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SPOT: A machine learning model that predicts specific substrates for transport proteins

Author(s): Kroll A; Niebuhr N; Butler G; Lercher MJ;

Transport proteins play a crucial role in cellular metabolism and are central to many aspects of molecular biology and medicine. Determining the function of transport proteins experimentally is challenging, as they become unstable when isolated from cell me ...

Article GUID: 39325691


Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses

Author(s): Steindorff AS; Aguilar-Pontes MV; Robinson AJ; Andreopoulos B; LaButti K; Kuo A; Mondo S; Riley R; Otillar R; Haridas S; Lipzen A; Grimwood ...

Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some member ...

Article GUID: 39266695


Exploiting protein language models for the precise classification of ion channels and ion transporters

Author(s): Ghazikhani H; Butler G;

This study introduces TooT-PLM-ionCT, a comprehensive framework that consolidates three distinct systems, each meticulously tailored for one of the following tasks: distinguishing ion channels (ICs) from membrane proteins (MPs), segregating ion transporters ...

Article GUID: 38656743


Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks

Author(s): Ghazikhani H; Butler G;

Transmembrane transport proteins (transporters) play a crucial role in the fundamental cellular processes of all organisms by facilitating the transport of hydrophilic substrates across hydrophobic membranes. Despite the availability of numerous membrane pr ...

Article GUID: 37497772


Integrative approach for detecting membrane proteins.

Author(s): Alballa M, Butler G

BACKGROUND: Membrane proteins are key gates that control various vital cellular functions. Membrane proteins are often detected using transmembrane topology prediction tools. While transmembrane topology prediction tools can detect integral membrane protein ...

Article GUID: 33349234


BENIN: Biologically enhanced network inference.

Author(s): Wonkap SK, Butler G

J Bioinform Comput Biol. 2020 Jun;18(3):2040007 Authors: Wonkap SK, Butler G

Article GUID: 32698722


TooT-T: discrimination of transport proteins from non-transport proteins.

Author(s): Alballa M, Butler G

BMC Bioinformatics. 2020 Apr 23;21(Suppl 3):25 Authors: Alballa M, Butler G

Article GUID: 32321420


TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information.

Author(s): Alballa M, Aplop F, Butler G

PLoS One. 2020;15(1):e0227683 Authors: Alballa M, Aplop F, Butler G

Article GUID: 31935244


Analytical and computational approaches to define the Aspergillus niger secretome.

Author(s): Tsang A, Butler G, Powlowski J, Panisko EA, Baker SE

Fungal Genet Biol. 2009 Mar;46 Suppl 1:S153-S160 Authors: Tsang A, Butler G, Powlowski J, Panisko EA, Baker SE

Article GUID: 19618504


SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.

Author(s): Reid I, O'Toole N, Zabaneh O, Nourzadeh R, Dahdouli M, Abdellateef M, Gordon PM, Soh J, Butler G, Sensen CW, Tsang A

BMC Bioinformatics. 2014 Jul 01;15:229 Authors: Reid I, O'Toole N, Zabaneh O, Nourzadeh R, Dahdouli M, Abdellateef M, Gordon PM, Soh J, Butler G, Sensen CW, Tsang A

Article GUID: 24980894


Machine learning for biomedical literature triage.

Author(s): Almeida H, Meurs MJ, Kosseim L, Butler G, Tsang A

PLoS One. 2014;9(12):e115892 Authors: Almeida H, Meurs MJ, Kosseim L, Butler G, Tsang A

Article GUID: 25551575


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