pypi: browser | Projects | Ecosyste.ms: Papers

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 15 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: about 11 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: over 13 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: almost 14 years ago

10.1186/1471-2164-12-165

Rice-Map: a new-generation rice genome browser
Cited by: 12
Author(s): Jun Wang, Lei Kong, Shuqi Zhao, He Zhang, Liang Tang, Zhe Li, Xiaocheng Gu, Jianxun Luo, Ge Gao
Software Mentions: 2
Published: over 15 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: about 10 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: about 15 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 11 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: over 7 years ago

10.1186/s12864-019-6087-1

Α de novo 3.8-Mb inversion affecting the EDA and XIST genes in a heterozygous female calf with generalized hypohidrotic ectodermal dysplasia
Cited by: 5
Author(s): Clémentine Escouflaire, Emmanuelle Rebours, Mathieu Charles, Sébastien Orellana, Margarita Cano, Julie Rivière, Cécile Grohs, Hélène Hayes, Aurélien Capitan
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2164-14-477

Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq
Cited by: 64
Author(s): Md. Shamimuzzaman, Lila O. Vodkin
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-016-2389-8

Cascade: an RNA-seq visualization tool for cancer genomics
Cited by: 2
Author(s): Aaron R. Shifman, Radia Marie Johnson, Brian T. Wilhelm
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-016-3110-7

Short- and long-term effects of 56Fe irradiation on cognition and hippocampal DNA methylation and gene expression
Cited by: 47
Author(s): Soren Impey, Timothy Jopson, Carl Pelz, Amanuel Tafessu, Fatema Fareh, Damian G. Zuloaga, Tessa Marzulla, Lara Kirstie Riparip, Blair Stewart, Susanna Rosi, Mitchell S. Turker, Jacob Raber
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-16-S8-S8

Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs)
Cited by: 3
Author(s): Samuel K. Handelman, Michał Seweryn, Ryan M. Smith, Katherine E. Hartmann, Daqing Wang, Maciej Pietrzak, Andrew D. Johnson, Andrzej Kloczkowski, Wolfgang Sadée
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-015-1737-4

Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress
Cited by: 22
Author(s): Valeria Wallace-Salinas, Daniel P. Brink, Dag Ahrén, Marie-Françoise Gorwa-Grauslund
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-017-3650-5

Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation
Cited by: 75
Author(s): Philip Kelleher, Francesca Bottacini, Jennifer Mahony, Kieran N. Kilcawley, Douwe van Sinderen
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-13-394

Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica
Cited by: 23
Author(s): Radhika Das, Nathan Anderson, Mary Ellen Koran, Jennifer R. Weidman, Tarjei S. Mikkelsen, Michael Kamal, Susan K. Murphy, Kerstin Linblad-Toh, John M. Greally, Randy L. Jirtle
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-14-84

An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury
Cited by: 34
Author(s): Li‐Wei Chang, Andreu Viader, Nobish Varghese, Jacqueline E. Payton, Jeffrey Milbrandt, Rakesh Nagarajan
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-15-619

Metabolic pathways for the whole community
Cited by: 51
Author(s): Niels W. Hanson, Kishori M. Konwar, Alyse K. Hawley, Tomer Altman, Peter D. Karp, Steven J. Hallam
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2164-13-424

H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
Cited by: 377
Author(s): Krishanpal Karmodiya, Arnaud R Krebs, Mustapha Oulad‐Abdelghani, Hiroshi Kimura, László Tora
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12864-015-1713-z

Genomic copy number variation in Mus musculus
Cited by: 37
Author(s): M Elizabeth O Locke, Maja Milojevic, Susan T Eitutis, Nisha Patel, Andrea E Wishart, Mark Daley, Kathleen A. Hill
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2164-14-397

Web-based visual analysis for high-throughput genomics
Cited by: 44
Author(s): Jeremy Goecks, Carl Eberhard, Tomithy Too, Anton Nekrutenko, James Taylor
Software Mentions: 2
Published: about 13 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: about 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: over 11 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 17 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: over 7 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: almost 15 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: 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: 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 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: over 9 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: almost 14 years ago

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: about 13 years ago

10.1186/1745-6150-5-67

Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers
Cited by: 5
Author(s): Georg Fuellen, Stephan Struckmann
Software Mentions: 2
Published: over 16 years ago

10.1242/bio.011585

The canonical eIF4E isoform of<i>C. elegans</i>regulates growth, embryogenesis, and germline sex-determination
Cited by: 8
Author(s): Richard S. Mangio, SarahBeth Votra, David Pruyne
Software Mentions: 2
Published: about 11 years ago

10.1186/s13293-017-0150-x

Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells
Cited by: 50
Author(s): Rachael J. Werner, Bryant M. Schultz, Jacklyn Huhn, Jaroslav Jelı́nek, Jozef Madžo, Nora Engel
Software Mentions: 2
Published: about 9 years ago

10.3390/biology10060500

Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer
Cited by: 9
Author(s): Jeeyong Lee, Joshua Kwon, Dayeon Kim, Misun Park, Kwang‐Seok Kim, In-Hwa Bae, Hyunkyung Kim, Joonseog Kong, Younjoo Kim, Ui-Sup Shin, EunJu Kim
Software Mentions: 2
Published: about 5 years ago

10.3390/biology1020370

Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP
Cited by: 59
Author(s): Michał T. Lorenc, Satomi Hayashi, Jiri Stiller, S. Hong Lee, Sahana Manoli, Pradeep Ruperao, Paul Visendi, Paul J. Berkman, Kaitao Lai, Jacqueline Batley, David Edwards
Software Mentions: 2
Published: almost 14 years ago

10.1155/2014/893501

AmalgamScope: Merging Annotations Data across the Human Genome
Cited by: 0
Author(s): Georgia Tsiliki, Konstantinos Tsaramirsis, Σοφία Κοσσίδα
Software Mentions: 2
Published: over 12 years ago

10.1155/2014/730814

BLAT-Based Comparative Analysis for Transposable Elements: BLATCAT
Cited by: 0
Author(s): Sang-Bum Lee, Sumin Oh, Keunsoo Kang, Kyudong Han
Software Mentions: 2
Published: over 12 years ago

10.1038/s41416-020-0907-6

BRD4 promotes metastatic potential in oral squamous cell carcinoma through the epigenetic regulation of the MMP2 gene
Cited by: 12
Author(s): Takaya Yamamoto, Akiyuki Hirosue, Masafumi Nakamoto, Ryoji Yoshida, Junki Sakata, Yuichiro Matsuoka, Katsunobu Kawahara, Yuka Nagao, Masashi Nagata, Nobuhiro Takahashi, Akimitsu Hiraki, Masanori Shinohara, Mitsuyoshi Nakao, Noriko Saitoh, Hideki Nakayama
Software Mentions: 2
Published: about 6 years ago

10.1186/1475-2867-5-29

Epigenetic inactivation and aberrant transcription of CSMD1 in squamous cell carcinoma cell lines
Cited by: 29
Author(s): Toni M. Richter, Benton D. Tong, Steven B. Scholnick
Software Mentions: 2
Published: almost 21 years ago

10.3390/life11040340

Cross-Validation of Next-Generation Sequencing Technologies for Diagnosis of Chromosomal Mosaicism and Segmental Aneuploidies in Preimplantation Embryos Model
Cited by: 6
Author(s): Anıl Biricik, Ettore Cotroneo, Maria Giulia Minasi, Pierfrancesco Greco, Sara Bono, Matteo Surdo, Federica Lecciso, Mariateresa Sessa, Francesco Fiorentino, Francesca Spinella, Ermanno Greco
Software Mentions: 2
Published: over 5 years ago

10.26508/lsa.201800115

Optimized ChIP-seq method facilitates transcription factor profiling in human tumors
Cited by: 40
Author(s): Abhishek A. Singh, Karianne Schuurman, Ekaterina Nevedomskaya, Suzan Stelloo, Simon Linder, Marjolein Droog, Yongsoo Kim, Joyce Sanders, Henk van der Poel, Andries M. Bergman, Lodewyk Wessels, Wilbert Zwart
Software Mentions: 2
Published: over 7 years ago

10.1097/MD.0000000000013094

Clinical, cytogenetic, and molecular findings in a fetus with ultrasonic multiple malformations, 4q duplication, and 7q deletion
Cited by: 6
Author(s): Fagui Yue, Yuting Jiang, Yang Yu, Xiao Yang, Hongguo Zhang, Ruizhi Liu, Ruixue Wang
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.ymeth.2018.11.005

Optimization of DamID for use in primary cultures of mouse hepatocytes
Cited by: 5
Author(s): Leonardo Gatticchi, Jose I. de las Heras, Rita Roberti, Eric C. Schirmer
Software Mentions: 2
Published: over 7 years ago

10.1007/978-1-4939-7737-6_4

PomBase: The Scientific Resource for Fission Yeast
Cited by: 31
Author(s): Antonia Lock, Kim Rutherford, Midori A. Harris, Valerie Wood
Software Mentions: 2
Published: over 8 years ago

10.1099/mgen.0.000210

Copy number variation is associated with gene expression change in archaea
Cited by: 11
Author(s): Keely Dulmage, Cynthia L. Darnell, Angie Vreugdenhil, Amy K. Schmid
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40168-018-0399-2

ReprDB and panDB: minimalist databases with maximal microbial representation
Cited by: 19
Author(s): Wei Zhou, Julia Oh
Software Mentions: 2
Published: over 8 years ago

10.1186/s13100-018-0142-3

Variation in proviral content among human genomes mediated by LTR recombination
Cited by: 63
Author(s): Jainy Thomas, Hervé Perron, Cédric Feschotte
Software Mentions: 2
Published: over 7 years ago

10.1186/2040-2392-4-48

Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism
Cited by: 43
Author(s): Varun Warrier, Simon Baron‐Cohen, Bhismadev Chakrabarti
Software Mentions: 2
Published: over 13 years ago

10.1093/molbev/msab050

The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects
Cited by: 46
Author(s): Parul Johri, Kellen Riall, Hannes Becher, Laurent Excoffier, Brian Charlesworth, Jeffrey D. Jensen
Software Mentions: 2
Published: over 5 years ago

10.1093/molbev/msaa296

dbCNS: A New Database for Conserved Noncoding Sequences
Cited by: 3
Author(s): Jun Inoue, Naruya Saitou
Software Mentions: 2
Published: almost 6 years ago

10.1093/molbev/msz060

Emergence of a Thrombospondin Superfamily at the Origin of Metazoans
Cited by: 5
Author(s): Deborah K. Shoemark, Berenice Ziegler, Hiroshi Watanabe, Jennifer Strompen, Richard P. Tucker, Suat Özbek, Josephine C. Adams
Software Mentions: 2
Published: over 7 years ago

10.1186/1476-4598-8-42

The novel RASSF6 and RASSF10 candidate tumour suppressor genes are frequently epigenetically inactivated in childhood leukaemias
Cited by: 105
Author(s): Luke B. Hesson, Thomas L. Dunwell, Wendy N. Cooper, Daniel Catchpoole, A.T. Brini, Raffaella Chiaramonte, Mike Griffiths, Andrew D. Chalmers, Eamonn R. Maher, Farida Latif
Software Mentions: 2
Published: about 17 years ago

10.1016/j.molcel.2019.10.002

R-Loops Promote Antisense Transcription across the Mammalian Genome
Cited by: 97
Author(s): Sue Mei Tan-Wong, Somdutta Dhir, Nick J. Proudfoot
Software Mentions: 2
Published: almost 7 years ago

10.15252/msb.20177548

Pervasive coexpression of spatially proximal genes is buffered at the protein level
Cited by: 78
Author(s): Georg Kustatscher, Piotr Grabowski, Juri Rappsilber
Software Mentions: 2
Published: about 9 years ago

10.1038/mt.2016.112

Long Non-coding RNA BGas Regulates the Cystic Fibrosis Transmembrane Conductance Regulator
Cited by: 26
Author(s): Sheena Saayman, Amanda Ackley, Jon Burdach, Matthew Clemson, Dieter C. Gruenert, Kiyoshi Tachikawa, Pad Chivukula, Marc S. Weinberg, Kevin V. Morris
Software Mentions: 2
Published: about 10 years ago

10.3390/v9070161

Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome
Cited by: 10
Author(s): Przemysław Decewicz, Monika Radlińska, Łukasz Dziewit
Software Mentions: 2
Published: about 9 years ago

10.3390/v13091764

The Evolving Faces of the SARS-CoV-2 Genome
Cited by: 14
Author(s): Maria Schmidt, Mamoona Arshad, Stephan H. Bernhart, Siras Hakobyan, Arsen Arakelyan, Henry Loeffler‐Wirth, Hans Binder
Software Mentions: 2
Published: almost 5 years ago

10.7717/peerj.6028

Comprehensive tissue-specific transcriptome profiling of pineapple (<i>Ananas comosus</i>) and building an eFP-browser for further study
Cited by: 6
Author(s): Qi Mao, Chengjie Chen, Tongxin Xie, Aiping Luan, Chaoyang Liu, Yehua He
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.11052

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily
Cited by: 13
Author(s): Sushma Naithani, Daemon Dikeman, Priyanka Garg, Noor Al-Bader, Pankaj Jaiswal
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.6230

Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time
Cited by: 5
Author(s): Jonas S. Almeida, Janos Hajagos, Joel Saltz, Mary Saltz
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj-cs.433

Multi-level aspect based sentiment classification of Twitter data: using hybrid approach in deep learning
Cited by: 6
Author(s): Sadaf Hussain Janjua, Ghazanfar Farooq Siddiqui, Muddassar Azam Sindhu, Umer Rashid
Software Mentions: 2
Published: over 5 years ago

10.1111/pbi.13327

High‐resolution expression profiling of selected gene sets during plant immune activation
Cited by: 19
Author(s): Pingtao Ding, Bruno Pok Man Ngou, Oliver J. Furzer, Toshiyuki Sakai, Ram Krishna Shrestha, Dan MacLean, Jonathan D. G. Jones
Software Mentions: 2
Published: over 6 years ago

10.1093/pcp/pcw207

TOMATOMICS: A Web Database for Integrated Omics Information in Tomato
Cited by: 18
Author(s): Toru Kudo, Mariko Kobayashi, Shin Terashima, Minami Katayama, Soichi Ozaki, Maasa Kanno, Misa Saito, Koji Yokoyama, Hajime Ohyanagi, Koh Aoki, Yasutaka Kubo, Kentarô Yano
Software Mentions: 2
Published: over 9 years ago

10.1186/1746-4811-7-31

Maize microarray annotation database
Cited by: 9
Author(s): Nanette Coetzer, Alexander Andrew Myburg, David Kenneth Berger
Software Mentions: 2
Published: almost 15 years ago

10.1007/s11103-016-0508-1

Elucidating and mining the Tulipa and Lilium transcriptomes
Cited by: 16
Author(s): Natalia M. Moreno-Pachon, Hendrika A.C.F. Leeggangers, Harm Nijveen, Edouard Severing, Henk W. M. Hilhorst, Richard G. H. Immink
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pbio.1000371

Most “Dark Matter” Transcripts Are Associated With Known Genes
Cited by: 384
Author(s): Harm van Bakel, Corey Nislow, Benjamin J. Blencowe, Timothy R. Hughes
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pcbi.1000147

A General Definition and Nomenclature for Alternative Splicing Events
Cited by: 211
Author(s): Michael Sammeth, Sylvain Foissac, Roderic Guigó
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pcbi.1007863

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation
Cited by: 3
Author(s): Luke Sargent, Yating Liu, Wilson Leung, Nathan T. Mortimer, David Lopatto, Jeremy Goecks, Sarah C. R. Elgin
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1005840

Significant associations between driver gene mutations and DNA methylation alterations across many cancer types
Cited by: 38
Author(s): Yunching Chen, Valer Gotea, Gennady Margolin, Laura Elnitski
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pcbi.1003153

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
Cited by: 350
Author(s): Umadevi Paila, Brad Chapman, Rory Kirchner, Aaron R. Quinlan
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pcbi.1007399

Direct prediction of regulatory elements from partial data without imputation
Cited by: 12
Author(s): Yu Zhang, Shaun Mahony
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pcbi.1000843

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq
Cited by: 55
Author(s): Augix Guohua Xu, Lin He, Zhongshan Li, Ying Xu, Mingfeng Li, Xing Fu, Yanyan Zheng, Yuan Yuan, Corinna Menzel, Na Li, Mehmet Somel, Hao Hu, Wei Chen, Svante Pääbo, Philipp Khaitovich
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0026837

Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma
Cited by: 95
Author(s): Volkhard Seitz, Peter Butzhammer, Burkhard Hirsch, Jochen Hecht, Ines Gütgemann, Anke Ehlers, Dido Lenze, Elisabeth Oker, Anke Sommerfeld, Edda von der Wall, Christoph König, Christian Zinser, Rainer Spang, Michael Hummel
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0131908

Mutagenesis Screen Identifies agtpbp1 and eps15L1 as Essential for T lymphocyte Development in Zebrafish
Cited by: 12
Author(s): Christoph Seiler, Nichole Gebhart, Yong Zhang, Susan A. Shinton, Yuesheng Li, Nicola L. Ross, Xingjun Liu, Qin Li, Alison N. Bilbee, Gaurav K. Varshney, Shawn M. Burgess, Jorune Balciuniene, Darius Balciunas, Richard R. Hardy, Dietmar J. Kappes, David L. Wiest, Jennifer Rhodes
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0067885

HLA Haplotyping from RNA-seq Data Using Hierarchical Read Weighting
Cited by: 50
Author(s): Hyunsung John Kim, Nader Pourmand
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0117415

A Non-Parametric Peak Calling Algorithm for DamID-Seq
Cited by: 5
Author(s): Renhua Li, Leonie U. Hempel, Tingbo Jiang
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0214816

SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome
Cited by: 21
Author(s): Kerstin Neininger, Tobias Marschall, Volkhard Helms
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0018180

Exploring Uncoupling Proteins and Antioxidant Mechanisms under Acute Cold Exposure in Brains of Fish
Cited by: 89
Author(s): Yung‐Che Tseng, Ruo Dong Chen, Magnus Lucassen, Maike Schmidt, Ralf Dringen, Doris Abele, Pung Pung Hwang
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0171661

Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer
Cited by: 88
Author(s): Federica Conte, Giulia Fiscon, Matteo Chiara, Teresa Colombo, Lorenzo Farina, Paola Paci
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0031621

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region
Cited by: 80
Author(s): Satish Sati, Vinay Singh Tanwar, Kalle Anand Kumar, Ashok Patowary, Vaibhav Jain, Sourav Ghosh, Shadab Ahmad, Meghna Singh, Sujatha Reddy, Giriraj Ratan Chandak, Manchala Raghunath, Sridhar Sivasubbu, Kausik Chakraborty, Vinod Scaria, Shantanu Sengupta
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0165176

The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family
Cited by: 44
Author(s): Saura R. Silva, Yani C. A. Diaz, Helen Alves Penha, Daniel Guariz Pinheiro, Camila Cesário Fernandes, Vitor F. O. Miranda, Todd P. Michael, Alessandro M. Varani
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0019481

Elevated miR-499 Levels Blunt the Cardiac Stress Response
Cited by: 130
Author(s): Joseph T.C. Shieh, Yu Huang, Jacqueline Gilmore, Deepak Srivastava
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0220378

Coordinated transcriptional regulation by thyroid hormone and glucocorticoid interaction in adult mouse hippocampus-derived neuronal cells
Cited by: 12
Author(s): Pia Bagamasbad, Jose Ezekiel C. Espina, Joseph R. Knoedler, Arasakumar Subramani, Ariel J. Harden, Robert J. Denver
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0138381

The Role of ARF6 in Biliary Atresia
Cited by: 51
Author(s): Mylarappa Ningappa, Juhoon So, Joseph T. Glessner, Chethan Ashokkumar, Sarangarajan Ranganathan, Jin‐Young Min, Brandon W. Higgs, Qing Sun, Kimberly Haberman, Lori Schmitt, Sílvia Vilarinho, Pramod K. Mistry, Gerard Vockley, Anil Dhawan, George K. Gittes, Hákon Hákonarson, Ronald Jaffe, Shankar Subramaniam, Donghun Shin, Rakesh Sindhi
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0000366

Human GLI3 Intragenic Conserved Non-Coding Sequences Are Tissue-Specific Enhancers
Cited by: 41
Author(s): Amir Ali Abbasi, Zissis Paparidis, Sajid Malik, Debbie K. Goode, Heather Callaway, Greg Elgar, Karl‐Heinz Grzeschik
Software Mentions: 2
Published: over 19 years ago

10.1371/journal.pone.0067222

Detailed Analysis of Focal Chromosome Arm 1q and 6p Amplifications in Urothelial Carcinoma Reveals Complex Genomic Events on 1q, and SOX4 as a Possible Auxiliary Target on 6p
Cited by: 10
Author(s): Pontus Eriksson, Mattias Aine, Gottfrid Sjödahl, Johan Staaf, David Lindgren, Mattias Höglund
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0182371

Long noncoding RNAs are dynamically regulated during β-cell mass expansion in mouse pregnancy and control β-cell proliferation in vitro
Cited by: 15
Author(s): Giorgia Sisino, Alex-Xianghua Zhou, Niklas Dahr, Alan Sabirsh, Mangala M. Soundarapandian, Ranjan J. Perera, Erik Larsson-Lekholm, Maria Chiara Magnone, Magnus Althage, Björn Tyrberg
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0203843

4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin
Cited by: 11
Author(s): Shraddha Shrestha, Dong-Ha Oh, J. Keller McKowen, Maheshi Dassanayake, Craig M. Hart
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0041709

Brain Transcriptional Responses to High-Fat Diet in Acads-Deficient Mice Reveal Energy Sensing Pathways
Cited by: 9
Author(s): Claudia Krüger, K. Ganesh Kumar, Randall L. Mynatt, Júlia Vólaufová, Brenda Richards
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0007479

Probe-Level Analysis of Expression Microarrays Characterizes Isoform-Specific Degradation during Mouse Oocyte Maturation
Cited by: 29
Author(s): Jesse Salisbury, Keith W. Hutchison, Karen Wigglesworth, John J. Eppig, Joel H. Graber
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pone.0054359

Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data
Cited by: 37
Author(s): Анна Герасимова, Lukas Chávez, Bin Li, Grégory Seumois, Jason A. Greenbaum, Anjana Rao, Pandurangan Vijayanand, Bjoern Peters
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0017125

Ontogenetic De Novo Copy Number Variations (CNVs) as a Source of Genetic Individuality: Studies on Two Families with MZD Twins for Schizophrenia
Cited by: 66
Author(s): Sujit Maiti, Kiran Kumar, Christina A Castellani, Richard O’Reilly, Shiva M. Singh
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0243791

PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence
Cited by: 9
Author(s): Caitlin Mills, Anushya Muruganujan, Dustin Ebert, Crystal N. Marconett, Juan Pablo Lewinger, Paul D. Thomas
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0082499

Metabolomics Coupled with Multivariate Data and Pathway Analysis on Potential Biomarkers in Gastric Ulcer and Intervention Effects of Corydalis yanhusuo Alkaloid
Cited by: 30
Author(s): Tianjiao Li, Shuai Wang, Xin-He Meng, Yong-Rui Bao, Shanshan Guan, Bo Liu, Chen Lü, Lei Wang, Xiaorong Ran
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0029758

Twist1 Directly Regulates Genes That Promote Cell Proliferation and Migration in Developing Heart Valves
Cited by: 40
Author(s): Mary P. Lee, Katherine E. Yutzey
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0123261

ClusTrack: Feature Extraction and Similarity Measures for Clustering of Genome-Wide Data Sets
Cited by: 3
Author(s): Halfdan Rydbeck, Geir Kjetil Sandve, Egil Ferkingstad, Boris Simovski, Morten Rye, Eivind Hovig
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0120296

Genome-Wide Transcript Profiling Reveals Novel Breast Cancer-Associated Intronic Sense RNAs
Cited by: 3
Author(s): Sang Woo Kim, Elane Fishilevich, Gustavo Arango-Argoty, Yuefeng Lin, Guodong Liu, Zhihua Li, A. Paula Monaghan, Mark Nichols, Bino John
Software Mentions: 2
Published: over 11 years ago

Projects: pypi: browser

Enhanced Analysis

Science Score: 65/100

Penalties:

Papers Mentioning browser 2,125