当前位置： SCI文献检索 > COMPUTATIONAL BIOLOGY AND CHEMISTRY期刊下所有文献 > Identification of evolutionarily conserved Momordica charantia microRNAs using computational approach and its utility in phylogeny analysis.

Identification of evolutionarily conserved Momordica charantia microRNAs using computational approach and its utility in phylogeny analysis.

Abstract：

:Momordica charantia (bitter gourd, bitter melon) is a monoecious Cucurbitaceae with anti-oxidant, anti-microbial, anti-viral and anti-diabetic potential. Molecular studies on this economically valuable plant are very essential to understand its phylogeny and evolution. MicroRNAs (miRNAs) are conserved, small, non-coding RNA with ability to regulate gene expression by bind the 3' UTR region of target mRNA and are evolved at different rates in different plant species. In this study we have utilized homology based computational approach and identified 27 mature miRNAs for the first time from this bio-medically important plant. The phylogenetic tree developed from binary data derived from the data on presence/absence of the identified miRNAs were noticed to be uncertain and biased. Most of the identified miRNAs were highly conserved among the plant species and sequence based phylogeny analysis of miRNAs resolved the above difficulties in phylogeny approach using miRNA. Predicted gene targets of the identified miRNAs revealed their importance in regulation of plant developmental process. Reported miRNAs held sequence conservation in mature miRNAs and the detailed phylogeny analysis of pre-miRNA sequences revealed genus specific segregation of clusters.

journal_name

Comput Biol Chem

journal_title

Computational biology and chemistry

authors

Thirugnanasambantham K,Saravanan S,Karikalan K,Bharanidharan R,Lalitha P,Ilango S,HairulIslam VI

doi

10.1016/j.compbiolchem.2015.04.011

subject

Has Abstract

pub_date

2015-10-01 00:00:00

pages

25-39

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(15)30001-3

journal_volume

58

pub_type

杂志文章

相关文献

COMPUTATIONAL BIOLOGY AND CHEMISTRY文献大全
  • Analysis of compensatory substitution and gene evolution on the MAGEA/CSAG-palindrome of the primate X chromosomes.

    abstract：:The human X chromosome contains a large number of inverted repeat DNA palindromes. Although arbitrary substitutions destroyed the inverted repeat structure of MAGEA/CSAG-palindrome during the evolutionary process of the primates, most of the substitutions are compensatory. Using maximum parsimony, it is demonstrated t...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2012.11.002

    authors： Qi Y,Lu H,Ai D

    更新日期：2013-02-01 00:00:00

  • Gene teams: a new formalization of gene clusters for comparative genomics.

    abstract：:This paper describes an efficient algorithm based on a new concept called gene team for detecting conserved gene clusters among an arbitrary number of chromosomes. Within the clusters, neither the order of the genes nor their orientation need be conserved. In addition, insertion of foreign genes within the clusters ar...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/s1476-9271(02)00097-x

    authors： Luc N,Risler JL,Bergeron A,Raffinot M

    更新日期：2003-02-01 00:00:00

  • Carboxylic acid derivatives display potential selectivity for human histone deacetylase 6: Structure-based virtual screening, molecular docking and dynamics simulation studies.

    abstract：:Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of α-tubulin, making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available, providing avenues for structu...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.05.004

    authors： Uba AI,Yelekçi K

    更新日期：2018-08-01 00:00:00

  • Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin.

    abstract：:Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from ri...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107245

    authors： Hussain A,Shahbaz M,Tariq M,Ibrahim M,Hong X,Naeem F,Khalid Z,Raza HMZ,Bo Z,Bin L

    更新日期：2020-06-01 00:00:00

  • Predicting human intestinal absorption of diverse chemicals using ensemble learning based QSAR modeling approaches.

    abstract：:Human intestinal absorption (HIA) of the drugs administered through the oral route constitutes an important criterion for the candidate molecules. The computational approach for predicting the HIA of molecules may potentiate the screening of new drugs. In this study, ensemble learning (EL) based qualitative and quanti...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.01.005

    authors： Basant N,Gupta S,Singh KP

    更新日期：2016-04-01 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

  • Structure based pharmacophore study to identify possible natural selective PARP-1 trapper as anti-cancer agent.

    abstract：:Inhibition of poly(ADP-ribose) polymerase-1 (PARP-1) has turned out an innovative approach for cancer therapy due to its involvement in DNA repair pathways. Although several potent PARP-1 inhibitors have been identified, they exhibit high toxicity, resistivity and diverse pharmacological profile in clinical trials, wh...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.04.018

    authors： Kumar C,P T V L,Arunachalam A

    更新日期：2019-06-01 00:00:00

  • ScGSLC: An unsupervised graph similarity learning framework for single-cell RNA-seq data clustering.

    abstract：:Accurate clustering of cells from single-cell RNA sequencing (scRNA-seq) data is an essential step for biological analysis such as putative cell type identification. However, scRNA-seq data has high dimension and high sparsity, which makes traditional clustering methods less effective to reflect the similarity between...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107415

    authors： Li J,Jiang W,Han H,Liu J,Liu B,Wang Y

    更新日期：2020-11-18 00:00:00

  • Natural compounds as potential Hsp90 inhibitors for breast cancer-Pharmacophore guided molecular modelling studies.

    abstract：:Breast cancer is one of the major impediments affecting women globally. The ATP-dependant heat shock protein 90 (Hsp90) forms the central component of molecular chaperone machinery that predominantly governs the folding of newly synthesized peptides and their conformational maturation. It regulates the stability and f...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107113

    authors： Rampogu S,Parate S,Parameswaran S,Park C,Baek A,Son M,Park Y,Park SJ,Lee KW

    更新日期：2019-12-01 00:00:00

  • Dynamic characterization of HLA-B*44 Alleles: A comparative molecular dynamics simulation study.

    abstract：:Human Leukocyte Antigens (HLA) are highly polymorphic proteins that play a key role in the immune system. HLA molecule is present on the cell membrane of antigen-presenting cells of the immune system and presents short peptides, originating from the proteins of invading pathogens or self-proteins, to the T-cell Recept...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.02.019

    authors： Ozbek P

    更新日期：2016-06-01 00:00:00

  • Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries.

    abstract：:In this paper, a problem of isothermic DNA sequencing by hybridization (SBH) is considered. In isothermic SBH a new type of oligonucleotide libraries is used. The library consists of oligonucleotides of different lengths depending on an oligonucleotide content. It is assumed that every oligonucleotide in such a librar...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2003.12.002

    authors： Błazewicz J,Formanowicz P,Kasprzak M,Markiewicz WT,Swiercz A

    更新日期：2004-02-01 00:00:00

  • Why does beta-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies.

    abstract：:Beta-secretase is a potential target for inhibitory drugs against Alzheimer's disease as it cleaves amyloid precursor protein (APP) to form insoluble amyloid plaques and vascular deposits in the brain. Beta-secretase is matured from its precursor protein, called beta-secretase zymogen, which, different from most of ot...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2007.03.007

    authors： Zuo Z,Gang C,Zou H,Mok PC,Zhu W,Chen K,Jiang H

    更新日期：2007-06-01 00:00:00

  • Protein function prediction using neighbor relativity in protein-protein interaction network.

    abstract：:There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interact...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2012.12.003

    authors： Moosavi S,Rahgozar M,Rahimi A

    更新日期：2013-04-01 00:00:00

  • DFT and QTAIM based investigation on the structure and antioxidant behavior of lichen substances Atranorin, Evernic acid and Diffractaic acid.

    abstract：:In this study, the structural and antioxidant behavior of the three lichen-derived natural compounds such as atranorin (AT), evernic acid (EV) and diffractaic acid (DF) has been investigated in the gas and water phase using both B3LYP and M06-2X functional level of density functional theory (DFT) with two different ba...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.03.009

    authors： Shameera Ahamed TK,Rajan VK,Sabira K,Muraleedharan K

    更新日期：2019-06-01 00:00:00

  • Guided macro-mutation in a graded energy based genetic algorithm for protein structure prediction.

    abstract：:Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more importantly, the use of effective sampling algorithms become crucial to address this pro...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.01.008

    authors： Rashid MA,Iqbal S,Khatib F,Hoque MT,Sattar A

    更新日期：2016-04-01 00:00:00

  • Protein complex prediction by date hub removal.

    abstract：:Proteins physically interact with each other and form protein complexes to perform their biological functions. The prediction of protein complexes from protein-protein interaction (PPI) network is usually difficult when the complexes are overlapping with each other in a dense region of the network. To address the prob...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.03.012

    authors： Pyrogova I,Wong L

    更新日期：2018-06-01 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

  • Genome-wide analysis of magnesium transporter genes in Solanum lycopersicum.

    abstract：:Magnesium (Mg) is an important micronutrient for various physiological processes in plants. In this study, putative Magnesium Transporter (MGT) genes have been identified in Solanum lycopersicum, Solanum tuberosum, Brachypodium distachyon, Fagaria vesca, Brassica juncea and were classified into 5 distinct groups based...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.05.014

    authors： Regon P,Chowra U,Awasthi JP,Borgohain P,Panda SK

    更新日期：2019-06-01 00:00:00

  • Cryptic tRNAs in chaetognath mitochondrial genomes.

    abstract：:The chaetognaths constitute a small and enigmatic phylum of little marine invertebrates. Both nuclear and mitochondrial genomes have numerous originalities, some phylum-specific. Until recently, their mitogenomes seemed containing only one tRNA gene (trnMet), but a recent study found in two chaetognath mitogenomes two...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.04.007

    authors： Barthélémy RM,Seligmann H

    更新日期：2016-06-01 00:00:00

  • The binding mode of picrotoxinin in GABAA-ρ receptors: Insight into the subunit's selectivity in the transmembrane domain.

    abstract：:The channel blocker picrotoxinin has been studied with GABAA-ρ1 and GABAA-ρ2 homology models based on the GluCl crystal structure. Picrotoxinin is tenfold more potent for GABAA-ρ2 than for GABAA-ρ1 homomeric channels. This intra-subunit selectivity arises from the unconserved residues at the 2' sites, which are the es...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.07.003

    authors： Naffaa MM,Samad A

    更新日期：2016-10-01 00:00:00

  • QSAR study of pyrazolo[4,3-e][1,2,4]triazine sulfonamides against tumor-associated human carbonic anhydrase isoforms IX and XII.

    abstract：:The QSAR models for a set of pyrazolo[4,3-e][1,2,4]triazines incorporating benzenesulfonamide moiety combined directly with the heterocyclic ring or by NH linkage were generated. The inhibitory potency of compounds against human carbonic anhydrase isoforms IX and XII and antiproliferative activity against human MCF-7 ...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2017.09.006

    authors： Matysiak J,Skrzypek A,Tarasiuk P,Mojzych M

    更新日期：2017-12-01 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

  • Simulating the Monty Hall problem in a DNA sequencing machine.

    abstract：:The Monty Hall problem is a decision problem with an answer that is surprisingly counter-intuitive yet provably correct. Here we simulate and prove this decision in a high-throughput DNA sequencing machine, using a simple encoding. All possible scenarios are represented by DNA oligonucleotides, and gameplay decisions ...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107122

    authors： Mamet N,Harari G,Zamir A,Bachelet I

    更新日期：2019-12-01 00:00:00

  • Characterizing the protonation states of the catalytic residues in apo and substrate-bound human T-cell leukemia virus type 1 protease.

    abstract：:Human T-cell leukemia virus type 1 (HTLV-1) protease is an attractive target when developing inhibitors to treat HTLV-1 associated diseases. To study the catalytic mechanism and design novel HTLV-1 protease inhibitors, the protonation states of the two catalytic aspartic acid residues must be determined. Free energy s...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2015.04.002

    authors： Ma S,Vogt KA,Petrillo N,Ruhoff AJ

    更新日期：2015-06-01 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

  • Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1.

    abstract：:Programmed cell death or apoptosis plays a vital physiological role in the development and homeostasis. Any discrepancy in apoptosis may trigger testicular and neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. Tcte3 (T-complex testis expressed 3) is an accessory component of a...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2014.10.005

    authors： Parveen Z,Bibi Z,Bibi N,Neesen J,Rashid S

    更新日期：2014-12-01 00:00:00

  • Putative dual inhibitors of Janus kinase 1 and 3 (JAK1/3): Pharmacophore based hierarchical virtual screening.

    abstract：:Janus kinase 1 and 3 are non-receptor protein tyrosine kinases, involved in the regulation of various cytokines implicated in the pathogenesis of autoimmune and inflammatory disease conditions. Thus, they serve as therapeutic targets for the designing of multi-targeted agents for the treatment of inflammatory-mediated...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.07.009

    authors： Jasuja H,Chadha N,Singh PK,Kaur M,Bahia MS,Silakari O

    更新日期：2018-10-01 00:00:00

  • Cytochrome P450 2C9 polymorphism: Effect of amino acid substitutions on protein flexibility in the presence of tamoxifen.

    abstract：:Tamoxifen is a prodrug and cytochrome P450 2C9 (CYP2C9) has a significant role in the formation of a therapeutically more potent metabolite (4-hydroxytamoxifen) than tamoxifen. Since CYP2C9 exhibits genetic polymorphism, it may contribute to different phenotypic drug response. Moreover, it may be misleading if the pos...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107166

    authors： Manish M,Lynn AM,Mishra S

    更新日期：2020-02-01 00:00:00

  • Identification of Casiopeina II-gly secondary targets through a systems pharmacology approach.

    abstract：:Casiopeinas are a group of copper-based compounds designed to be used as less toxic, more efficient chemotherapeutic agents. In this study, we analyzed the in vitro effects of Casiopeina II-gly on the expression of canonical biological pathways. Using microarray data from HeLa cell lines treated with Casiopeina II-gly...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.11.021

    authors： de Anda-Jáuregui G,Espinal-Enríquez J,Hur J,Alcalá-Corona SA,Ruiz-Azuara L,Hernández-Lemus E

    更新日期：2019-02-01 00:00:00

  • In silico analyses of a new group of fungal and plant RecQ4-homologous proteins.

    abstract：:Bacterial and eukaryotic RecQ helicases comprise a family of homologous proteins necessary for maintaining genomic integrity during the cell cycle and DNA repair. There is one known bacterial RecQ helicase, and five eukaryotic RecQ helicases that have been described: RecQ1p, RecQ4p, RecQ5p, Bloom, and Werner. While th...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2008.07.005

    authors： Barea F,Tessaro S,Bonatto D

    更新日期：2008-10-01 00:00:00