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10.1371/journal.pgen.1002641

Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies
Cited by: 121
Author(s): Joseph P. Jarvis, Laura B. Scheinfeldt, Sameer Soi, Charla Lambert, Larsson Omberg, Bart Ferwerda, Alain Froment, Jean-Marie Bodo, William Beggs, Gabriel E. Hoffman, Jason G. Mezey, Sarah A. Tishkoff
Software Mentions: 2
Published: over 12 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

10.1093/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

10.1186/1748-7188-6-4

Fast local fragment chaining using sum-of-pair gap costs
Cited by: 14
Author(s): Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0074132

Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates
Cited by: 25
Author(s): Joana Pereira, Warren E. Johnson, Stephen J. O’Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 2
Published: almost 10 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

10.1371/journal.pgen.1000163

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq
Cited by: 518
Author(s): Alexandra Sittka, Sacha Lucchini, Kai Papenfort, Cynthia M. Sharma, Katarzyna Rolle, Tim T. Binnewies, Jay C. D. Hinton, Jörg Vogel
Software Mentions: 2
Published: over 16 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

10.1186/1471-2164-15-765

Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature
Cited by: 80
Author(s): Alba Nicoletta Mininni, Massimo Milan, Serena Ferraresso, T. Petochi, Patrizia Di Marco, G. Marino, Silvia Livi, Chiara Romualdi, Luca Bargelloni, Tomaso Patarnello
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2148-9-85

Origin and evolution of the RIG-I like RNA helicase gene family
Cited by: 224
Author(s): Jun Zou, Ming Chang, Pin Nie, Chris J. Secombes
Software Mentions: 2
Published: almost 16 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

10.1371/journal.pgen.1008827

Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution
Cited by: 53
Author(s): Christian D. Huber, Bernard Kim, Kirk E. Lohmueller
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1005947

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies
Cited by: 91
Author(s): Qiongshi Lu, Ryan L. Powles, Qian Wang, B. Julie He, Hongyu Zhao
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-015-1533-1

Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea
Cited by: 17
Author(s): Gustavo Rodríguez-Esteban, Alejandro González-Sastre, José Ignacio Rojo-Laguna, Emili Saló, Josep F. Abril
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2148-9-207

Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family
Cited by: 47
Author(s): William J. Gillis, John St. John, Bruce Bowerman, Stephan Schneider
Software Mentions: 2
Published: over 15 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

10.1371/journal.pgen.0020024

SPA: A Probabilistic Algorithm for Spliced Alignment
Cited by: 25
Author(s): Erik van Nimwegen, Nicodème Paul, Robert P. Sheridan, Mihaela Zavolan
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pgen.1006700

Probing the canonicity of the Wnt/Wingless signaling pathway
Cited by: 37
Author(s): Alexandra Franz, Daria Shlyueva, Erich Brunner, Alexander Stark, Konrad Basler
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-10-215

Regression based predictor for p53 transactivation
Cited by: 7
Author(s): Sivakumar Gowrisankar, Anil G. Jegga
Software Mentions: 2
Published: over 15 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

10.1186/1471-2156-12-27

PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
Cited by: 10
Author(s): Ram Vinay Pandey, Robert Kofler, Pablo Orozco‐terWengel, Viola Nolte, Christian Schlötterer
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1001116

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data
Cited by: 484
Author(s): Abigail W. Bigham, Marc Bauchet, Dalila Pinto, Xiaole Mao, Joshua M. Akey, Rui Mei, Stephen W. Scherer, Colleen G. Julian, Megan J. Wilson, David López Herráez, Tom D. Brutsaert, Esteban J. Parra, Lorna G. Moore, Mark D. Shriver
Software Mentions: 2
Published: about 14 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/s41598-018-36927-7

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/s41598-018-37678-1

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

10.1371/journal.pgen.1008694

WHIMP links the actin nucleation machinery to Src-family kinase signaling during protrusion and motility
Cited by: 7
Author(s): Shail Kabrawala, Margaret D. Zimmer, Kenneth Campellone
Software Mentions: 2
Published: over 4 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

10.1038/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/s41598-017-04642-4

Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population
Cited by: 56
Author(s): Sang Moon Lee, Jihae Seo, Jinman Park, Jae Yong Nam, Ahyoung Choi, Jason S. Ignatius, Robert Bjornson, Jong Hee Chae, In Jin Jang, Sanghyuk Lee, Woong-Yang Park, Daehyun Baek, Murim Choi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1008977

Systematic identification of functional SNPs interrupting 3’UTR polyadenylation signals
Cited by: 21
Author(s): Eldad D. Shulman, Ran Elkon
Software Mentions: 2
Published: over 4 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

10.1186/1471-2172-9-7

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.1005050

Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication
Cited by: 52
Author(s): Christine R. Beck, Claudia M.B. Carvalho, Linda Banser, Tomasz Gambin, Danielle Stubbolo, Bo Yuan, Karen Sperle, Suzanne M. McCahan, Marco Henneke, Pavel Seeman, James Garbern, Grace M. Hobson, James R. Lupski
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1001134

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome
Cited by: 461
Author(s): Robert S. Illingworth, Ulrike Gruenewald-Schneider, Shaun Webb, Alastair Kerr, Keith James, Daniel J. Turner, Colin Smith, David J. Harrison, Robert Andrews, Adrian Bird
Software Mentions: 2
Published: about 14 years ago

10.1186/s12859-021-04359-2

Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders
Cited by: 0
Author(s): Quentin Ferré, Jeanne Chèneby, Denis Puthier, Cécile Capponi, Benoît Ballester
Software Mentions: 2
Published: about 3 years ago

10.1038/s41598-020-74687-5

Evaluation of blood gene expression levels in facioscapulohumeral muscular dystrophy patients
Cited by: 10
Author(s): Mirko Signorelli, Amanda G. Mason, Karlien Mul, Teresinha Evangelista, Hailiang Mei, N.C. Voermans, Stephen J. Tapscott, Roula Tsonaka, B.G.M. van Engelen, Silvère M. van der Maarel, Pietro Spitali
Software Mentions: 2
Published: about 4 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/s41598-021-81387-1

Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus
Cited by: 17
Author(s): Vitor Lima Coelho, Tarcísio Fontenele de Brito, Ingrid Alexandre de Abreu Brito, Maira Arruda Cardoso, Mateus Berni, Helena Araujo, Michael Sammeth, Andrea Pane
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1004885

Interactions of Chromatin Context, Binding Site Sequence Content, and Sequence Evolution in Stress-Induced p53 Occupancy and Transactivation
Cited by: 49
Author(s): Dan Su, Xuting Wang, Michelle R. Campbell, Lingyun Song, Alexias Safi, Gregory E. Crawford, Douglas A. Bell
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-021-90422-0

Simplification of culture conditions and feeder-free expansion of bovine embryonic stem cells
Cited by: 24
Author(s): Delia Alba Soto, Micaela Navarro, Canbin Zheng, Michelle M. Halstead, Chuan Zhou, Carly Guiltinan, Jun Wu, Pablo J. Ross
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-13-253

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
Cited by: 15
Author(s): Danielle G. Lemay, William Martin, Angie S. Hinrichs, Monique Rijnkels, J. Bruce German, Ian F Korf, Katherine S. Pollard
Software Mentions: 2
Published: about 12 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

10.3390/s18082633

PHAROS—PHysical Assistant RObot System
Cited by: 42
Author(s): Ângelo Costa, Ester Martínez-Martín, Miguel Cazorla, Vicente Julián
Software Mentions: 2
Published: over 6 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

10.1186/s13029-015-0032-8

LocusTrack: Integrated visualization of GWAS results and genomic annotation
Cited by: 28
Author(s): Gabriel Cuéllar-Partida, Miguel E. Renteriá, Stuart MacGregor
Software Mentions: 2
Published: almost 10 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

10.1371/journal.pgen.1007581

Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation
Cited by: 20
Author(s): Patrick Torbey, Elodie Thierion, Samuel Collombet, Anne De Cian, Carole Desmarquet-Trin-Dinh, Mathilde Dura, Jean-Paul Concordet, Patrick Charnay, Pascale Gilardi-Hebenstreit
Software Mentions: 2
Published: over 6 years ago

10.1186/s13287-019-1270-5

The long non-coding RNA Snhg3 is essential for mouse embryonic stem cell self-renewal and pluripotency
Cited by: 16
Author(s): Weisi Lu, Jianping Yu, Fang Shi, Jianing Zhang, Rui Huang, Shanshan Yin, Zhou Songyang, Junjiu Huang
Software Mentions: 2
Published: over 5 years ago

10.1002/stem.2294

Jun-Mediated Changes in Cell Adhesion Contribute to Mouse Embryonic Stem Cell Exit from Ground State Pluripotency
Cited by: 16
Author(s): Giulia Veluscek, Yaoyong Li, Shen-Hsi Yang, Andrew D. Sharrocks
Software Mentions: 2
Published: almost 9 years ago

10.7150/thno.47039

Comprehensive characterization of functional eRNAs in lung adenocarcinoma reveals novel regulators and a prognosis-related molecular subtype
Cited by: 18
Author(s): Na Qin, Zijuan Ma, Cheng Wang, Erbao Zhang, Yuancheng Li, Mingtao Huang, Congcong Chen, Chang Zhang, Jingyi Fan, Yayun Gu, Xin Xu, Yang Liu, Xiaoxia Wei, Rong Yin, Yue Jiang, Juncheng Dai, Guangfu Jin, Lin Xu, Hongbing Shen, Hongxia Ma
Software Mentions: 2
Published: almost 5 years ago

10.7150/thno.48744

Proteasome activator PA200 maintains stability of histone marks during transcription and aging
Cited by: 14
Author(s): Tiancai Jiang, Shuang Ma, Xia Han, Zi-Yu Luo, Qianqian Zhu, Tomoki Chiba, Wei Xie, Kui Lin, Xiao‐Bo Qiu
Software Mentions: 2
Published: almost 4 years ago

10.7150/thno.51931

Functional roles of antisense enhancer RNA for promoting prostate cancer progression
Cited by: 22
Author(s): Chun-Wu Pan, Simeng Wen, Lei Chen, Yulei Wei, Yuanjie Niu, Yu Zhao
Software Mentions: 2
Published: almost 4 years ago

10.7150/thno.53170

Tanshinone I, a new EZH2 inhibitor restricts normal and malignant hematopoiesis through upregulation of MMP9 and ABCG2
Cited by: 22
Author(s): Ying Huang, Shanhe Yu, Wenxuan Zhen, Cheng Tien, Dan Wang, Jiebo Lin, Yuxin Wu, Yifan Wang, Yi Chen, Liping Shu, Yi Wang, Xiao Jian Sun, Yi Zhou, Fan Yang, Chih-Hung Hsu, Pengfei Xu
Software Mentions: 2
Published: almost 4 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

10.1038/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/s41398-020-00966-4

Integration of postmortem amygdala expression profiling, GWAS, and functional cell culture assays: neuroticism-associated synaptic vesicle glycoprotein 2A (SV2A) gene is regulated by miR-133a and miR-218
Cited by: 9
Author(s): Magdalena Jurkiewicz, Dirk Moser, Antonius Koller, Lei Yu, Emily I. Chen, David A. Bennett, Turhan Canli
Software Mentions: 2
Published: about 4 years ago

10.1038/s41398-020-01056-1

Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder
Cited by: 12
Author(s): Katarina Truvé, Toshima Z. Parris, Dzeneta Vizlin‐Hodzic, Susanne Salmela, Evelin Berger, Hans Ǻgren, Keiko Funa
Software Mentions: 2
Published: about 4 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

10.1128/mBio.02367-19

Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications
Cited by: 37
Author(s): Bernhard Blank‐Landeshammer, Ines Teichert, Ramona Märker, Minou Nowrousian, Ulrich Kück, Albert Sickmann
Software Mentions: 2
Published: about 5 years ago

10.1186/s12881-016-0359-2

Sacral agenesis: a pilot whole exome sequencing and copy number study
Cited by: 15
Author(s): Robert M. Porsch, Elisa Merello, Patrizia De Marco, Gregory Yin Ming Cheng, Laura Rodriguez, Man-Ting So, Pak C. Sham, Paul Kwong Hang Tam, Valeria Capra, Stacey S. Cherny, Maria Mercè García-Barceló, Desmond Campbell
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1009613

A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila
Cited by: 4
Author(s): Clara Poupault, Diane Choi, Khanh Lam-Kamath, Deepshe Dewett, Ansa Razzaq, Joseph Bunker, Alexis Perry, Irene Cho, Jens Rister
Software Mentions: 2
Published: over 3 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

10.1007/s00439-017-1838-z

Enrichment of putatively damaging rare variants in the DYX2 locus and the reading-related genes CCDC136 and FLNC
Cited by: 8
Author(s): Andrew Adams, Shelley D. Smith, Dongnhu T. Truong, Erik G. Willcutt, Richard K. Olson, John C. DeFries, Bruce F. Pennington, Jeffrey R. Gruen
Software Mentions: 2
Published: about 7 years ago

10.1007/s00439-014-1454-0

A single codon insertion in PICALM is associated with development of familial subvalvular aortic stenosis in Newfoundland dogs
Cited by: 13
Author(s): Joshua A. Stern, Stephen N. White, Linda B. Lehmkuhl, Yamir Reina-Doreste, Jordan L. Ferguson, Nanette Nascone‐Yoder, Kathryn M. Meurs
Software Mentions: 2
Published: over 10 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

10.1186/s40246-021-00342-3

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism
Cited by: 11
Author(s): Evin M. Padhi, Tristan J. Hayeck, Cheng Zhang, Satadal Chatterjee, Brandon J. Mannion, Marta Byrska-Bishop, Marjolaine Willems, Lucile Pinson, Sylvia Redon, Caroline Bénech, Kévin Uguen, Séverine Audebert‐Bellanger, Cédric Le Marechal, Claude Férec, Stéphanie Efthymiou, Fatima Rahman, Shazia Maqbool, Reza Maroofian, Henry Houlden, Rajeeva Musunuri, Giuseppe Narzisi, Avinash Abhyankar, Riana D Hunter, Jennifer A. Akiyama, Lauren Fries, Jeffrey Ng, Elvisa Mehinovic, Nicholas Stong, Andrew S. Allen, Diane E. Dickel, Raphael Bernier, David U. Gorkin, L Pennacchio, Michael C. Zody, Tychele N. Turner
Software Mentions: 2
Published: over 3 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

10.1371/journal.pgen.1008036

LINE-2 transposable elements are a source of functional human microRNAs and target sites
Cited by: 42
Author(s): Rebecca Petri, Per Ludvik Brattås, Yogita Sharma, Marie E. Jönsson, Karolina Pircs, Johan Bengzon, Johan Jakobsson
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1005702

Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish
Cited by: 70
Author(s): Adi Shamay-Ramot, Khen Khermesh, Hagit T. Porath, Michal Barák, Yishay Pinto, Chaim Wachtel, Alona Zilberberg, Tali Lerer-Goldshtein, Sol Efroni, Erez Y. Levanon, Lior Appelbaum
Software Mentions: 2
Published: almost 9 years ago

10.1093/hmg/ddv272

Homozygous loss-of-function variants in European cosmopolitan and isolate populations
Cited by: 25
Author(s): Vera B. Kaiser, Victoria Svinti, James Prendergast, You-Ying Chau, Archie Campbell, Inga Patarčić, Inês Barroso, Peter K. Joshi, Nicholas D. Hastie, Ana Miljković, Martin S. Taylor, Generation Scotland, Uk K, Stefan Enroth, Yasin Memari, Anja Kolb-Kokocinski, Alan F. Wright, Ulf Gyllensten, Richard Durbin, Igor Rudan, Harry Campbell, Ozren Polašek, Åsa Johansson, Sascha Sauer, David J. Porteous, Ross M. Fraser, Camilla Drake, Véronique Vitart, Caroline Hayward, Colin A. Semple, James F. Wilson
Software Mentions: 2
Published: over 9 years ago

10.1002/humu.22842

Facilitating Collaboration in Rare Genetic Disorders Through Effective Matchmaking in DECIPHER
Cited by: 35
Author(s): Eleni A. Chatzimichali, Simon Brent, Benjamin Hutton, Daniel Perrett, Caroline F. Wright, A. Paul Bevan, Matthew E. Hurles, Helen V. Firth, Ganesh Swaminathan
Software Mentions: 2
Published: over 9 years ago

10.1002/humu.22471

A 129-kb Deletion on Chromosome 12 Confers Substantial Protection Against Rheumatoid Arthritis, Implicating the GeneSLC2A3
Cited by: 21
Author(s): Colin Veal, Katherine Reekie, Johnny C. Lorentzen, Peter K. Gregersen, Leonid Padyukov, Anthony J. Brookes
Software Mentions: 2
Published: almost 11 years ago

10.1002/humu.22594

Genetic Variations and Diseases in UniProtKB/Swiss‐Prot: The Ins and Outs of Expert Manual Curation
Cited by: 49
Author(s): Maria Livia Famiglietti, Anne Estreicher, Arnaud Gos, Jerven Bolleman, Sébastien Géhant, Lionel Breuza, Alan Bridge, Sylvain Poux, Nicole Redaschi, Lydie Bougueleret, Ioannis Xénarios
Software Mentions: 2
Published: over 10 years ago

10.1093/humrep/deab099

Exome sequencing reveals variants in known and novel candidate genes for severe sperm motility disorders
Cited by: 28
Author(s): Manon S Oud, Brendan J Houston, Ludmila Voložonoka, Francesco K. Mastrorosa, Giles Holt, Bilal Alobaidi, P F deVries, Galuh D.N. Astuti, Liliana Ramos, Robert I McLachlan, Moira K O'Bryan, Joris A. Veltman, H Chemes, Harsh Sheth
Software Mentions: 2
Published: over 3 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

10.1371/journal.pgen.1006682

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus
Cited by: 37
Author(s): Anchel de Jaime-Soguero, Francesco Aulicino, Gökhan Ertaylan, Anna Griego, Aniello Cerrato, Aravind Tallam, Antonio del Sol, María Pía Cosma, Frederic Lluı́s
Software Mentions: 2
Published: over 7 years ago

10.3390/jof7080600

Transcription Factors in the Fungus Aspergillus nidulans: Markers of Genetic Innovation, Network Rewiring and Conflict between Genomics and Transcriptomics
Cited by: 6
Author(s): Oier Etxebeste
Software Mentions: 2
Published: over 3 years ago

10.1186/1755-8794-2-31

Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease
Cited by: 8
Author(s): Charles G. Danko, Arkady M. Pertsov
Software Mentions: 2
Published: over 15 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

10.3892/ijo.2012.1724

Epigenetic silencing of miR-335 and its host gene MEST in hepatocellular carcinoma
Cited by: 70
Author(s): Osamu Dohi, Kohichiroh Yasui, Yasuyuki Gen, Hisashi Takada, Mio Endo, Kazuhiro Tsuji, Chika Konishi, Naotaka Yamada, Hironori Mitsuyoshi, Nobuaki Yagi, Yuji Naito, Shinji Tanaka, Shigeki Arii, Toshikazu Yoshikawa
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pgen.1000672

Genetic Determinants of Circulating Sphingolipid Concentrations in European Populations
Cited by: 185
Author(s): Andrew A. Hicks, Peter P. Pramstaller, Åsa Johansson, Véronique Vitart, Igor Rudan, Péter Ugocsai, Yurii S. Aulchenko, Christopher S. Franklin, Gerhard Liebisch, Jeanette Erdmann, Inger Jonasson, Irina V. Zorkoltseva, Cristian Pattaro, Caroline Hayward, Aaron Isaacs, Christian Hengstenberg, Susan Campbell, Carsten Gnewuch, A. Cecile J.W. Janssens, A. V. Kirichenko, Inke R. König, Fabio Marroni, Ozren Polašek, Ayşe Demirkan, Ivana Kolčić, Christine Schwienbacher, Wilmar Igl, Zrinka Biloglav, Jacqueline C. M. Witteman, Irene Pichler, Ghazal Zaboli, Tatiana I. Axenovich, Annette Peters, Stefan Schreiber, H‐Erich Wichmann, Heribert Schunkert, Nick Hastie, Ben A. Oostra, Sarah H. Wild, Thomas Meitinger, Ulf Gyllensten, Cornelia M. van Duijn, James F. Wilson, Alan F. Wright, Gerd Schmitz, Harry Campbell
Software Mentions: 2
Published: about 15 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

10.1038/onc.2017.37

Serine hydroxymethyl transferase 1 stimulates pro-oncogenic cytokine expression through sialic acid to promote ovarian cancer tumor growth and progression
Cited by: 29
Author(s): Romi Gupta, Qinghua Yang, Shaillay Kumar Dogra, Narendra Wajapeyee
Software Mentions: 2
Published: over 7 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

10.1186/1471-2164-16-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

10.1371/journal.pgen.1006754

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Cited by: 52
Author(s): Wareed Ahmed, Claudia Sala, Shubhada R. Hegde, Rajiv Kumar Jha, Stewart T. Cole, Valakunja Nagaraja
Software Mentions: 2
Published: over 7 years ago

10.1038/oncsis.2017.32

The prohibitin-repressive interaction with E2F1 is rapidly inhibited by androgen signalling in prostate cancer cells
Cited by: 17
Author(s): Sarah Koushyar, G Economides, S Zaat, Wen Guo Jiang, Charlotte Bevan, Dafydd Alwyn Dart
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1002390

Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development
Cited by: 61
Author(s): Sushma Nagaraja Grellscheid, Caroline Dalgliesh, Markus Storbeck, Andrew Best, Yilei Liu, Miriam Jakubik, Ylva Mende, Ingrid Ehrmann, Tomaž Curk, Kristina Roßbach, Cyril F. Bourgeois, James Stévenin, David Grellscheid, Michael S. Jackson, Brunhilde Wirth, David J. Elliott
Software Mentions: 2
Published: almost 13 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

10.1007/s00109-020-01898-8

S100A4 mRNA-protein relationship uncovered by measurement noise reduction
Cited by: 0
Author(s): Angelos Theodoros Athanasiou, Thomas Nußbaumer, Stefan Kummer, Martin Hofer, Iain G. Johnston, Moritz Staltner, Daniela Maria Allmer, Milcah C. Scott, Claus Vogl, Joelle M. Fenger, Jaime F. Modiano, Ingrid Walter, Ralf Steinborn
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.54782

Epigenetic regulation of Wnt7b expression by the cis-acting long noncoding RNA Lnc-Rewind in muscle stem cells
Cited by: 17
Author(s): Andrea Cipriano, Martina Macino, Giulia Buonaiuto, Tiziana Santini, Beatrice Biferali, Giovanna Peruzzi, Alessio Colantoni, Chiara Mozzetta, Monica Ballarino
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.11155

Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway
Cited by: 112
Author(s): Zhiyun Ge, Bao Lin Quek, Karen Beemon, J. Robert Hogg
Software Mentions: 2
Published: almost 9 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

10.7554/eLife.29550

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo
Cited by: 76
Author(s): Michael Stadler, Jenna E. Haines, Michael B. Eisen
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.56697

Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction
Cited by: 5
Author(s): Jan Hendrik van Weerd, Rajiv A Mohan, Karel van Duijvenboden, Ingeborg B. Hooijkaas, Vincent Wakker, Bastiaan J. Boukens, Phil Barnett, Vincent M. Christoffels
Software Mentions: 2
Published: over 4 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

10.1186/s12920-015-0087-z

Systems biology of myasthenia gravis, integration of aberrant lncRNA and mRNA expression changes
Cited by: 19
Author(s): Zhaohui Luo, Ye Li, Xiaofang Liu, Mingyao Luo, Liqun Xu, Yue‐Bei Luo, Bo Xiao, Huan Yang
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.41444

The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci
Cited by: 35
Author(s): Anand Kumar Singh, Subhendu Roy Choudhury, Sandip De, Jie Zhang, Stephen Kissane, Vibha Dwivedi, Preethi Ramanathan, Marija Petrić, Luisa Orsini, Daniel Hebenstreit
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.23670

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids
Cited by: 101
Author(s): Sebastián Cánovas, Elena Ivanova, Raquel Romar, Soledad García-Martínez, Cristina Soriano‐Úbeda, Francisco Alberto García–Vázquez, Heba Saadeh, Simon Andrews, Gavin Kelsey, Pilar Coy
Software Mentions: 2
Published: almost 8 years ago

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