Keyword search (3,448 papers available)


Simulation and computer modeling of asphaltene in different solvents on oil-water interfaces using a molecular dynamic methodology.

Author(s): Yuan J, Elektorowicz M, Chen Z, Segun GA, Vakili M, Zhong L, Wang B, Zhu J, Wu Y

J Mol Graph Model. 2019 Sep 13;93:107450 Authors: Yuan J, Elektorowicz M, Chen Z, Segun GA, Vakili M, Zhong L, Wang B, Zhu J, Wu Y

Article GUID: 31542686
Backbone Flexibility Influences Nucleotide Incorporation by Human Translesion DNA Polymerase η opposite Intrastrand Cross-Linked DNA.

Author(s): O'Flaherty DK, Guengerich FP, Egli M, Wilds CJ

Biochemistry. 2015 Dec 29;54(51):7449-56 Authors: O'Flaherty DK, Guengerich FP, Egli M, Wilds CJ

Article GUID: 26624500
Diagnostic accuracy of the Depression subscale of the Hospital Anxiety and Depression Scale (HADS-D) for detecting major depression: protocol for a systematic review and individual patient data meta-analyses.

Author(s): Thombs BD, Benedetti A, Kloda LA, Levis B, Azar M, Riehm KE, Saadat N, Cuijpers P, Gilbody S, Ioannidis JP, McMillan D, Patten SB, Shrier I,...

BMJ Open. 2016 Apr 13;6(4):e011913 Authors: Thombs BD, Benedetti A, Kloda LA, Levis B, Azar M, Riehm KE, Saadat N, Cuijpers P, Gilbody S, Ioannidis JP, McMillan D, Patten SB, Shrier I, Steele RJ, ...

Article GUID: 27075844
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
A Lithium-Sulfur Battery using a 2D Current Collector Architecture with a Large-Sized Sulfur Host Operated under High Areal Loading and Low E/S Ratio.

Author(s): Li M, Zhang Y, Bai Z, Liu WW, Liu T, Gim J, Jiang G, Yuan Y, Luo D, Feng K, Yassar RS, Wang X, Chen Z, Lu J

Adv Mater. 2018 Nov;30(46):e1804271 Authors: Li M, Zhang Y, Bai Z, Liu WW, Liu T, Gim J, Jiang G, Yuan Y, Luo D, Feng K, Yassar RS, Wang X, Chen Z, Lu J

Article GUID: 30368935
Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η.

Author(s): O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ

Chem Sci. 2016 Aug 01;7(8):4896-4904 Authors: O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ

Article GUID: 27574558
O6-2'-Deoxyguanosine-butylene-O6-2'-deoxyguanosine DNA Interstrand Cross-Links Are Replication-Blocking and Mutagenic DNA Lesions.

Author(s): Xu W, Kool D, O'Flaherty DK, Keating AM, Sacre L, Egli M, Noronha A, Wilds CJ, Zhao L

Chem Res Toxicol. 2016 11 21;29(11):1872-1882 Authors: Xu W, Kool D, O'Flaherty DK, Keating AM, Sacre L, Egli M, Noronha A, Wilds CJ, Zhao L

Article GUID: 27768841
The Effect of Synbiotic Supplementation on Growth Parameters in Mild to Moderate FTT Children Aged 2-5 Years.

Author(s): Aflatoonian M, Taghavi Ardakani A, Modarresi SZ, Modaresi V, Karimi M, Ordooei M, Vakili M, Pakseresht B

Probiotics Antimicrob Proteins. 2019 Jan 09;: Authors: Aflatoonian M, Taghavi Ardakani A, Modarresi SZ, Modaresi V, Karimi M, Ordooei M, Vakili M, Pakseresht B

Article GUID: 30627885
Multimodal 18F-Fluciclovine PET/MRI and Ultrasound-Guided Neurosurgery of an Anaplastic Oligodendroglioma.

Author(s): Karlberg A, Berntsen EM, Johansen H, Myrthue M, Skjulsvik AJ, Reinertsen I, Esmaeili M, Dai HY, Xiao Y, Rivaz H, Borghammer P, Solheim O, Eikenes L

World Neurosurg. 2017 Dec;108:989.e1-989.e8 Authors: Karlberg A, Berntsen EM, Johansen H, Myrthue M, Skjulsvik AJ, Reinertsen I, Esmaeili M, Dai HY, Xiao Y, Rivaz H, Borghammer P, Solheim O, Eikenes L

Article GUID: 28844925
A comparison of muscle activation and knee mechanics during gait between patients with non-traumatic and post-traumatic knee osteoarthritis.

Author(s): Robbins SM, Morelli M, Martineau PA, St-Onge N, Boily M, Dimentberg R, Antoniou J

A comparison of muscle activation and knee mechanics during gait between patients with non-traumatic and post-traumatic knee osteoarthritis.
Osteoarthritis Cartilage. 2019 Mar 18;:
Authors: Robbins SM, Morelli M, Martineau PA, St-Onge N, Boily M, Di...

Article GUID: 30898621
Title:SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.
Authors:Reid I,  O'Toole N,  Zabaneh O,  Nourzadeh R,  Dahdouli M,  Abdellateef M,  Gordon PM,  Soh J,  Butler G,  Sensen CW,  Tsang A
Link:https://www.ncbi.nlm.nih.gov/pubmed/24980894?dopt=Abstract
DOI:10.1186/1471-2105-15-229
Category:BMC Bioinformatics
PMID:24980894
Dept Affiliation: GENOMICS
1 Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St, W, Montreal, QC H4B 1R6, Canada. ian.reid@concordia.ca.

Description:

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

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

Abstract

BACKGROUND: Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them.

RESULTS: SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data.

CONCLUSIONS: SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/.

PMID: 24980894 [PubMed - indexed for MEDLINE]