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10.1093/bioinformatics/btt330

Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation
Cited by: 9
Author(s): Colin Veal, Hang Xu, Katherine Reekie, Robert C. Free, Robert J. Hardwick, David G. McVey, Anthony J. Brookes, Edward J. Hollox, Chris J. Talbot
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-020-57753-w

Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications
Cited by: 20
Author(s): Jingwei Liu, Huihua Hu, Stéphane Panserat, Lucie Marandel
Software Mentions: 2
Published: almost 5 years ago

10.1093/bioinformatics/bts382

REVEAL--visual eQTL analytics
Cited by: 0
Author(s): Günter Jäger, Florian Battke, Kay Nieselt
Software Mentions: 2
Published: about 12 years ago

10.1038/s41598-017-06351-4

Integrin α6β4 Upregulates Amphiregulin and Epiregulin through Base Excision Repair-Mediated DNA Demethylation and Promotes Genome-wide DNA Hypomethylation
Cited by: 9
Author(s): Brittany L. Carpenter, Jinpeng Liu, Lei Qi, Chi Wang, Kathleen L. O’Connor
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-43292-6

Identification of regulatory variants associated with genetic susceptibility to meningococcal disease
Cited by: 3
Author(s): Lisa Borghini, Eileen Png, Alexander Binder, Victoria J. Wright, Ellie Pinnock, Ronald de Groot, Jan A. Hazelzet, Marieke Emonts, Michiel van der Flier, Luregn J Schlapbach, Suzanne T. Anderson, Fatou Secka, Antonio Salas, Colin G. Fink, Enitan D. Carrol, Andrew J. Pollard, Lachlan Coin, Taco W. Kuijpers, Federico Martinón‐Torres, Werner Zenz, Michael Levin, Martin L. Hibberd, Sonia Dávila
Software Mentions: 2
Published: over 5 years ago

10.1093/bioinformatics/btx007

ASCIIGenome: a command line genome browser for console terminals
Cited by: 3
Author(s): Dario Beraldi
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-36927-7

High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue
Cited by: 23
Author(s): Saori Fujiwara, Songjoon Baek, Lyuba Varticovski, Sohyoung Kim, Gordon L. Hager
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-37294-z

STAT3 is activated in multicellular spheroids of colon carcinoma cells and mediates expression of IRF9 and interferon stimulated genes
Cited by: 7
Author(s): Elin Edsbäcker, Jason T. Serviss, Iryna Kolosenko, Caroline Palm-Apergi, Angelo De Milito, Katja Pokrovskaja Tamm
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-37678-1

Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio)
Cited by: 11
Author(s): Markus Ojanen, Meri Uusi-Mäkelä, Sanna-Kaisa E. Harjula, Anni Saralahti, Kaisa Oksanen, Niklas Kähkönen, Juha Määttä, Vesa P. Hytönen, Marko Pesu, Mika Rämet
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-019-43403-3

Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models
Cited by: 0
Author(s): Alexander Shein, Anton Zaikin, Maria Poptsova
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-78907-w

Genome-wide association identifies several QTLs controlling cysteine and methionine content in soybean seed including some promising candidate genes
Cited by: 11
Author(s): Sidiki Malle, Milad Eskandari, Malcolm J. Morrison, François Belzile
Software Mentions: 2
Published: almost 4 years ago

10.1038/onc.2017.256

High-depth, high-accuracy microsatellite genotyping enables precision lung cancer risk classification
Cited by: 8
Author(s): Karthik Raja Velmurugan, Robin Varghese, Natalie C. Fonville, Harold R. Garner
Software Mentions: 2
Published: over 7 years ago

10.1186/s13040-021-00251-0

Indels in SARS-CoV-2 occur at template-switching hotspots
Cited by: 23
Author(s): Brianna Chrisman, Kelley Paskov, Nate Stockham, Kevin Tabatabaei, Jae-Yoon Jung, Peter Washington, Maya Varma, Min Sun, Sepideh Maleki, Dennis P. Wall
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-13-S3-S13

Comparative analysis and visualization of multiple collinear genomes
Cited by: 54
Author(s): Jeremy Wang, Fernando Pardo Manuel de Villena, Leonard McMillan
Software Mentions: 2
Published: over 12 years ago

10.1186/s12917-018-1752-1

Inherited selective cobalamin malabsorption in Komondor dogs associated with a CUBN splice site variant
Cited by: 9
Author(s): John C. Fyfe, Shelby L. Hemker, Alycia Frampton, Karthik Raj, Péter L. Nagy, Kristi J. Gibbon, Urs Giger
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-29074-6

Culture of haploid blastocysts in FGF4 favors the derivation of epiblast stem cells with a primed epigenetic and transcriptional landscape
Cited by: 2
Author(s): Runsheng He, Benjamin L. Kidder
Software Mentions: 2
Published: over 6 years ago

10.1186/s13073-016-0320-1

Comprehensive promoter level expression quantitative trait loci analysis of the human frontal lobe
Cited by: 19
Author(s): Cornelis Blauwendraat, Margherita Francescatto, J. Raphael Gibbs, Iris E. Jansen, Javier Simón‐Sánchez, Dena G. Hernandez, Allissa Dillman, Andrew B. Singleton, Mark Cookson, Patrizia Rizzu, Peter Heutink
Software Mentions: 2
Published: over 8 years ago

10.1186/s13073-018-0562-1

Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Cited by: 36
Author(s): Sabrina Grasse, Matthias Lienhard, Steffen Frese, Martin Kerick, Anne Steinbach, Christina Grimm, Michelle Hussong, Jana Rolff, Michael W. Becker, Felix Dreher, Uwe Schirmer, Stefan Boerno, Anna Ramisch, Gunda Leschber, Bernd Timmermann, Christian Grohé, H Lüders, Martin Vingron, Iduna Fichtner, Sebastian Klein, Margarete Odenthal, Reinhard Büttner, Hans Lehrach, Holger Sültmann, Ralf Herwig, Michal R. Schweiger
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-19494-9

Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing
Cited by: 5
Author(s): Mari Mito, Mitsutaka Kadota, Kaori Tanaka, Yasuhide Furuta, Kuniya Abe, Shigeo Iwasaki, Shinichi Nakagawa
Software Mentions: 2
Published: almost 7 years ago

10.1093/gbe/evy029

Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome
Cited by: 15
Author(s): Larissa Maranhão Dias, Adriana Ribeiro Carneiro Folador, Amanda M.S. Oliveira, Rommel Thiago Jucá Ramos, Artur M. S. Silva, Rafael Azevedo Baraúna
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-018-5376-4

GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution
Cited by: 9
Author(s): Peter J. Hansen, Salaheddine Ali, Hannah Blau, Daniel Daniš, Jochen Hecht, Uwe Kornak, Darío G. Lupiáñez, Stefan Mundlos, Robin Steinhaus, Peter N. Robinson
Software Mentions: 2
Published: almost 6 years ago

10.1186/1756-0500-7-845

Experience of using an open source clinical trials data management software system in Kenya
Cited by: 15
Author(s): Moses Ngari, Naomi Waithira, Roma Chilengi, Patricia Njuguna, Trudie Lang, Greg Fegan
Software Mentions: 2
Published: almost 11 years ago

10.1093/gbe/evu142

Sequence-Level Mechanisms of Human Epigenome Evolution
Cited by: 17
Author(s): James Prendergast, Emily Chambers, Colin A. Semple
Software Mentions: 2
Published: over 10 years ago

10.1093/gbe/evab183

nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over
Cited by: 7
Author(s): Andrea Talenti, James Prendergast
Software Mentions: 2
Published: over 3 years ago

10.1186/1756-0500-4-405

EcoBrowser: a web-based tool for visualizing transcriptome data of Escherichia coli
Cited by: 3
Author(s): Xiao Chang, Yun Li, Jie Ping, Xiaobin Xing, Han Sun, Peng Jia, Chuan Wang, Yuanyuan Li, Yixue Li
Software Mentions: 2
Published: about 13 years ago

10.18632/aging.101867

Tubastatin A inhibits HDAC and Sirtuin activity rather than being a HDAC6-specific inhibitor in mouse oocytes
Cited by: 8
Author(s): Yun‐Jung Choi, Min-Hee Kang, Kwonho Hong, Jin‐Hoi Kim
Software Mentions: 2
Published: over 5 years ago

10.1186/gm486

BAIT: Organizing genomes and mapping rearrangements in single cells
Cited by: 31
Author(s): Matthew J. Hills, Kieran O’Neill, Ester Falconer, Ryan R. Brinkman, Peter M. Lansdorp
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12870-019-1651-z

Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness
Cited by: 21
Author(s): Javier Terol, María José Nueda, Daniel Ventimilla, Francisco R. Tadeo, Manuel Talón
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-11-239

Using caching and optimization techniques to improve performance of the Ensembl website
Cited by: 7
Author(s): Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard, James Smith, Stephen J. Trevanion
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2229-9-50

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences
Cited by: 54
Author(s): Martin Trick, Foo Cheung, Nizar Drou, F C Fråser, Edward K. Lobenhofer, Patrick Hurban, Andreas Magusin, Christopher D. Town, Ian Bancroft
Software Mentions: 2
Published: over 15 years ago

10.1186/s13059-019-1893-y

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
Cited by: 44
Author(s): Lin An, Tao Yang, Jingquan Yang, Johannes Nuebler, Guanjue Xiang, R Hardison, Qunhua Li, Yu Zhang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12870-014-0412-2

NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome
Cited by: 16
Author(s): Hamed Bostan, Maria Luisa Chiusano
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13059-016-1142-6

Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies
Cited by: 145
Author(s): Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Saixia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael Feolo, Nataliya Sharopova, Anne Sturcke, Alejandro A. Schäffer, Nancy L. Heard‐Costa, Han Chen, Poching Liu, Thomas J. Wang, Kimberly A. Woodhouse, Kahraman Tanrıverdi, Jane E. Freedman, Nalini Raghavachari, Josée Dupuis, Andrew D. Johnson, Christopher J. O’Donnell, Daniel Levy, Peter J. Munson
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-018-2219-x

mySyntenyPortal: an application package to construct websites for synteny block analysis
Cited by: 6
Author(s): Jongin Lee, Daehwan Lee, Mikang Sim, Daehong Kwon, Ju‐Yeon Kim, Yun Woong Ko, Jaebum Kim
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-015-0835-6

Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2
Cited by: 30
Author(s): Young Chae Kim, Sangwon Byun, Yang Zhang, Sunmi Seok, Byron Kemper, Jian Ma, Jongsook Kim Kemper
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13059-017-1161-y

Software tools for visualizing Hi-C data
Cited by: 49
Author(s): Galip Gürkan Yardımcı
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-33629-y

LncRNA BLAT1 is Upregulated in Basal-like Breast Cancer through Epigenetic Modifications
Cited by: 25
Author(s): Yoo Jane Han, Sonja Boatman, Jing Zhang, Xinxin Du, Albert C. Yeh, Yonglan Zheng, Jeffrey Mueller, Olufunmilayo I. Olopade
Software Mentions: 2
Published: about 6 years ago

10.1186/s13059-014-0578-9

Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds
Cited by: 51
Author(s): Carolina Frankl-Vilches, Heiner Kuhl, Martin Werber, Sven Klages, Martin Kerick, Antje Bakker, Edivaldo Herculano Corrêa de Oliveira, Christina Reusch, Floriana Capuano, Jakob Vowinckel, Stefan Leitner, Markus Ralser, Bernd Timmermann, Manfred Gahr
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-015-1414-7

The salinity tolerant poplar database (STPD): a comprehensive database for studying tree salt-tolerant adaption and poplar genomics
Cited by: 7
Author(s): Ying Ma, Ting Xu, Dongshi Wan, Tao Ma, Shengjun Shi, Jianquan Liu, Quanjun Hu
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-014-0469-0

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes
Cited by: 137
Author(s): Adam Blattler, Lijing Yao, Heather Witt, Yu Guo, Charles M. Nicolet, Benjamin P. Berman, Peggy J. Farnham
Software Mentions: 2
Published: about 10 years ago

10.1038/s41598-017-09810-0

Evidence-based tailoring of bioinformatics approaches to optimize methods that predict the effects of nonsynonymous amino acid substitutions in glucokinase
Cited by: 9
Author(s): Daniela Šimčíková, Lucie Kocková, Kateřina Vackářová, Miroslav Těšínský, Petr Heneberg
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2105-8-320

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation
Cited by: 6
Author(s): Kathrin Klee, Rebecca Ernst, Manuel Spannagl, Klaus Mayer
Software Mentions: 2
Published: about 17 years ago

10.1186/s12860-021-00378-2

Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity
Cited by: 2
Author(s): Atefeh Atefi, Pendar Shojaei kojouri, Fereshteh Karamali, Shiva Irani, Mohammad Hossein Nasr-Esfahani
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-020-03806-w

oposSOM-Browser: an interactive tool to explore omics data landscapes in health science
Cited by: 10
Author(s): Henry Loeffler‐Wirth, Jasmin Reikowski, Siras Hakobyan, Jonas Wagner, Hans Binder
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2105-13-206

CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes
Cited by: 39
Author(s): Ivan Borozan, Shane Wilson, Paola Blanchette, Philippe Laflamme, Stuart Watt, Paul M. Krzyzanowski, Fabrice Sircoulomb, Robert Rottapel, Philip E. Branton, Vincent Ferretti
Software Mentions: 2
Published: over 12 years ago

10.1186/gb-2014-15-1-r8

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast
Cited by: 153
Author(s): Shaun Webb, Ralph D. Hector, Grzegorz Kudla, Sander Granneman
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-12-305

A tissue-specific landscape of sense/antisense transcription in the mouse intestine
Cited by: 19
Author(s): Ulrich C. Klostermeier, Matthias Barann, Michael Wittig, Robert Häsler, André Franke, Olga Gavrilova, Benjamin Kreck, Christian Sina, Markus B. Schilhabel, Stefan Schreiber, Philip Rosenstiel
Software Mentions: 2
Published: over 13 years ago

10.1186/s12874-016-0164-9

ODMedit: uniform semantic annotation for data integration in medicine based on a public metadata repository
Cited by: 28
Author(s): Martin Dugas, Alexandra Meidt, Philipp Neuhaus, Michael Storck, Julian Varghese
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-016-2794-z

MBDDiff: an R package designed specifically for processing MBDcap-seq datasets
Cited by: 3
Author(s): Yuanhang Liu, Desiree Wilson, Robin J. Leach, Yidong Chen
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0005008

Transcriptional Network of p63 in Human Keratinocytes
Cited by: 42
Author(s): Silvia Pozzi, Federico Zambelli, Daniele Merico, Giulio Pavesi, Amélie Robert, Peggy Maltère, Xavier Gidrol, Roberto Mantovani, M. Alessandra Viganò
Software Mentions: 2
Published: over 15 years ago

10.1186/gb-2014-15-1-r1

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis
Cited by: 1,195
Author(s): Peng Cui, Shoudong Zhang, Feng Ding, Shahjahan Ali, Liming Xiong
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13059-015-0727-9

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
Cited by: 107
Author(s): Pelin Sahlén, Ilgar Abdullayev, Daniel Ramsköld, Liudmila Matskova, Nemanja Rilakovic, Britta Lötstedt, Thomas Albert, Joakim Lundeberg, Rickard Sandberg
Software Mentions: 2
Published: over 9 years ago

10.1186/gb-2010-11-4-r36

Optimized design and data analysis of tag-based cytosine methylation assays
Cited by: 76
Author(s): Masako Suzuki, Jun Qiang, Daniel Lia, Marién Pascual, Andrew McLellan, John M. Greally
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2010-11-2-r22

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
Cited by: 254
Author(s): Guoliang Li, Melissa J. Fullwood, Xu Han, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius B. Vega, Pramila Ariyaratne, Yusoff Bin Mohamed, Hong Ooi, Chandana Tennakoon, Chia Lin Wei, Yijun Ruan, Wing-Kin Sung
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2010-11-4-r42

Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis
Cited by: 66
Author(s): Qiang Gan, Dustin E. Schones, Suk Ho Eun, Gang Wei, Kairong Cui, Keji Zhao, Xin Chen
Software Mentions: 2
Published: almost 15 years ago

10.1186/1755-8794-6-1

Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C
Cited by: 72
Author(s): Daria Grafodatskaya, Barian H Y Chung, Darci T. Butcher, Andrei L. Turinsky, Sarah J. Goodman, Sana Choufani, Yi‐An Chen, Youliang Lou, Cheng Zhao, Rageen Rajendram, Fatima Abidi, Cindy Skinner, James Stavropoulos, Carolyn A. Bondy, Jill Hamilton, Shoshana J. Wodak, Stephen W. Scherer, Charles E. Schwartz, Rosanna Weksberg
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2164-13-636

Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects
Cited by: 184
Author(s): Kristel R. van Eijk, Simone de Jong, Marco P. Boks, Terry Langeveld, Fabrice Colas, Jan H. Veldink, Carolien G.F. de Kovel, Esther Janson, Eric Strengman, Peter Langfelder, René S. Kahn, Leonard H van den Berg, Steve Horvath, Roel A. Ophoff
Software Mentions: 2
Published: about 12 years ago

10.1186/gb-2008-9-12-r170

FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
Cited by: 75
Author(s): Rongrong Chen, Alex Morgan, Joel T. Dudley, Tarangini Deshpande, Li Li, Keiichi Kodama, An‐Jen Chiang, Atul J. Butte
Software Mentions: 2
Published: almost 17 years ago

10.1186/gb-2010-11-3-r34

Global and unbiased detection of splice junctions from RNA-seq data
Cited by: 87
Author(s): Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2006-7-7-r58

Cited by: 22
Author(s): Matthew D. Wilkerson, Shannon D. Schlueter, Volker Brendel
Software Mentions: 2
Published: almost 19 years ago

10.1534/genetics.115.185363

Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae
Cited by: 27
Author(s): Katarzyna B. Hooks, Samina Naseeb, Steven J. Parker, Sam Griffiths-Jones, Daniela Delneri
Software Mentions: 2
Published: over 8 years ago

10.1186/gb-2006-7-s1-s9

Cited by: 59
Author(s): Jonathan Allen, William H. Majoros, Mihaela Pertea, Steven L. Salzberg
Software Mentions: 2
Published: almost 19 years ago

10.1371/journal.pntd.0000543

Anti-schistosomal Intervention Targets Identified by Lifecycle Transcriptomic Analyses
Cited by: 117
Author(s): Jennifer M. Fitzpatrick, Emily Peak, Samïrah Perally, Iain W. Chalmers, John Barrett, Timothy P. Yoshino, Alasdair Ivens, Karl F. Hoffmann
Software Mentions: 2
Published: about 15 years ago

10.1002/dvg.22963

Transcriptional regulation of the proto‐oncogeneZfp521by SPI1 (PU.1) and HOXC13
Cited by: 11
Author(s): Ming Yu, Salma Aldallal, Latifa Al‐Haj, Shiraj Panjwani, Akina S. McCartney, Sarah Edwards, Pooja Manjunath, Catherine Walker, Alexander Awgulewitsch, Kathryn E. Hentges
Software Mentions: 2
Published: about 8 years ago

10.18632/genesandcancer.113

Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development
Cited by: 12
Author(s): Meng Chen, Nathaniel Rothman, Yuanqing Ye, Jian Gu, Paul Scheet, Maosheng Huang, David W. Chang, Colin P.N. Dinney, Debra T. Silverman, Jonine D. Figueroa, Stephen J. Chanock, Xifeng Wu
Software Mentions: 2
Published: over 8 years ago

10.1186/s12711-020-0528-9

pCADD: SNV prioritisation in Sus scrofa
Cited by: 16
Author(s): Christian Groß, Martijn F.L. Derks, Hendrik Jan Megens, Mirte Bosse, M.A.M. Groenen, Marcel J. T. Reinders, Dick de Ridder
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2164-14-611

Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes
Cited by: 159
Author(s): James R. Doroghazi, William W. Metcalf
Software Mentions: 2
Published: almost 12 years ago

10.3390/genes12020221

Evaluation of OpenArray™ as a Genotyping Method for Forensic DNA Phenotyping and Human Identification
Cited by: 7
Author(s): Michele Reni, Giulio Puleri, Valeria Errichiello, L Manzo, Laura Luzzi, Saverio Potenza, Claudia Strafella, Cristina Peconi, Fabio Nicastro, Valerio Caputo, Emiliano Giardina
Software Mentions: 2
Published: almost 4 years ago

10.3390/genes12060870

Age Prediction of Human Based on DNA Methylation by Blood Tissues
Cited by: 5
Author(s): Jiansheng Zhang, Hongli Fu, Yan Xu
Software Mentions: 2
Published: over 3 years ago

10.1186/s12920-021-01007-9

Epigenetic landscapes of intracranial aneurysm risk haplotypes implicate enhancer function of endothelial cells and fibroblasts in dysregulated gene expression
Cited by: 5
Author(s): Kerry E. Poppenberg, Haley R Zebraski, Naval Avasthi, Muhammad Waqas, Adnan H. Siddiqui, James N. Jarvis, Vincent M. Tutino
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1005117

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis
Cited by: 20
Author(s): Erin Osborne Nishimura, Jay C. Zhang, Adam D. Werts, Bob Goldstein, Jason D. Lieb
Software Mentions: 2
Published: over 9 years ago

10.3390/genes11121486

citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement
Cited by: 8
Author(s): Naveen Duhan, Manish Meshram, Cristian D Loaiza, Rakesh Kaundal
Software Mentions: 2
Published: almost 4 years ago

10.3390/genes12081249

Proof of Gene Doping in a Mouse Model with a Human Erythropoietin Gene Transferred Using an Adenoviral Vector
Cited by: 7
Author(s): Takehito Sugasawa, Takuro Nakano, Shin‐ichiro Fujita, Yuki Matsumoto, Genki Ishihara, Kai Aoki, Koki Yanazawa, S. Ono, Shinsuke Tamai, Lev Manevich, Hiroshi Ueda, Noriyo Ishibashi, Kenshirou Tamai, Yasuharu Kanki, Yasuko Yoshida, Koichi Watanabe, Tohru Takemasa, Yasushi Kawakami, Kazuhiro Takekoshi
Software Mentions: 2
Published: over 3 years ago

10.3390/genes7030011

Genome-Wide Identification and Characterization of Long Non-Coding RNAs from Mulberry (Morus notabilis) RNA-seq Data
Cited by: 35
Author(s): Xin Song, Liang Sun, Haitao Luo, Qingguo Ma, Yi Zhao, Dong Pei
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-16-S8-S2

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
Cited by: 68
Author(s): Adam Frankish, Barbara Uszczyńska, Graham R. S. Ritchie, Jose M. Gonzalez, Dmitri D. Pervouchine, Robert Petryszak, Jonathan M. Mudge, Nuno A. Fonseca, Alvis Brāzma, Roderic Guigó, Jennifer Harrow
Software Mentions: 2
Published: over 9 years ago

10.3390/genes8010014

mRNA Expression and DNA Methylation Analysis of Serotonin Receptor 2A (HTR2A) in the Human Schizophrenic Brain
Cited by: 29
Author(s): Sern-Yih Cheah, Bruce R. Lawford, Ross McD. Young, Charles P. Morris, Joanne Voisey
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1006296

Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer
Cited by: 37
Author(s): Jian Gong, Carolyn M. Hutter, Polly A. Newcomb, Cornelia M. Ulrich, Stephanie A. Bien, Peter T. Campbell, John A. Baron, Sonja I. Berndt, Stéphane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang–Claude, Mengmeng Du, David Duggan, Jane C. Figueiredo, Steven Gallinger, Edward Giovannucci, Robert W. Haile, Tabitha A. Harrison, Richard B. Hayes, Michael Hoffmeister, John L. Hopper, Thomas J. Hudson, Jihyoun Jeon, Mark A. Jenkins, Jonathan Kocarnik, Sébastien Küry, Loı̈c Le Marchand, Yi Lin, Noralane M. Lindor, Reiko Nishihara, Shuji Ogino, John D. Potter, Anja Rudolph, Robert E. Schoen, Petra Schrotz‐King, Daniela Seminara, Martha L. Slattery, Stephen N. Thibodeau, Mark Thornquist, Réka Tóth, Robert B. Wallace, Emily White, Shuo Jiao, Mathieu Lemire, Li Hsu, Ulrike Peters
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2105-11-10

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
Cited by: 52
Author(s): Guanqun Shi, Liqing Zhang, Tao Jiang
Software Mentions: 2
Published: almost 15 years ago

10.3390/genes5041115

Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential
Cited by: 18
Author(s): Y. Kurihara, Yuko Makita, Mika Kawashima, Hidefumi Hamasaki, Yoshiharu Y. Yamamoto, Minami Matsui
Software Mentions: 2
Published: almost 10 years ago

10.3390/genes12091388

A Recurrent De Novo Terminal Duplication of 14q32 in Korean Siblings Associated with Developmental Delay and Intellectual Disability, Growth Retardation, Facial Dysmorphism, and Cerebral Infarction: A Case Report and Literature Review
Cited by: 2
Author(s): Ji Yoon Han, Joonhong Park
Software Mentions: 2
Published: about 3 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/s13059-015-0736-8

Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions
Cited by: 83
Author(s): Elena M. Pugacheva, Samuel Rivero-Hinojosa, Celso A. Espinoza, Claudia Fabiola Méndez-Catalá, Sungyun Kang, Tomohiko Suzuki, Natsuki Kosaka-Suzuki, Susan Robinson, Vijayaraj Nagarajan, Zhen Ye, Abdelhalim Boukaba, John E.J. Rasko, Alexander Strunnikov, Dmitri Loukinov, Bing Ren, Victor Lobanenkov
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1002384

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
Cited by: 892
Author(s): A. P. Jason de Koning, Wanjun Gu, Todd A. Castoe, Mark A. Batzer, David D. Pollock
Software Mentions: 2
Published: almost 13 years ago

10.1534/g3.112.003194

Microarray-Based Capture of Novel Expressed Cell Type–Specific Transfrags (CoNECT) to Annotate Tissue-Specific Transcription in Drosophila melanogaster
Cited by: 0
Author(s): Xiaojing Hong, Harshavardhan Doddapaneni, Josep M. Comeron, Matthew J. Rodesch, Heather A. Halvensleben, Chung Yi Nien, F. Bolei, Raghu Metpally, Todd Richmond, Thomas Albert, J. Robert Manak
Software Mentions: 2
Published: over 12 years ago

10.1534/g3.115.021386

Identification of Genes Uniquely Expressed in the Germ-Line Tissues of the Jewel WaspNasonia vitripennis
Cited by: 15
Author(s): Patrick M. Ferree, Christopher Fang, Mariah Mastrodimos, Bruce A. Hay, Henry Amrhein, Omar S. Akbari
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1005946

MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO
Cited by: 17
Author(s): Nicole Kohrs, Stephan Kolodziej, Olga N. Kuvardina, Julia Herglotz, Jasmin Yillah, Stefanie Herkt, Alexander Piechatzek, Gabriela Salinas Riester, Thomas Lingner, Christian Wichmann, Halvard Bönig, Erhard Seifried, Uwe Platzbecker, Hind Medyouf, Manuel Grez, Jörn Lausen
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-9-21

LeARN: a platform for detecting, clustering and annotating non-coding RNAs
Cited by: 10
Author(s): Céline Noirot, Christine Gaspin, Thomas Schiex, Jérôme Gouzy
Software Mentions: 2
Published: almost 17 years ago

10.3389/fpls.2019.00072

Cold Induced Antisense Transcription of FLOWERING LOCUS C in Distant Grasses
Cited by: 16
Author(s): Fuchao Jiao, Kanchan Pahwa, Murray Manning, Niklas Dochy, Koen Geuten
Software Mentions: 2
Published: almost 6 years ago

10.1136/annrheumdis-2018-214930

Altered DNA methylation in children born to mothers with rheumatoid arthritis during pregnancy
Cited by: 7
Author(s): Hilal Ince-Askan, Pooja R. Mandaviya, Janine F. Felix, Liesbeth Duijts, Joyce B. J. van Meurs, Johanna M. W. Hazes, Radboud J E M Dolhain
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2017.02218

Nictaba Homologs from Arabidopsis thaliana Are Involved in Plant Stress Responses
Cited by: 13
Author(s): Lore Eggermont, Karolina Stefanowicz, Els J. M. Van Damme
Software Mentions: 2
Published: almost 7 years ago

10.3389/fnmol.2017.00279

Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder
Cited by: 14
Author(s): Krzysztof J. Szkop, Peter I. C. Cooke, Joanne A. Humphries, Viktoria Kalna, David S. Moss, Eugene F. Schuster, Irene Nobeli
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2105-13-2

ABrowse - a customizable next-generation genome browser framework
Cited by: 18
Author(s): Lei Kong, Jun Wang, Shuqi Zhao, Xiaocheng Gu, Jianxun Luo, Ge Gao
Software Mentions: 2
Published: almost 13 years ago

10.3389/fnmol.2016.00013

Recombinant Human Myelin-Associated Glycoprotein Promoter Drives Selective AAV-Mediated Transgene Expression in Oligodendrocytes
Cited by: 35
Author(s): Georg von Jonquières, Dominik Fröhlich, Claudia B. Klugmann, Xin Wen, Anne E. Harasta, Roshini Ramkumar, Ziggy H. T. Spencer, Gary D. Housley, Matthias Klugmann
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1005709

Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes
Cited by: 110
Author(s): Thomas Arbogast, Abdel‐Mouttalib Ouagazzal, Claire Chevalier, Maksym V. Kopanitsa, Nurudeen O. Afinowi, Eugenia Migliavacca, Belinda S. Cowling, Marie‐Christine Birling, Marie‐France Champy, Alexandre Reymond, Yann Hérault
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2021.636284

Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016
Cited by: 4
Author(s): Yujie Hu, Scott V. Nguyen, Wei Wang, Xin Gan, Yinping Dong, Chang Liu, Xiquan Cui, Jin Xu, Fengqin Li, Séamus Fanning
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2172-9-7

The Innate Immune Database (IIDB)
Cited by: 44
Author(s): Martin Korb, Alistair G. Rust, Vésteinn Thórsson, Christophe Battail, Bin Li, Daehee Hwang, Kathleen A. Kennedy, Jared C. Roach, Carrie M. Rosenberger, Mark Gilchrist, Daniel E. Zak, Carrie D. Johnson, Bruz Marzolf, Alan Aderem, Ilya Shmulevich, Hamid Bolouri
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pgen.1008026

Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency
Cited by: 13
Author(s): Jinli Li, Yi Chen, Tao Zheng, Lingxin Kong, Sucheng Zhu, Yihua Sun, Zixin Deng, Litao Yang, Delin You
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-11-119

Prodigal: prokaryotic gene recognition and translation initiation site identification
Cited by: 7,098
Author(s): Doreene R. Hyatt, Gwo Liang Chen, Philip F. LoCascio, Miriam Land, Frank W. Larimer, Loren Hauser
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pgen.1009290

Natural variation in temperature-modulated immunity uncovers transcription factor bHLH059 as a thermoresponsive regulator in Arabidopsis thaliana
Cited by: 19
Author(s): Friederike Bruessow, Jaqueline Bautor, Gesa Hoffmann, Ipek Yildiz, Jürgen Zeier, Jane E. Parker
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1004507

KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development
Cited by: 94
Author(s): Karl B. Shpargel, Joshua Starmer, Della Yee, Michael Pohlers, Terry Magnuson
Software Mentions: 2
Published: over 10 years ago

Projects: pypi: browser

Papers Mentioning browser 2,125