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Akademický článek

Multi-label classification with XGBoost for metabolic pathway prediction

Autor: Hyunwhan Joe, Hong-Gee Kim

Publikováno v: BMC Bioinformatics, Vol 25, Iss 1, Pp 1-15 (2024)

Abstract Background Metabolic pathway prediction is one possible approach to address the problem in system biology of reconstructing an organism’s metabolic network from its genome sequence. Recently there have been developments in machine learning

Externí odkaz: https://doaj.org/article/053bec36905745f6946f4a92c67377b4

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Akademický článek

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Akademický článek

Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics

Autor: Peter D. Karp, Peter E. Midford, Ron Caspi, Arkady Khodursky

Publikováno v: BMC Genomics, Vol 22, Iss 1, Pp 1-11 (2021)

Abstract Background Enrichment or over-representation analysis is a common method used in bioinformatics studies of transcriptomics, metabolomics, and microbiome datasets. The key idea behind enrichment analysis is: given a set of significantly expre

Externí odkaz: https://doaj.org/article/2d9bd4ebc1624d689a01172f053f63dc

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Akademický článek

Metabolic route computation in organism communities

Autor: Markus Krummenacker, Mario Latendresse, Peter D Karp

Publikováno v: Microbiome, Vol 7, Iss 1, Pp 1-8 (2019)

Abstract Background Microbiomes are complex aggregates of organisms, each of which has its own extensive metabolic network. A variety of metabolites are exchanged between the microbes. The challenge we address is understanding the overall metabolic c

Externí odkaz: https://doaj.org/article/0abf236cb2894e519d232a4385b75158

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Akademický článek

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Akademický článek

Using Pathway Covering to Explore Connections among Metabolites

Autor: Peter E. Midford, Mario Latendresse, Paul E. O’Maille, Peter D. Karp

Publikováno v: Metabolites, Vol 9, Iss 5, p 88 (2019)

Interpreting changes in metabolite abundance in response to experimental treatments or disease states remains a major challenge in metabolomics. Pathway Covering is a new algorithm that takes a list of metabolites (compounds) and determines a minimum

Externí odkaz: https://doaj.org/article/b6909947531a4088a59e75f928131611

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From genomes to metabolism reconstruction: companion collections of databases to study symbiotic interactions between insects and their bacterial symbionts

Autor: Baa-Puyoulet, Patrice, Parisot, Nicolas, Peignier, Sergio, Calevro, Federica, Charles, Hubert

Publikováno v: 12. Rencontre du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA)
12. Rencontre du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), May 2022, Nice, France
13ème Réunion du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA)
13ème Réunion du Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), 2020, Nice (virtuel), France

International audience

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::b370a293cd2107da603fea3f076d8c03
https://hal.inrae.fr/hal-03810352

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Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation

Autor: Ingrid M. Keseler, Peter D. Karp, Suzanne M. Paley, Markus Krummenacker

Publikováno v: Frontiers in Microbiology
Frontiers in Microbiology, Vol 12 (2021)

Updating genome databases to reflect newly published molecular findings for an organism was hard enough when only a single strain of a given organism had been sequenced. With multiple sequenced strains now available for many organisms, the challenge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0bb65f49320d060c6e5f69ff02bed3af

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Identification of Potential Drug Targets in Helicobacter pylori Using In Silico Subtractive Proteomics Approaches and Their Possible Inhibition through Drug Repurposing

Autor: Mohammed A. Ramadan, Omneya M. Helmy, Tharwat R Elkhamissy, Kareem A Ibrahim, Mona T. Kashef

Publikováno v: Pathogens, Vol 9, Iss 747, p 747 (2020)
Pathogens
Volume 9
Issue 9

The class 1 carcinogen, Helicobacter pylori, is one of the World Health Organization&rsquo
s high priority pathogens for antimicrobial development. We used three subtractive proteomics approaches using protein pools retrieved from: chokepoint re

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::36b3fa28879ea76381eefc7345f2cf06
https://www.mdpi.com/2076-0817/9/9/747

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Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics

Autor: Peter D. Karp, Arkady B. Khodursky, Peter E. Midford, Ron Caspi

Publikováno v: BMC Genomics
BMC Genomics, Vol 22, Iss 1, Pp 1-11 (2021)

Background Enrichment or over-representation analysis is a common method used in bioinformatics studies of transcriptomics, metabolomics, and microbiome datasets. The key idea behind enrichment analysis is: given a set of significantly expressed gene

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::db4f3fc996cc84872a6e0dacfd943b1f
https://pubmed.ncbi.nlm.nih.gov/33726670

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