P D Karp
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Explore the profile of P D Karp including associated specialties, affiliations and a list of published articles.
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31
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2122
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Recent Articles
1.
Baltsavia I, Stamoulos G, Tziavaras K, Bouas C, Katikaridou I, Dermaris A, et al.
iScience
. 2025 Jan;
28(1):111546.
PMID: 39834858
The genome of () DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new...
2.
Karp P
Comp Funct Genomics
. 2008 Jul;
2(1):25-7.
PMID: 18628940
A survey of Genbank entries for complete microbial genomes reveals that the majority do not conform to the Genbank standard. Typical deviations from the Genbank standard include records with information...
3.
Green M, Karp P
Nucleic Acids Res
. 2006 Aug;
34(13):3687-97.
PMID: 16893953
Different biological notions of pathways are used in different pathway databases. Those pathway ontologies significantly impact pathway computations. Computational users of pathway databases will obtain different results depending on the...
4.
Green M, Karp P
Nucleic Acids Res
. 2005 Jul;
33(13):4035-9.
PMID: 16034025
We report on a new type of systematic annotation error in genome and pathway databases that results from the misinterpretation of partial Enzyme Commission (EC) numbers such as '1.1.1.-'. This...
5.
Karp P, Paley S, Krieger C, Zhang P
Pac Symp Biocomput
. 2004 Mar;
:190-201.
PMID: 14992503
An important emerging need in Model Organism Databases (MODs) and other bioinformatics databases (DBs) is that of capturing the scientific evidence that supports the information within a DB. This need...
6.
Romero P, Karp P
Bioinformatics
. 2004 Jan;
20(5):709-17.
PMID: 14751985
Motivation: The prediction of transcription units (TUs, which are similar to operons) is an important problem that has been tackled using many different approaches. The availability of complete microbial genomes...
7.
Wood D, Setubal J, Kaul R, Monks D, Kitajima J, Okura V, et al.
Science
. 2001 Dec;
294(5550):2317-23.
PMID: 11743193
The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of...
8.
Karp P
Science
. 2001 Sep;
293(5537):2040-4.
PMID: 11557880
A pathway database (DB) is a DB that describes biochemical pathways, reactions, and enzymes. The EcoCyc pathway DB (see http://ecocyc.org) describes the metabolic, transport, and genetic-regulatory networks of Escherichia coli....
9.
Karp P, Paley S, Zhu J
Bioinformatics
. 2001 Jun;
17(6):526-32; discussion 533-4.
PMID: 11395429
Problem Statement: We have studied the relationships among SWISS-PROT, TrEMBL, and GenBank with two goals. First is to determine whether users can reliably identify those proteins in SWISS-PROT whose functions...
10.
Karp P
Bioinformatics
. 2000 Jun;
16(3):269-85.
PMID: 10869020
Motivations: A number of important bioinformatics computations involve computing with function: executing computational operations whose inputs or outputs are descriptions of the functions of biomolecules. Examples include performing functional queries...