Recent developments and future directions in computational genomics (Q34020017)

30 July 2017

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title

Recent developments and future directions in computational genomics (English)

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ORCID Public Data File 2021

30 July 2017

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computational genomics

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author name string

Tsoka S

series ordinal

1

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PubMed ID

10967327

30 July 2017

Ouzounis CA

series ordinal

2

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PubMed ID

10967327

30 July 2017

language of work or name

English

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publication date

1 August 2000

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30 July 2017

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30 July 2017

480

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30 July 2017

1

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30 July 2017

42-48

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Representation of function: the next step.

30 July 2017

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Genomics and computational molecular biology

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

From protein sequence to function

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

From genes to protein structure and function: novel applications of computational approaches in the genomic era.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Systems for categorizing functions of gene products.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Alignment of whole genomes

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Bioinformatics: from genome data to biological knowledge.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Positional characterisation of false positives from computational prediction of human splice sites

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Intrinsic and extrinsic approaches for detecting genes in a bacterial genome

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Novel coding regions in four complete archaeal genomes

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Evaluation of gene structure prediction programs.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

GeneMark.hmm: new solutions for gene finding

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Microbial gene identification using interpolated Markov models

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Gene-finding approaches for eukaryotes

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Predicting coiled coils from protein sequences

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Machine learning approaches for the prediction of signal peptides and other protein sorting signals

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Non-globular domains in protein sequences: automated segmentation using complexity measures

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Analysis of compositionally biased regions in sequence databases

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Issues in searching molecular sequence databases

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Methods and statistics for combining motif match scores

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Hidden Markov models for detecting remote protein homologies

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Benchmarking PSI-BLAST in genome annotation.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Superior performance in protein homology detection with the Blocks Database servers

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

The Pfam protein families database.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

A genomic perspective on protein families

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Highly specific protein sequence motifs for genome analysis

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Detecting protein function and protein-protein interactions from genome sequences

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Protein interaction maps for complete genomes based on gene fusion events

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Effective use of sequence correlation and conservation in fold recognition

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

The relationship between protein structure and function: a comprehensive survey with application to the yeast genome

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Late-night thoughts on the sequence annotation problem

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Whole-genome sequence annotation: 'Going wrong with confidence'.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

The EcoCyc and MetaCyc databases

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

SGD: Saccharomyces Genome Database

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

FlyBase: a Drosophila database. The FlyBase consortium

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Integrated access to metabolic and genomic data

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Reconstruction of amino acid biosynthesis pathways from the complete genome sequence.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

KEGG: kyoto encyclopedia of genes and genomes

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

GAIA: framework annotation of genomic sequence

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Gene ontology: tool for the unification of biology

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Bioinformatics--principles and potential of a new multidisciplinary tool

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Differential genome analysis applied to the species-specific features of Helicobacter pylori

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Conserved clusters of functionally related genes in two bacterial genomes.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Conservation of gene order: a fingerprint of proteins that physically interact

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

The use of gene clusters to infer functional coupling

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

A reconstruction of the metabolism of Methanococcus jannaschii from sequence data.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Variation and evolution of the citric-acid cycle: a genomic perspective.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Global properties of the metabolic map of Escherichia coli

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

A combined algorithm for genome-wide prediction of protein function

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Comparative genomics of the eukaryotes

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Phylogenetic classification and the universal tree

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Genome phylogeny based on gene content

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Computational comparisons of model genomes

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

EUCLID: automatic classification of proteins in functional classes by their database annotations.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Structural genomics: beyond the human genome project

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Expectations from structural genomics

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

From protein structure to function.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Advances in structural genomics

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Biological function made crystal clear - annotation of hypothetical proteins via structural genomics

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Finding function through structural genomics

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

DNA chips: promising toys have become powerful tools

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Gene expression informatics--it's all in your mine.

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

A computational genomics approach to the identification of gene networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

E-CELL: software environment for whole-cell simulation

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Mapping regulatory networks in microbial cells

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Towards a circuit engineering discipline

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

The genexpress IMAGE knowledge base of the human muscle transcriptome: a resource of structural, functional, and positional candidate genes for muscle physiology and pathologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

'Going wrong with confidence': misleading sequence analyses of CiaB and ClpX

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Differential genome display

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Universal Protein Families and the Functional Content of the Last Universal Common Ancestor

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Automated genome sequence analysis and annotation

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Using metabolic pathway databases for functional annotation

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Integrated pathway–genome databases and their role in drug discovery

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

A database for cell signaling networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

DATABANKS - a catalogue database of molecular biology databases

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Prediction of membrane proteins based on classification of transmembrane segments

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

What we do not know about sequence analysis and sequence databases

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Errors in genome annotation

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Reproducibility in genome sequence annotation: the Plasmodium falciparum chromosome 2 case

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Orthology: another terminology muddle

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Functional classes in the three domains of life

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

A comparative analysis of ABC transporters in complete microbial genomes

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

Analysis of the pathway structure of metabolic networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FS0014-5793%2800%2901776-2

10.1016/S0014-5793(00)01776-2

21 January 2018

Identifiers

DOI

1 reference

30 July 2017

1 reference

PubMed ID

10967327