GADS software for parametric linkage analysis of quantitative traits distributed as a point-mass mixture.

Abstract:

:Often the quantitative data coming from proteomics and metabolomics studies have irregular distribution with a spike. None of the wide used methods for human QTL mapping are applicable to such traits. Researchers have to reduce the sample, excluding the spike, and analyze only continuous measurements. In this study, we propose a method for the parametric linkage analysis of traits with a spike in the distribution, and a software GADS, which implements this method. Our software includes not only the programs for parametric linkage analysis, but also the program for complex segregation analysis, which allows the estimation of the model parameters used in linkage. We tested our method on the real data about vertical cup-to-disc ratio, the important characteristic of the optic disc associated with glaucoma, in a large pedigree from a Dutch isolated population. Significant linkage signal was identified on chromosome 6 with the help of GADS, whereas the analysis of the normal distributed part of the sample demonstrated only a suggestive linkage peak on this chromosome. The software GADS is freely available at http://mga.bionet.nsc.ru/soft/index.html.

journal_name

Comput Biol Chem

authors

Axenovich TI,Zorkoltseva IV

doi

10.1016/j.compbiolchem.2011.11.004

subject

Has Abstract

pub_date

2012-02-01 00:00:00

pages

13-4

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(11)00122-8

journal_volume

36

pub_type

杂志文章
  • Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides.

    abstract::Annular structures have been observed experimentally in aggregates of polyglutamine-containing proteins and other proteins associated with diseases of the brain. Here we report the observation of annular structures in molecular-level simulations of large systems of model polyglutamine peptides. A system of 24 polyglut...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2006.01.003

    authors: Marchut AJ,Hall CK

    更新日期:2006-06-01 00:00:00

  • A vibrational entropy term for DNA docking with autodock.

    abstract::DNA interacts with small molecules, from water to endogenous reactive oxygen and nitrogen species, environmental mutagens and carcinogens, and pharmaceutical anticancer molecules. Understanding and predicting the physical interactions of small molecules with DNA via docking is key not only for the comprehension of mol...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.03.027

    authors: McElfresh GW,Deligkaris C

    更新日期:2018-06-01 00:00:00

  • An unusual 500,000 bases long oscillation of guanine and cytosine content in human chromosome 21.

    abstract::An oscillation with a period of around 500 kb in guanine and cytosine content (GC%) is observed in the DNA sequence of human chromosome 21. This oscillation is localized in the rightmost one-eighth region of the chromosome, from 43.5 Mb to 46.5 Mb. Five cycles of oscillation are observed in this region with six GC-ric...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2004.09.011

    authors: Li W,Holste D

    更新日期:2004-12-01 00:00:00

  • MODULEWRITER: a program for automatic generation of database interfaces.

    abstract::MODULEWRITER is a PERL object relational mapping (ORM) tool that automatically generates database specific application programming interfaces (APIs) for SQL databases. The APIs consist of a package of modules providing access to each table row and column. Methods for retrieving, updating and saving entries are provide...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/s1476-9271(03)00021-5

    authors: Zheng CL,Fana F,Udupi PV,Gribskov M

    更新日期:2003-05-01 00:00:00

  • Identification of novel vaccine candidates against carbapenem resistant Klebsiella pneumoniae: A systematic reverse proteomic approach.

    abstract::Klebsiella pneumoniae is declared as antibiotic resistant by WHO, with the critical urgency of developing novel antimicrobial therapeutics as drug resistance is the second most dangerous threat after terrorism. Besides many attempts still, there is no effective vaccine available against K. pneumoniae. By utilizing all...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2020.107380

    authors: Mehmood A,Naseer S,Ali A,Fatimah H,Rehman S,Kiani AK

    更新日期:2020-12-01 00:00:00

  • Exploring the effect of aplidin on low molecular weight protein tyrosine phosphatase by molecular docking and molecular dynamic simulation study.

    abstract::The low molecular weight protein tyrosine phosphatase (LMW-PTP) could regulate many signaling pathways, and it had drawn attention as a potential target for cancer. As previous report has indicated that the aplidin could inhibit the LMW-PTP, and thus, the relevant cancer caused by the abnormal regulation of the LMW-PT...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.107123

    authors: Sun YZ,Wu JW,Lu XH,Ma Y,Wang RL

    更新日期:2019-12-01 00:00:00

  • The effect of structure on improvement of the PNA Young modulus: A study of steered molecular dynamics.

    abstract::Prefoldin is a molecular chaperone and acts as a nano-actuator in cargo carriage and drug delivery for disease treatment. Investigating the mechanical properties of nano-actuator helps predict its behavior and measure its performance under various environmental conditions, like external forces that are applied. Accord...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.107133

    authors: Ghasemi RH,Keramati M,Mojarrad MHS

    更新日期:2019-12-01 00:00:00

  • Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis.

    abstract::The Egyptian flora is rich with a large number of Triticum plants, which are very difficult to discriminate between in the early developmental stages. This study assesses the significance of using two DNA Barcoding loci (matK and rbcL) in distinguishing between 18 different Triticum accessions in Egypt. We isolated an...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2017.09.003

    authors: Awad M,Fahmy RM,Mosa KA,Helmy M,El-Feky FA

    更新日期:2017-12-01 00:00:00

  • On interaction of arginine, cysteine and guanine with a nano-TiO2 cluster.

    abstract::Nanoscopic properties of TiO2 augmented with its physicochemical properties and biocompatibility make it a material interest in the biomedical field. Efficient methods to design of such materials require a thorough understanding of associated nano-bio interfaces. In the present study, density functional theory calcula...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2020.107236

    authors: Sai Phani Kumar V,Verma M,Deshpande PA

    更新日期:2020-06-01 00:00:00

  • Genome-wide identification and expression analysis of StTCP transcription factors of potato (Solanum tuberosum L.).

    abstract::The plant-specific TCP transcription factors, which play critical roles in diverse aspects of biological processes, have been identified and analyzed in various plant species. However, no systematical study of TCP family genes in potato (Solanum tuberosum L.) has been undertaken. In this study, a total of 31 non-redun...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.11.009

    authors: Wang Y,Zhang N,Li T,Yang J,Zhu X,Fang C,Li S,Si H

    更新日期:2019-02-01 00:00:00

  • Genome-wide predicting disease-related protein complexes by walking on the heterogeneous network based on data integration and laplacian normalization.

    abstract:BACKGROUND:Associating protein complexes to human inherited diseases is critical for better understanding of biological processes and functional mechanisms of the disease. Many protein complexes have been identified and functionally annotated by computational and purification methods so far, however, the particular rol...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2017.04.007

    authors: Liu Z,Luo J

    更新日期:2017-08-01 00:00:00

  • DNA strand break: structural and electrostatic properties studied by molecular dynamics simulation.

    abstract::Due to their lethal consequences and a relatively high probability of introduction of repair errors and mutations, single and double strand breaks are among the most important and dangerous DNA lesions. However, the mechanisms of their recognition and repair processes are only poorly known at present. This work define...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2005.12.001

    authors: Bunta JK,Laaksonen A,Pinak M,Nemoto T

    更新日期:2006-04-01 00:00:00

  • Biocomputational identification and validation of novel microRNAs predicted from bubaline whole genome shotgun sequences.

    abstract::MicroRNAs (miRNAs) are small (19-25 base long), non-coding RNAs that regulate post-transcriptional gene expression by cleaving targeted mRNAs in several eukaryotes. The miRNAs play vital roles in multiple biological and metabolic processes, including developmental timing, signal transduction, cell maintenance and diff...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2017.08.005

    authors: Manku HK,Dhanoa JK,Kaur S,Arora JS,Mukhopadhyay CS

    更新日期:2017-10-01 00:00:00

  • Hybrid docking-QSAR studies of DPP-IV inhibition activities of a series of aminomethyl-piperidones.

    abstract::In this study, the dipeptidyl peptidase-IV (DPP-IV) inhibition activities of a series of novel aminomethyl-piperidones were investigated by molecular docking studies and modeled by quantitative structure-activity relationship (QSAR) methodology. Molecular docking studies were used to find the best conformations of the...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.08.003

    authors: Amini Z,Fatemi MH,Gharaghani S

    更新日期:2016-10-01 00:00:00

  • RNA-binding residues in sequence space: conservation and interaction patterns.

    abstract::RNA-binding proteins (RBPs) perform fundamental and diverse functions within the cell. Approximately 15% of proteins sequences are annotated as RNA-binding, but with a significant number of proteins without functional annotation, many RBPs are yet to be identified. A percentage of uncharacterised proteins can be annot...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2009.07.012

    authors: Spriggs RV,Jones S

    更新日期:2009-10-01 00:00:00

  • From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity.

    abstract::The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assem...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.02.016

    authors: Misas E,Muñoz JF,Gallo JE,McEwen JG,Clay OK

    更新日期:2016-04-01 00:00:00

  • Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach.

    abstract::Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) fac...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.07.008

    authors: Kumar A,Kumar S,Kumar U,Suravajhala P,Gajula MN

    更新日期:2016-10-01 00:00:00

  • Protein subcellular location prediction using optimally weighted fuzzy k-NN algorithm.

    abstract::Optimally weighted fuzzy k-nearest neighbors (OWFKNN) algorithm has been used to predict proteins' subcellular locations based on their amino acid composition, in this paper. The datasets used consists of two species which are 997 prokaryotic and 2427 eukaryotic protein sequences. The overall prediction accuracy achie...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2008.07.011

    authors: Nasibov E,Kandemir-Cavas C

    更新日期:2008-12-01 00:00:00

  • Temperature effect on the structure and conformational fluctuations in two zinc knuckles from the mouse mammary tumor virus.

    abstract::Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.03.005

    authors: Nedjoua D,Krallafa AM

    更新日期:2018-06-01 00:00:00

  • Mutually exclusive binding of APPL(PH) to BAR domain and Reptin regulates β-catenin dependent transcriptional events.

    abstract::Reptin functions in a wide range of biological processes including chromatin remodelling, nucleolar organization and transcriptional regulation of WNT signalling. As β-catenin dependent transcriptional repression and activation events involve binding of Reptin and histone deacetylase 1 to APPL endocytic proteins, this...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2013.05.005

    authors: Rashid S,Parveen Z,Ferdous S,Bibi N

    更新日期:2013-12-01 00:00:00

  • Pharmacoinformatics exploration of polyphenol oxidases leading to novel inhibitors by virtual screening and molecular dynamic simulation study.

    abstract::Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2017.02.012

    authors: Hassan M,Abbas Q,Ashraf Z,Moustafa AA,Seo SY

    更新日期:2017-06-01 00:00:00

  • Spectroscopic, quantum computational and molecular docking studies on 1-phenylcyclopentane carboxylic acid.

    abstract::The vibrational wavenumbers of optimized molecular structure of 1-phenylcyclopentane carboxylic acid (1PCPCA) molecule have been calculated by quantum chemical theory and compared with experimental results. The density functional theory (DFT) approach is followed using the method B3LYP and 6-311++G(d,p) basis set. Usi...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.05.011

    authors: Raajaraman BR,Sheela NR,Muthu S

    更新日期:2019-10-01 00:00:00

  • Inhibitory activity of hibifolin on adenosine deaminase- experimental and molecular modeling study.

    abstract::Adenosine deaminase (ADA) is an enzyme involved in purine metabolism. ADA converts adenosine to inosine and liberates ammonia. Because of their critical role in the differentiation and maturation of cells, the regulation of ADA activity is considered as a potential therapeutic approach to prevent malignant and inflamm...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.08.005

    authors: Arun KG,Sharanya CS,Sandeep PM,Sadasivan C

    更新日期:2016-10-01 00:00:00

  • Generating SNP barcode to evaluate SNP-SNP interaction of disease by particle swarm optimization.

    abstract::Genome-wide association analysis involved many single-nucleotide polymorphisms (SNPs) data is challenging mathematically and computationally. Hence, we propose the odds ratio-based discrete binary particle swarm optimization (OR-DBPSO) method that uses the OR as a new quantitative measure of disease risk among many SN...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2008.07.029

    authors: Chang HW,Yang CH,Ho CH,Wen CH,Chuang LY

    更新日期:2009-02-01 00:00:00

  • Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay.

    abstract::Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 pandemic is ongoing, with no proven safe and effective vaccine to date. Further, effective therapeutic agents for COVID-19 are limited, and as a result, the identification of potential small molecule antiviral drugs is of particul...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2020.107408

    authors: Pitsillou E,Liang J,Karagiannis C,Ververis K,Darmawan KK,Ng K,Hung A,Karagiannis TC

    更新日期:2020-12-01 00:00:00

  • Ab-initio prediction and reliability of protein structural genomics by PROPAINOR algorithm.

    abstract::We have formulated the ab-initio prediction of the 3D-structure of proteins as a probabilistic programming problem where the inter-residue 3D-distances are treated as random variables. Lower and upper bounds for these random variables and the corresponding probabilities are estimated by nonparametric statistical metho...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/s0097-8485(02)00074-8

    authors: Joshi RR,Jyothi S

    更新日期:2003-07-01 00:00:00

  • Modelling the role of dual specificity phosphatases in herceptin resistant breast cancer cell lines.

    abstract:BACKGROUND:Breast cancer remains the most lethal type of cancer for women. A significant proportion of breast cancer cases are characterised by overexpression of the human epidermal growth factor receptor 2 protein (HER2). These cancers are commonly treated by Herceptin (Trastuzumab), but resistance to drug treatment f...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.03.018

    authors: Buiga P,Elson A,Tabernero L,Schwartz JM

    更新日期:2019-06-01 00:00:00

  • A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model.

    abstract::The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world,...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.107192

    authors: Hattori LT,Gutoski M,Vargas Benítez CM,Nunes LF,Lopes HS

    更新日期:2020-02-01 00:00:00

  • Identification and characterization of lysine-methylated sites on histones and non-histone proteins.

    abstract::Protein methylation is a kind of post-translational modification (PTM), and typically takes place on lysine and arginine amino acid residues. Protein methylation is involved in many important biological processes, and most recent studies focused on lysine methylation of histones due to its critical roles in regulating...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2014.01.009

    authors: Lee TY,Chang CW,Lu CT,Cheng TH,Chang TH

    更新日期:2014-06-01 00:00:00

  • Novel 2,4-disubstituted quinazolines as cytotoxic agents and JAK2 inhibitors: Synthesis, in vitro evaluation and molecular dynamics studies.

    abstract::Recent studies reported the involvement of JAK2/STAT3 pathway in various solid tumours including breast, ovarian, prostate and lung cancers. Clinical literature also reported the lowered burden in breast and ovarian cancers by targeting JAK2 pathway. In this study, a series of novel 2,4-disubstituted quinazolines (2a-...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.01.008

    authors: Jyothi Buggana S,Paturi MC,Perka H,Gade DR,Vvs RP

    更新日期:2019-04-01 00:00:00