pypi: browser | Projects | Ecosyste.ms: Papers

10.3389/fimmu.2015.00616

Bad News: Analysis of the Quality of Information on Influenza Prevention Returned by Google in English and Italian
Cited by: 21
Author(s): Ali Maki, Roger Evans, Pietro Ghezzi
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-11-519

Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated
Cited by: 99
Author(s): Mun-Kit Choy, Mehregan Movassagh, Hock Guan Goh, Martin R. Bennett, Thomas A. Down, Roger Foo
Software Mentions: 2
Published: about 16 years ago

10.1186/1471-2164-9-398

Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray
Cited by: 54
Author(s): Hongying Jiang, Ming Yi, Jianbing Mu, Louie Zhang, Alasdair Ivens, Leszek J. Klimczak, Yentram Huyen, Robert M. Stephens, Xin-zhuan Su
Software Mentions: 2
Published: about 18 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 12 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: over 16 years ago

10.3389/fgene.2017.00042

Characterization of X-Chromosome Gene Expression in Bovine Blastocysts Derived by In vitro Fertilization and Somatic Cell Nuclear Transfer
Cited by: 10
Author(s): Byungkuk Min, Jung Sun Park, Kyuheum Jeon, Yong‐Kook Kang
Software Mentions: 2
Published: over 9 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 16 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.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 6 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

10.1186/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 5 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.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: over 6 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.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: 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 15 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 11 years ago

10.3389/fgene.2018.00025

Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2
Cited by: 8
Author(s): Øivind Skare, Rolv Terje Lie, Øystein Ariansen Haaland, Miriam Gjerdevik, Julia Romanowska, Håkon K. Gjessing, Astanand Jugessur
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2015.00167

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds
Cited by: 56
Author(s): Beatriz Gutiérrez-Gil, Juan José Arranz, Pamela Wiener
Software Mentions: 2
Published: over 11 years ago

10.1186/s12862-018-1306-y

The evolution of ependymin-related proteins
Cited by: 15
Author(s): Carmel McDougall, Michael Hammond, Simon Christopher Dailey, Ildikó Maureen Lara Somorjai, Scott F. Cummins, Bernard M. Degnan
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2018.00214

Screening of the LAMB2, WT1, NPHS1, and NPHS2 Genes in Pediatric Nephrotic Syndrome
Cited by: 6
Author(s): Aiysha Abid, Saba Shahid, Madiha Shakoor, Ali Lanewala, Seema Hashmi, Shagufta Khaliq
Software Mentions: 2
Published: over 8 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

10.1038/s41598-017-07539-4

Reactivity of human AGO2 monoclonal antibody 11A9 with the SWI/SNF complex: A case study for rigorously defining antibody selectivity
Cited by: 9
Author(s): Roderick A. P. M. van Eijl, Teun van den Brand, Luan N. Nguyen, Klaas W. Mulder
Software Mentions: 2
Published: about 9 years ago

10.3389/fgene.2020.00766

Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice
Cited by: 12
Author(s): Nannan Zhao, Kang Zhang, Chunchao Wang, Hengyu Yan, Yue Liu, Wenying Xu, Zhen Su
Software Mentions: 2
Published: about 6 years ago

10.1093/database/baz056

LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species
Cited by: 6
Author(s): Leiming You, Jiaqi Chi, Shengfeng Huang, Ting Yu, Guangrui Huang, Yuchao Feng, Xiaopu Sang, Xinhui Gao, Tingan Li, Zirui Yue, Aijie Liu, Shangwu Chen, Anlong Xu
Software Mentions: 2
Published: almost 8 years ago

10.1093/database/bat034

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
Cited by: 120
Author(s): Deeksha Bhartiya, Koustav Pal, Sourav Ghosh, Shruti Kapoor, Saakshi Jalali, Bharat Panwar, Sakshi Jain, Satish Sati, Shantanu Sengupta, Chetana Sachidanandan, Gajendra P. S. Raghava, Sridhar Sivasubbu, Vinod Scaria
Software Mentions: 2
Published: almost 14 years ago

10.1093/database/bax059

BioSearch: a semantic search engine for Bio2RDF
Cited by: 19
Author(s): Wei Hu, Honglei Qiu, Junhui Huang, Michel Dumontier
Software Mentions: 2
Published: almost 10 years ago

10.1093/database/bav103

WaspAtlas: aNasonia vitripennisgene database and analysis platform
Cited by: 17
Author(s): Nathaniel J. Davies, Eran Tauber
Software Mentions: 2
Published: almost 12 years ago

10.1093/database/baw162

viruSITE—integrated database for viral genomics
Cited by: 47
Author(s): Matej Stano, Gábor Beke, Ľuboš Klučár
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-15-1060

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor
Cited by: 64
Author(s): Michael N Romanov, Marta Farré, Pamela E Lithgow, Katie E. Fowler, Benjamin M. Skinner, Rebecca E O'Connor, Gothami Fonseka, Niclas Backström, Yoichi Matsuda, Chizuko Nishida, Peter Houde, Erich D. Jarvis, Hans Ellegren, David W. Burt, Denis M. Larkin, Darren K. Griffin
Software Mentions: 2
Published: almost 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: about 12 years ago

10.1093/database/baz009

The radish genome database (RadishGD): an integrated information resource for radish genomics
Cited by: 11
Author(s): Hee‐Ju Yu, Seung-Hoon Baek, Young-Joon Lee, Ara Cho, Jeong‐Hwan Mun
Software Mentions: 2
Published: almost 8 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: over 10 years ago

10.1186/1471-2148-7-199

Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies
Cited by: 37
Author(s): Aurora Ruiz‐Herrera, Terence J. Robinson
Software Mentions: 2
Published: almost 20 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: about 15 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: about 8 years ago

10.1186/s12862-018-1311-1

Rapid microevolution during recent range expansion to harsh environments
Cited by: 26
Author(s): Yiyong Chen, Noa Shenkar, Ping Ni, Ya‐Ping Lin, Shiguo Li, Aibin Zhan
Software Mentions: 2
Published: almost 8 years ago

10.1093/database/bax074

Echinobase: an expanding resource for echinoderm genomic information
Cited by: 60
Author(s): Parul Kudtarkar, R. Andrew Cameron
Software Mentions: 2
Published: almost 10 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

10.1111/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

10.1186/s13148-018-0470-7

Methylated genomic loci encoding microRNA as a biomarker panel in tissue and saliva for head and neck squamous cell carcinoma
Cited by: 15
Author(s): Yu Cao, Katherine Green, Steve Quattlebaum, Ben Milam, Ling Lu, Dexiang Gao, Hui He, Ningning Li, Liwei Gao, F. De Havilland Hall, Matthew Whinery, Elyse Handley, Yi Ma, Tao Xu, Feng Jin, Jing Xiao, Minjie Wei, Derek E. Smith, Sophia Bornstein, Neil D. Gross, Dohun Pyeon, John I. Song, Shi Lu
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2148-9-286

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites
Cited by: 26
Author(s): Alan M. Moses
Software Mentions: 2
Published: almost 18 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

10.1186/s13148-016-0269-3

MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics
Cited by: 10
Author(s): Ram Vinay Pandey, Walter Pulverer, Rainer Kallmeyer, Gabriel Beikircher, Stephan Pabinger, Albert Kriegner, Andreas Weinhäusel
Software Mentions: 2
Published: about 10 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

10.1371/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 5 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.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: almost 8 years ago

10.1186/1471-2105-9-432

easyExon – A Java-based GUI tool for processing and visualization of Affymetrix exon array data
Cited by: 18
Author(s): Ting‐Yu Chang, Yin-Yi Li, C.-L. Jen, Tsun-Po Yang, Chi‐Hung Lin, Ming Hsu, Hsei‐Wei Wang
Software Mentions: 2
Published: almost 18 years ago

10.3390/cells9010147

IGF-1 Signalling Regulates Mitochondria Dynamics and Turnover through a Conserved GSK-3β–Nrf2–BNIP3 Pathway
Cited by: 46
Author(s): Sarah Riis, Jack Murray, Rosemary O’Connor
Software Mentions: 2
Published: almost 7 years ago

10.3390/cells1041029

A Novel Type III Endosome Transmembrane Protein, TEMP
Cited by: 1
Author(s): Rajith Aturaliya, Markus C. Kerr, Rohan D. Teasdale
Software Mentions: 2
Published: almost 14 years ago

10.1186/s13148-017-0386-7

CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel
Cited by: 44
Author(s): Luca Morandi, Davide Bartolomeo Gissi, Achille Tarsitano, Sofia Asioli, Andrea Gabusi, Claudio Marchetti, Lucio Montebugnoli, Maria Pia Foschini
Software Mentions: 2
Published: about 9 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 7 years ago

10.1016/j.cellsig.2007.01.010

Genomic tagging of endogenous Type IIβ Phosphatidylinositol 5-phosphate 4-kinase in DT40 cells reveals a nuclear localisation
Cited by: 31
Author(s): Jonathan P. Richardson, Minchuan Wang, Jonathan H. Clarke, Ketan Patel, Robin F. Irvine
Software Mentions: 2
Published: over 19 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 10 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: about 5 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 9 years ago

10.1038/cr.2017.25

De novo DNA methylation during monkey pre-implantation embryogenesis
Cited by: 42
Author(s): Fei Gao, Yuyu Niu, Yi Sun, Hanlin Lu, Yongchang Chen, Siguang Li, Yu Kang, Yuan Luo, Chenyang Si, Juehua Yu, Li Chang, Nianqin Sun, Wei Si, Hong Wang, Weizhi Ji, Tao Tan
Software Mentions: 2
Published: over 9 years ago

10.1038/s41422-021-00477-x

Formative pluripotent stem cells show features of epiblast cells poised for gastrulation
Cited by: 42
Author(s): Xiaoxiao Wang, Yunlong Xiang, Yang Yu, Ran Wang, Yu Zhang, Qianhua Xu, Hao Sun, Zhen Zhao, Xiangxiang Jiang, Xiaoqing Wang, Xukun Lu, Dandan Qin, Yujun Quan, Jiaqi Zhang, Ng Shyh‐Chang, Hongmei Wang, Naihe Jing, Wei Xie, Lei Li
Software Mentions: 2
Published: over 5 years ago

10.1186/s13148-019-0666-5

DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer
Cited by: 20
Author(s): Christoph Weigel, Jittiporn Chaisaingmongkol, Yassen Assenov, Christine Kuhmann, Volker Winkler, Irene Santi, Olga Bogatyrova, Simone Kaucher, Justo Lorenzo Bermejo, Suet Yi Leung, Tsun Leung Chan, Felix Lasitschka, M. Bohrer, Alexander Marx, Roland Heyny-von Haußen, Christel Herold‐Mende, Gerhard Dyckhoff, Petra Boukamp, K.-W. Delank, K. Hörmann, Burkhard M. Lippert, G. Baier, Andreas Dietz, Christopher C. Oakes, Christoph Plass, Heiko Becher, Peter Schmezer, Heribert Ramroth, Odilia Popanda
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-6-95

Cited by: 12
Author(s): Judith E. Stenger, Hong Xu, Carol Haynes, Elizabeth R. Hauser, Margaret A. Pericak‐Vance, Pascal J. Goldschmidt‐Clermont, Jeffery M. Vance
Software Mentions: 2
Published: almost 22 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: over 9 years ago

10.1016/j.celrep.2015.10.030

Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis
Cited by: 33
Author(s): Mayuri Rege, Vidya Subramanian, Chenchen Zhu, Tsung Han Hsieh, Assaf Weiner, Nir Friedman, Sandra Clauder‐Münster, Lars M. Steinmetz, Oliver J. Rando, Laurie A. Boyer, Craig L. Peterson
Software Mentions: 2
Published: almost 11 years ago

10.1111/cmi.12890

Systematic gene overexpression in<i>Candida albicans</i>identifies a regulator of early adaptation to the mammalian gut
Cited by: 35
Author(s): Sadri Znaidi, Lasse van Wijlick, Arturo Hernández‐Cervantes, Natacha Sertour, Jean‐Luc Desseyn, Frédéric Vincent, Ralitsa Atanassova, Valérie Gouyer, Carol A. Munro, Sophie Bachellier‐Bassi, Frédéric Dalle, Thierry Jouault, Marie‐Elisabeth Bougnoux, Christophe d’Enfert
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-15-685

Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing
Cited by: 18
Author(s): Yu Liu, Mehmet Koyutürk, Sean Maxwell, Min Xiang, Marty L Veigl, Richard S. Cooper, Bamidele O. Tayo, Li Li, Thomas LaFramboise, Benlian Wang, Xiaofeng Zhu, Mark R. Chance
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-12-637

Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers
Cited by: 29
Author(s): Hugo J. Parker, Paul Piccinelli, Tatjana Sauka‐Spengler, Marianne Bronner‐Fraser, Greg Elgar
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2105-13-S15-S4

Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
Cited by: 12
Author(s): Joseph S. Reddy, Ranjit Kumar, James Watt, Mark L. Lawrence, Shane C. Burgess, Bindu Nanduri
Software Mentions: 2
Published: about 14 years ago

10.1038/s41421-018-0039-9

DNA methylation reprogramming of functional elements during mammalian embryonic development
Cited by: 43
Author(s): Congru Li, Yong Fan, Guoqiang Li, Xiaocui Xu, Jialei Duan, Rong Li, Xiangjin Kang, Xin Ma, Xuepeng Chen, Youqi Ke, Jie Yan, Ying Lian, Ping Liu, Yue Zhao, Haiquan Zhao, Yaoyong Chen, Yang Yu, Jiang Liu
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-019-6356-z

JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants
Cited by: 6
Author(s): Xuan Zhang, Bang-Zhen Pan, Maosheng Chen, Wen Chen, Jing Li, Zeng-Fu Xu, Changning Liu
Software Mentions: 2
Published: almost 7 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

10.1371/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 9 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 15 years ago

10.1038/s41419-018-0777-5

An antisense RNA capable of modulating the expression of the tumor suppressor microRNA-34a
Cited by: 7
Author(s): Jason T. Serviss, Nathanael Andrews, Jimmy Van den Eynden, Felix Clemens Richter, Miranda Houtman, Mattias Vesterlund, Laura Schwarzmueller, Per Johnsson, Erik Larsson, Dan Grandér, Katja Pokrovskaja Tamm
Software Mentions: 2
Published: over 8 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

10.1186/1471-2164-9-586

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics
Cited by: 17
Author(s): Ki Won Jung, Jongsun Park, Jaeyoung Choi, Bong Soo Park, Seungill Kim, Kyohun Ahn, Jaehyuk Choi, Doil Choi, Seogchan Kang, Yong Hwan Lee
Software Mentions: 2
Published: almost 18 years ago

10.3390/cancers13133180

Immunity Depletion, Telomere Imbalance, and Cancer-Associated Metabolism Pathway Aberrations in Intestinal Mucosa upon Short-Term Caloric Restriction
Cited by: 0
Author(s): Evan Maestri, Kalina Duszka, Vladimir A. Kuznetsov
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-213X-10-105

zTrap: zebrafish gene trap and enhancer trap database
Cited by: 148
Author(s): Koichi Kawakami, Gembu Abe, Tokuko Asada, Kazuhide Asakawa, Ryūji Fukuda, Aki Ito, Pradeep Lal, Naruaki Mouri, Akira Muto, Maximilliano L. Suster, Hitomi Takakubo, Akihiro Urasaki, Hironori Wada, Mikio Yoshida
Software Mentions: 2
Published: almost 16 years ago

10.1038/s41419-021-04017-8

Tissue-specific expression of p73 and p63 isoforms in human tissues
Cited by: 10
Author(s): Clayton B. Marshall, J. Scott Beeler, Brian D. Lehmann, Paula I. González-Ericsson, Violeta Sánchez, Melinda E. Sanders, Kelli L. Boyd, Jennifer A. Pietenpol
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-14-566

Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing
Cited by: 125
Author(s): Christos Palaiokostas, Michaël Bekaert, Andrew Davie, Mairi Cowan, Münevver Oral, John B. Taggart, Karim Gharbi, Brendan McAndrew, David J. Penman, Hervé Migaud
Software Mentions: 2
Published: about 13 years ago

10.1038/s41419-019-2201-1

Epigenetic priming by Dot1l in lymphatic endothelial progenitors ensures normal lymphatic development and function
Cited by: 11
Author(s): Hyunjin Yoo, Young Jae Lee, Chanhyeok Park, Dabin Son, Dong Yoon Choi, Ji Hyun Park, Hee-Jin Choi, Hyun Woo La, Yun Jung Choi, Eun Hye Moon, Dieter Saur, Hyung Min Chung, Hyuk Song, Jeong Tae, Hoon Jang, Dong Ryul Lee, Chankyu Park, Ok Hee Lee, Ssang-Goo Cho, Seok Ho Hong, Gu Kong, Jin‐Hoi Kim, Yun‐Sang Choi, Kwonho Hong
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0003012

A Resource for Transcriptomic Analysis in the Mouse Brain
Cited by: 11
Author(s): Charles Plessy, Michela Fagiolini, Akiko Wagatsuma, Norihiro Harasawa, Takenobu Kuji, Atsuko Asaka-Oba, Yukari Kanzaki, Sayaka Fujishima, Kazunori Waki, Hiroyuki Nakahara, Takao K. Hensch, Piero Carninci
Software Mentions: 2
Published: about 18 years ago

10.1186/s12864-017-4220-6

An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes
Cited by: 22
Author(s): Nora Hohmann, Marcus A. Koch
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0047157

Distinct Distribution of Ectopically Expressed Histone Variants H2A.Bbd and MacroH2A in Open and Closed Chromatin Domains
Cited by: 19
Author(s): E. S. Ioudinkova, Ana Barat, Andrey Pichugin, Eva Markovà, Ilya Sklyar, Iryna Pirozhkova, Chloé Robin, Marc Lipinski, Vasily Ogryzko, Yegor S. Vassetzky, Sergey V. Razin
Software Mentions: 2
Published: almost 14 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: over 13 years ago

10.1016/j.heliyon.2020.e05243

Fast, easy, cheap, robust and safe method of analysis of Sudan dyes in chilli pepper powder
Cited by: 5
Author(s): Joseph Kweku Adjei, Vigil Ahormegah, Alex Kissi Boateng, Harry Kwaku Megbenu, Samuel Asiedu Owusu
Software Mentions: 2
Published: about 6 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

10.1371/journal.pone.0097568

Genome-Wide Quantitative Analysis of Histone H3 Lysine 4 Trimethylation in Wild House Mouse Liver: Environmental Change Causes Epigenetic Plasticity
Cited by: 12
Author(s): Angelika Börsch-Haubold, Inka Montero, Kathryn Konrad, Bernhard Haubold
Software Mentions: 2
Published: over 12 years ago

10.3390/cancers12082137

Epigenetic Targeting of Mcl-1 Is Synthetically Lethal with Bcl-xL/Bcl-2 Inhibition in Model Systems of Glioblastoma
Cited by: 14
Author(s): Enyuan Shang, Trang Nguyen, Chang Shu, Mike‐Andrew Westhoff, Georg Karpel‐Massler, Markus D. Siegelin
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0038240

Genome-Wide Study of Gene Variants Associated with Differential Cardiovascular Event Reduction by Pravastatin Therapy
Cited by: 31
Author(s): Dov Shiffman, Stella Trompet, Judy Z. Louie, Charles M. Rowland, Joseph J. Catanese, Olga A. Iakoubova, Todd G. Kirchgessner, Rudi G. J. Westendorp, Anton J. M. de Craen, P. Eline Slagboom, Brendan M. Buckley, David J. Stott, Naveed Sattar, James J. Devlin, Christopher J. Packard, Ian Ford, Frank M. Sacks, J. Wouter Jukema
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0071691

Differential DNA Methylation Regions in Cytokine and Transcription Factor Genomic Loci Associate with Childhood Physical Aggression
Cited by: 61
Author(s): Nadine Provençal, Matthew Suderman, Doretta Caramaschi, Dongsha Wang, Michael Hallett, Frank Vitaro, Richard E. Tremblay, Moshe Szyf
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0072670

A Minimal Set of Tissue-Specific Hypomethylated CpGs Constitute Epigenetic Signatures of Developmental Programming
Cited by: 20
Author(s): Alejandro Colaneri, Tianyuan Wang, Vijayakanth Pagadala, Jaya Kittur, Nickolas G. Staffa, Shyamal D. Peddada, Elvira Isganaitis, Mary Elizabeth Patti, Lutz Birnbaumer
Software Mentions: 2
Published: about 13 years ago

10.1093/database/bat067

BBGRE: brain and body genetic resource exchange
Cited by: 3
Author(s): Joo Wook Ahn, Abhishek Dixit, Caroline Johnston, Caroline Mackie Ogilvie, David A. Collier, Sarah Curran, Richard Dobson
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0128916

An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples
Cited by: 41
Author(s): Jonathan Scolnick, Michelle Dimon, I‐Ching Wang, Stephanie C. Huelga, Douglas A. Amorese
Software Mentions: 2
Published: over 11 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 10 years ago

10.1371/journal.pone.0250669

Distinct expression of select and transcriptome-wide isolated 3’UTRs suggests critical roles in development and transition states
Cited by: 1
Author(s): Shaoyi Ji, Zihui Yang, Leonardi Gozali, Thomas Kenney, Arif Kocabas, Carolyn Jinsook Park, Mary Hynes
Software Mentions: 2
Published: over 5 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 15 years ago

10.1186/2041-1480-2-S2-S3

HyQue: evaluating hypotheses using Semantic Web technologies
Cited by: 33
Author(s): Alison Callahan, Michel Dumontier, Nigam H. Shah
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0098635

Gene Expression Profiling Analysis of Bisphenol A-Induced Perturbation in Biological Processes in ER-Negative HEK293 Cells
Cited by: 20
Author(s): Rong Yin, Liang Gu, Min Li, Cizhong Jiang, Tongcheng Cao, Xiaobai Zhang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0150768

High Throughput Sequencing Identifies Misregulated Genes in the Drosophila Polypyrimidine Tract-Binding Protein (hephaestus) Mutant Defective in Spermatogenesis
Cited by: 4
Author(s): Vinod Sridharan, Joseph Heimiller, Mark D. Robida, Ravinder Singh
Software Mentions: 2
Published: over 10 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: about 14 years ago

Projects: pypi: browser

Enhanced Analysis

Science Score: 65/100

Penalties:

Papers Mentioning browser 2,125