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Understanding the disease genome: gene essentiality and the interplay of selection, recombination and mutation

Reuben J. Pengelly, Alejandra Vergara-Lope, Dareen Alyousfi, M. Reza Jabalameli, Andrew Collins
2017 Briefings in Bioinformatics  
Increasing understanding of the interplay between genetic recombination, selection and mutation and their relationship to gene essentiality suggests that gene-specific information may be useful for the  ...  Considered alongside additional distinctive properties of the disease genome, such as the timing of the evolutionary emergence of genes and the roles of their products in protein networks, the case for  ...  Gene essentiality and the disease genome Essential genes are critical for cell viability.  ... 
doi:10.1093/bib/bbx110 pmid:28968721 fatcat:trzatwxqabhg5dntdgs7r6y73m

Combined use of feature engineering and machine-learning to predict essential genes in Drosophila melanogaster

Tulio L Campos, Pasi K Korhonen, Andreas Hofmann, Robin B Gasser, Neil D Young
2020 NAR Genomics and Bioinformatics  
Here, we harnessed comprehensive genomic-phenomic datasets publicly available for D. melanogaster and a machine-learning-based workflow to predict essential genes of this fly.  ...  We discovered strong predictors of such genes, paving the way for computational predictions of essentiality in less-studied arthropod pests and vectors of infectious diseases.  ...  For D. melanogaster, studies have sought to infer essential genes computationally using features based 2 NAR Genomics and Bioinformatics, 2020, Vol. 2, No. 3 on gene homology/orthology/ontology, PPI/  ... 
doi:10.1093/nargab/lqaa051 pmid:33575603 pmcid:PMC7671374 fatcat:x5sixw7yxvae7hqt2jdtx7izpm

1P232 Feasibility of the essential maps derived from the microbial genomes(Bioinformatics-structural, functional, and comparative genomics,Oral Presentations)
1P232 微生物ゲノムから同定された必須マップに関する実現性の検証(生命情報科学(構造・機能・比較ゲノミクス),口頭発表,第45回日本生物物理学会年会)

Yusuke Azuma, Motonori Ota
2007 Seibutsu Butsuri  
丘id as 蜘 ents め genome sequenoes and SCOPEC ;adataba5e ot ' catalytic domain ofenzymes , 、 、 ・ eb 岨 しan en 甲 11a血 data 呂et .  ...  lebyex ustiv 鰯 q 風 λ eRcecompurisonbut actUtiUy , noL W 白 pre 日 t a hsUc app ch to compare genomes a5 a whde and pmvide 凱 a 丘Ule・ um ・ 峨 ・ fdata abcu 匸曲 曲 ue .  ...  . ・ 生命 t 青報 PhyiogeneticAnalysesefEssendal Genes by Using OR レGENE Himoshi Kaw 目 皿 o ω , } 五deaki Mixuno 〔 2)and Ak 血 Dri Sarai ω . ( 1: Dep 匸 of thoscience日 nd Bioinformatics , Graduate翫hool Df Computer  ... 
doi:10.2142/biophys.47.s81_3 fatcat:y5eyqgg5fvfmvppu23ozkwdqk4

1P230 Phylogenetic Analyses of Essential Genes by Using ORI-GENE(Bioinformatics-comparative genomics and molecular evolution,Poster Presentations)
1P230 ORI-GENEを用いた必須遺伝子の進化系統解析(生命情報科学(比較ゲノミクス・分子進化),ポスター発表,第45回日本生物物理学会年会)

Hirotoshi Kawano, Hideaki Mizuno, Akinori Sarai
2007 Seibutsu Butsuri  
丘id as 蜘 ents め genome sequenoes and SCOPEC ;adataba5e ot ' catalytic domain ofenzymes , 、 、 ・ eb 岨 しan en 甲 11a血 data 呂et .  ...  lebyex ustiv 鰯 q 風 λ eRcecompurisonbut actUtiUy , noL W 白 pre 日 t a hsUc app ch to compare genomes a5 a whde and pmvide 凱 a 丘Ule・ um ・ 峨 ・ fdata abcu 匸曲 曲 ue .  ...  . ・ 生命 t 青報 PhyiogeneticAnalysesefEssendal Genes by Using OR レGENE Himoshi Kaw 目 皿 o ω , } 五deaki Mixuno 〔 2)and Ak 血 Dri Sarai ω . ( 1: Dep 匸 of thoscience日 nd Bioinformatics , Graduate翫hool Df Computer  ... 
doi:10.2142/biophys.47.s81_1 fatcat:2humu4dhybapdjdafrfwcf5z6q

Index [chapter]

Essentials of Genomics and Bioinformatics  
project 32ff, 48 -maps 32 -number ofgenes 34 188 167 202ff 177 -telomeres 34 drug discovery, and bioinformatics 105ff -gene-centric-107 -target-centric -107 drug targets, identification  ...  Turner syndrome 75 twin studies 80 two-dimensional gel electrophoresis see 2D gel two-locus analysis 151 Genome and Human Rights 385 working draft of human genome sequence 48 Web-based database intergration  ... 
doi:10.1002/9783527612642.index fatcat:u5eldwcccjfm5og25lj4moi7ai

Introduction to minitrack: computational issues in bioinformatics

H.H. Ali
2003 36th Annual Hawaii International Conference on System Sciences, 2003. Proceedings of the  
Employing algorithmic approaches are expected to be essential to the development and advancement of many fields in biosciences.  ...  A true multidisciplinary field of study, Bioinformatics deals with the development and use of mathematical and computational methods to assist in modeling and solving problems in biosciences.  ...  In the first paper, "Comparative Genome Anotation for Mapping, Prediction and discovery of Genes," by Kappen and Salbaum, the analysis of specific chromosomes in two genomes, the human genome and the muse  ... 
doi:10.1109/hicss.2003.1174801 fatcat:hxybzz4dengnho3y4khop6rska

An adaptive landscape for training in the essentials of next gen sequencing data acquisition and bioinformatic analysis

Mark Farman, Patrick Calie, Jerzy Jaromczyk, Jolanta Jaromczyk, Neil Moore, Daniel Harris, Chris Schardl
2014 BMC Bioinformatics  
P O S T E R P R E S E N T A T I O N Open Access An adaptive landscape for training in the essentials of next gen sequencing data acquisition and bioinformatic analysis Mark Farman 1,2 , Patrick Calie 3  ...  RNASeq data to a reference genome, construction of in silico gene models, and populating a genome browser, to name a few.  ... 
doi:10.1186/1471-2105-15-s10-p25 pmcid:PMC4196053 fatcat:r5do5f5mrnhijaqfywzydjk7rm

Page 650 of Journal of Clinical Oncology Vol. 30, Issue 6 [page]

2012 Journal of Clinical Oncology  
As detailed in Table 2, these bioinformatic functions are an essential component of cancer genomics.  ...  Role of Bioinformatics in Cancer Genomics Bioinformatics Function Background Genome alignment Alignment and reconstruction requires reads and sufficiently long enough to be mapped accurately reconstruction  ... 

Bioinformatics in cancer therapeutics—hype or hope?

Richard Simon
2005 Nature Clinical Practice Oncology  
Development and use of bioinformatics is essential for the future of cancer therapeutics.  ...  Development and application of bioinformatics by multidisciplinary teams conducting focused translational research is essential for all steps of this process.  ... 
doi:10.1038/ncponc0176 pmid:16264939 fatcat:33t6jfuf55g7xmnpmsme6pll7a

Response to Hertz-Fowler and Berriman: Continuing tsetse and Trypanosoma genome sequencing projects

Alberto M.R. Dávila, Phelix A.O. Majiwa, Edmundo C. Grisard, Serap Aksoy, Winston Hide
2004 Trends in Parasitology  
The recent genome initiatives of the neglected parasites Trypanosoma vivax and Trypanosoma congolense, and the vector tsetse [1,2] are promising with regards to the Corresponding author: Alberto M.R.  ...  Acknowledgements A.M.R.D. and E.C.G. are recipients of research productivity fellowships, in addition to bioinformatics research grants from the Brazilian Council for Research and Development.  ...  We stated [1] that both bioinformatics and research are becoming more necessary and essential in DECs.  ... 
doi:10.1016/j.pt.2004.04.014 fatcat:w35jn2nzprfgdoa7vkjxd5hdua

In silico identification and characterization of novel drug targets and outer membrane proteins in the fish pathogen Edwardsiella tarda

Karunasagar, Mohammed Neema, Karunasagar
2011 Open Access Bioinformatics  
The complete genome of the fish pathogen Edwardsiella tarda and the host Danio rerio (zebrafish) was subjected to subtractive genome analysis with the objective of identifying potential drug targets and  ...  The nonparalogous proteins were analyzed for sequence homology with the Database of Essential Genes to determine the essentiality of the proteins for the bacteria.  ...  Acknowledgments The Bioinformatics Sub-distributed Information Centre, Department of Biotechnology (DBT), Government of India and DBT Indo-Norwegian project on fish and shell fish vaccine are gratefully  ... 
doi:10.2147/oab.s15581 fatcat:eongownihnfvfaeorodtij4vke

Bioinformatics: Essential Infrastructure for Global Biology1

ROBERT J. ROBBINS
1996 Journal of Computational Biology  
(Data supplied by MichaelCinkosky and Dennis Benson.) ): A...major...goal of genome informatics should be the integration of genome and genome-related databases.  ...  Despite this, the advance of bioinformatics is essential for much of biology. ⇒ Needed: Coordinated, international efforts to develop better means for supporting worthy bioinformatics activities.  ... 
doi:10.1089/cmb.1996.3.465 pmid:8891960 fatcat:twxmdwnczrcjfjtnzn6q2lqkoy

Think Outside of the Box—Think Genomic

Ram Samudrala
2003 Cell Biology Education  
Discovering Genomics, Proteomics, and Bioinformatics, a book by A.  ...  The book begins by introducing us to basic biological issues and relates this to the sequencing of whole genomes and the questions that the genome sequences can answer.  ...  Discovering Genomics, Proteomics, and Bioinformatics, a book by A.  ... 
doi:10.1187/cbe.03-06-0028 pmcid:PMC256978 fatcat:uv4rrgkbcvgp3evikyyi7wmf5a

Genomics research at Bioinformatics of Genome Regulation and Structure\ Systems Biology (BGRS\SB) conferences in Novosibirsk

Yuriy L. Orlov, Alex V. Kochetov, Guoliang Li, Nikolay A. Kolchanov
2019 BMC Genomics  
In this Special Issue of BMC Genomics we present the studies on computational genomics discussed at BGRS\SB-2018 (Bioinformatics of Genome Regulation and Structure\Systems Biology) multi-conference (http  ...  Parallel special issues of BioMed Central journals after the BGRS conference series include manuscripts in the fields of plant biology, genomics, bioinformatics and genetics, and collated as  ...  The BGRS\SB-2018 conference organization and computer genomics session were supported by the Russian Foundation of Basic Research, Russian-German and Sino-Russian Virtual Bioinformatics Network.  ... 
doi:10.1186/s12864-019-5707-0 pmid:32039700 fatcat:kfidr6jaercq7iguvhsmc2hsr4
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