietinus/P. tristis</i>)
Cited by: 4
Author(s): Venkat Talla, Faheema Kalsoom, Daria Shipilina, И. М. Марова, Niclas Backström
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0192858

High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets
Cited by: 1
Author(s): Piotr Madanecki, Magdalena Bałut, Patrick G. Buckley, J. Renata Ochocka, Rafał Bartoszewski, David K. Crossman, Ludwine Messiaen, Arkadiusz Piotrowski
Software Mentions: 5
Published: almost 7 years ago

10.1534/g3.116.030783

ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress
Cited by: 47
Author(s): Benoît Castandet, Amber M. Hotto, Susan R. Strickler, David B. Stern
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1009784

R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements
Cited by: 1
Author(s): D. S. Ellis, Félix Reyes-Martín, María Rodríguez-López, Cristina Cotobal, Xi‐Ming Sun, Quentin Saintain, Daniel C. Jeffares, Samuel Marguerat, Juan Jiménez, Jürg Bähler
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-15-76

Combinatorial epigenetic patterns as quantitative predictors of chromatin biology
Cited by: 16
Author(s): Marcin Cieślik, Stefan Bekiranov
Software Mentions: 5
Published: almost 11 years ago

10.3389/fgene.2021.613808

Characterization of SALL2 Gene Isoforms and Targets Across Cell Types Reveals Highly Conserved Networks
Cited by: 3
Author(s): Carlos Farkas, Aracelly Quiroz, Claudia Álvarez, Viviana E. Hermosilla, Carlos F. Aylwin, Alejandro Lomniczi, Ariel F. Castro, Matías I. Hepp, Roxana Pincheira
Software Mentions: 5
Published: almost 4 years ago

10.1038/s42003-021-02097-y

Multi Locus View: an extensible web-based tool for the analysis of genomic data.
Cited by: 3
Author(s): Martin J. Sergeant, Jim R. Hughes, Lance D. Hentges, Gerton Lunter, Damien J. Downes, Stephen Taylor
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-019-2637-4

CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features
Cited by: 4
Author(s): Yao Yao, Zheng Liu, Qi Wei, Stephen A. Ramsey
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0160227

Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers
Cited by: 19
Author(s): Stephan Pabinger, Karina Ernst, Walter Pulverer, Rainer Kallmeyer, Ana M. Valdes, Sarah Metrustry, Denis Katic, Angelo Nuzzo, Albert Kriegner, Klemens Vierlinger, Andreas Weinhaeusel
Software Mentions: 4
Published: over 8 years ago

10.1016/j.dib.2018.11.034

Differential gene expression analysis and SNP/InDel marker discovery in resistant wild Asparagus kiusianus and susceptible A. officinalis in response to Phomopsis asparagi infection
Cited by: 4
Author(s): Mostafa Abdelrahman, Mai Mitoma, Takao Ikeuchi, Motoyuki Mori, Kyoko Murakami, Yukio Ozaki, Masaru Matsumoto, Atsuko Uragami, Akira Kanno
Software Mentions: 4
Published: about 6 years ago

10.3390/genes8120383

Differential Expression of Serum MicroRNAs Supports CD4+ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma
Cited by: 33
Author(s): Alicja Pacholewska, Matthias Kraft, Vinzenz Gerber, Vidhya Jagannathan
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2105-15-S1-S2

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
Cited by: 11
Author(s): Marco Masseroli, Barend Mons, Erik Bongcam‐Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-15-808

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes
Cited by: 47
Author(s): Pallavi Chauhan, Bengt Hansson, Ken Kraaijeveld, Peter de Knijff, Erik I. Svensson, Maren Wellenreuther
Software Mentions: 3
Published: almost 11 years ago

10.7717/peerj.4040

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples
Cited by: 19
Author(s): Zeeshan Ahmed, Duygu Ucar
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1008476

Photodamage repair pathways contribute to the accurate maintenance of the DNA methylome landscape upon UV exposure
Cited by: 15
Author(s): Stéfanie Graindorge, Valérie Cognat, Philippe Johann to Berens, Jérôme Mutterer, Jean Molinier
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0076276

Differential Expression of Tomato Spotted Wilt Virus-Derived Viral Small RNAs in Infected Commercial and Experimental Host Plants
Cited by: 56
Author(s): Neena Mitter, Vikas Koundal, Sarah Williams, H. R. Pappu
Software Mentions: 3
Published: about 11 years ago

10.1093/database/baab032

MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses
Cited by: 15
Author(s): Sébastien A. Choteau, Audrey Wagner, Philippe Pierre, Lionel Spinelli, Catherine Brun
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2021.638960

Remus: A Web Application for Prioritization of Regulatory Regions and Variants in Monogenic Diseases
Cited by: 1
Author(s): Paweł Sztromwasser, Damian Skrzypczak, Arkadiusz Michalak, Wojciech Fendler
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-6-124

Cited by: 80
Author(s): Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven Van Vooren, Joris Robert Vermeesch, Yves Moreau, Bart De Moor, Stefan Vermeulen, Frank Speleman, Jo Vandesompele
Software Mentions: 3
Published: almost 20 years ago

10.1186/gb-2008-9-2-r31

Text-mining assisted regulatory annotation
Cited by: 38
Author(s): Stein Aerts, Maximilian Haeussler, Steven Van Vooren, Obi L. Griffith, Paco Hulpiau, Steven J.M. Jones, Stephen B. Montgomery, Casey M. Bergman
Software Mentions: 3
Published: almost 17 years ago

10.1038/s41438-020-00452-4

Induced defense response in red mango fruit against Colletotrichum gloeosporioides
Cited by: 22
Author(s): Sudheeran Pradeep Kumar, Noa Sela, Mira Carmeli-Weissberg, Rinat Ovadia, Sayantan Panda, Oleg Feygenberg, Dalia Maurer, Michal Oren-Shamir, Asaph Aharoni, Noam Alkan
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.51452

Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation
Cited by: 22
Author(s): Ryoji Amamoto, Mauricio D. Garcia, Emma R. West, Jiho Choi, Sylvain W. Lapan, Elizabeth A. Lane, Norbert Perrimon, Constance L. Cepko
Software Mentions: 3
Published: about 5 years ago

10.3791/57633

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Cited by: 3
Author(s): Christoph N. Schlaffner, Georg J. Pirklbauer, Andreas Bender, Judith A. Steen, Jyoti S. Choudhary
Software Mentions: 3
Published: over 6 years ago

10.3389/fcell.2014.00039

Fingerprints of a message: integrating positional information on the transcriptome
Cited by: 1
Author(s): Erik Dassi, Alessandro Quattrone
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.23813

Human biallelic MFN2 mutations induce mitochondrial dysfunction, upper body adipose hyperplasia, and suppression of leptin expression
Cited by: 56
Author(s): Nuno Rocha, David A Bulger, Andrea Frontini, Hannah Titheradge, Sigrid Bjerge Gribsholt, Rachel Knox, Matthew J. Page, Julie Harris, Felicity Payne, Claire Adams, Alison Sleigh, John R. Crawford, Anette P. Gjesing, Jette Bork-Jensen, Oluf Pedersen, Inês Barroso, Torben Hansen, Helen Cox, Mary Reilly, Rebecca J. Brown, Simeon I. Taylor, Duncan McHale, Martin Armstrong, Elif A Oral, Vladimı́r Saudek, Stephen O’Rahilly, Eamonn R. Maher, Bjørn Richelsen, David B. Savage, Robert K. Semple
Software Mentions: 2
Published: over 7 years ago

10.1186/gb-2013-14-6-r59

Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome
Cited by: 251
Author(s): Emanuela Sani, Paweł Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-017-1377-x

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
Cited by: 17
Author(s): Gerben Menschaert, Xiaojing Wang, Andrew R. Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W. Deutsch, Tobias Ternent, Juan Antonio Vizcaíno
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13073-014-0067-5

VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites
Cited by: 21
Author(s): Andrea Calabria, Simone Leo, Fabrizio Benedicenti, Daniela Cesana, Giulio Spinozzi, Massimilano Orsini, Stefania Merella, Elia Stupka, Gianluigi Zanetti, Eugenio Montini
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-12-494

Identifying elemental genomic track types and representing them uniformly
Cited by: 24
Author(s): Sveinung Gundersen, Matúš Kalaš, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Kjetil Sandve
Software Mentions: 2
Published: about 13 years ago

10.1155/2021/8884229

Next Generation Exome Sequencing of Pediatric Asthma Identifies Rare and Novel Variants in Candidate Genes
Cited by: 4
Author(s): Neda M. Bogari, Amr Amin, Husni H Rayes, Ahmed Abdelmotelb, Mohiuddin M. Taher, Faisal A. Al‐Allaf, Abdellatif Bouazzaoui, Luke O’Gorman, John W. Holloway
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0063407

Transcription Factors That Convert Adult Cell Identity Are Differentially Polycomb Repressed
Cited by: 17
Author(s): Fred P. Davis, Sean R. Eddy
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0086761

ArchiLD: Hierarchical Visualization of Linkage Disequilibrium in Human Populations
Cited by: 2
Author(s): Rossella Melchiotti, Olaf Rötzschke, Michael Poidinger
Software Mentions: 2
Published: almost 11 years ago

10.3389/fonc.2020.00490

Electron Density and Biologically Effective Dose (BED) Radiomics-Based Machine Learning Models to Predict Late Radiation-Induced Subcutaneous Fibrosis
Cited by: 18
Author(s): Michele Avanzo, G. Pirrone, Lorenzo Vinante, Angela Caroli, Joseph Stancanello, A. Drigo, Samuele Massarut, Mario Mileto, Martina Urbani, Marco Trovò, Issam El Naqa, Antonino De Paoli, G. Sartor
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.56337

KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage
Cited by: 68
Author(s): Gernot Wolf, Alberto De Iaco, Ming-an Sun, Melania Bruno, Matthew Tinkham, Don Hoang, Apratim Mitra, Sherry Ralls, Didier Trono, Todd S. Macfarlan
Software Mentions: 2
Published: over 4 years ago

10.3390/nu9111274

Emotion Regulation in Binge Eating Disorder: A Review
Cited by: 181
Author(s): Alexandra E. Dingemans, Unna N. Danner, Melissa Parks
Software Mentions: 1
Published: about 7 years ago

10.1186/s13072-016-0067-3

Distinct epigenetic features of differentiation-regulated replication origins
Cited by: 46
Author(s): Owen K. Smith, RyanGuk Kim, Haiqing Fu, Melvenia M. Martin, Chii M. Lin, Koichi Utani, Zhang Ya, Anna B. Marks, Marc Lalande, Stormy J. Chamberlain, Maxwell W. Libbrecht, Eric E. Bouhassira, Michaël Ryan, William Stafford Noble, Mirit I. Aladjem
Software Mentions: 1
Published: over 8 years ago

10.3389/fonc.2021.709829

Genetic Variants of CLPP and M1AP Are Associated With Risk of Non-Small Cell Lung Cancer
Cited by: 1
Author(s): Xianghan Li, Yiran Zou, Teng Li, Thomas K. F. Wong, Ryan T. Bushey, Michael J. Campa, Elizabeth B. Gottlin, Hongliang Liu, Qingyi Wei, Allen G. Rodrigo, Edward F. Patz
Software Mentions: 1
Published: over 3 years ago

10.1186/1475-925X-14-S2-S7

cMRI-BED: A novel informatics framework for cardiac MRI biomarker extraction and discovery applied to pediatric cardiomyopathy classification
Cited by: 16
Author(s): Vanathi Gopalakrishnan, Prahlad G. Menon, Shobhit Madan
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-018-5201-0

Exploration of exosomal microRNA expression profiles in pigeon ‘Milk’ during the lactation period
Cited by: 16
Author(s): Yao Ma, Siyuan Feng, Xun Wang, Izhar Hyder Qazi, Keren Long, Yi Luo, Guojun Li, Chunyou Ning, Yixin Wang, Silu Hu, Juan Xiao, Xiaokai Li, Dan Lan, Yaodong Hu, Qianzi Tang, Jideng Ma, Long Jin, Anan Jiang, Mingzhou Li
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0239144

coPLINK: A complementary tool to PLINK
Cited by: 1
Author(s): Han-Ming Liu, Zhao-Fa Liu, Jin-Ping Zheng, Dan Yang, Shengzhou Hu, Yan Shen-hai, Xian-Wen He
Software Mentions: 1
Published: over 4 years ago

10.3390/nu11010054

Executive Functioning in Obesity, Food Addiction, and Binge-Eating Disorder
Cited by: 40
Author(s): Marie Blume, Ricarda Schmidt, Anja Hilbert
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.cell.2012.03.026

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency
Cited by: 753
Author(s): Hendrik Marks, Tüzer Kalkan, Roberta Menafra, Sergey Denissov, Kevin Jones, Helmut Hofemeister, Jennifer Nichols, Andrea Kranz, Aengus Stewart, Austin Smith, Hendrik G. Stunnenberg
Software Mentions: 1
Published: over 12 years ago

Projects: cran: BED

Papers Mentioning BED 49