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Evolutionary Bioinformatics Online

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https://www.readbyqxmd.com/read/30364489/how-to-reveal-magnitude-of-gene-signals-hierarchical-hypergeometric-complementary-cumulative-distribution-function
#1
Bongsong Kim
This article introduces a new method for genome-wide association study (GWAS), hierarchical hypergeometric complementary cumulative distribution function (HH-CCDF). Existing GWAS methods, e.g. the linear model and hierarchical association coefficient algorithm , calculate the association between a marker variable and a phenotypic variable. The ideal GWAS practice is to calculate the association between a marker variable and a gene-signal variable. If the gene-signal variable and phenotypic variable are imperfectly proportional, the existing methods do not properly reveal the magnitude of the association between the gene-signal variable and marker variable...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30364468/rooting-phylogenies-and-the-tree-of-life-while-minimizing-ad-hoc-and-auxiliary-assumptions
#2
REVIEW
Gustavo Caetano-Anollés, Arshan Nasir, Kyung Mo Kim, Derek Caetano-Anollés
Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a "model" of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30245567/s-plot2-rapid-visual-and-statistical-analysis-of-genomic-sequences
#3
Laurynas Kalesinskas, Evan Cudone, Yuriy Fofanov, Catherine Putonti
With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30210232/systematic-identification-and-classification-of-%C3%AE-lactamases-based-on-sequence-similarity-criteria-%C3%AE-lactamase-annotation
#4
Melise Chaves Silveira, Rangeline Azevedo da Silva, Fábio Faria da Mota, Marcos Catanho, Rodrigo Jardim, Ana Carolina R Guimarães, Antonio B de Miranda
β-lactamases, the enzymes responsible for resistance to β-lactam antibiotics, are widespread among prokaryotic genera. However, current β-lactamase classification schemes do not represent their present diversity. Here, we propose a workflow to identify and classify β-lactamases. Initially, a set of curated sequences was used as a model for the construction of profiles Hidden Markov Models (HMM), specific for each β-lactamase class. An extensive, nonredundant set of β-lactamase sequences was constructed from 7 different resistance proteins databases to test the methodology...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30116102/a-novel-approach-for-identifying-relevant-genes-for-breast-cancer-survivability-on-specific-therapies
#5
REVIEW
Ashraf Abou Tabl, Abedalrhman Alkhateeb, Huy Quang Pham, Luis Rueda, Waguih ElMaraghy, Alioune Ngom
Analyzing the genetic activity of breast cancer survival for a specific type of therapy provides a better understanding of the body response to the treatment and helps select the best course of action and while leading to the design of drugs based on gene activity. In this work, we use supervised and nonsupervised machine learning methods to deal with a multiclass classification problem in which we label the samples based on the combination of the 5-year survivability and treatment; we focus on hormone therapy, radiotherapy, and surgery...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30083050/transcriptome-analysis-and-microsatellite-markers-development-of-a-traditional-chinese-medicinal-herb-halenia-elliptica-d-don-gentianaceae
#6
Mingliu Yang, Nanyu Han, Heng Li, Lihua Meng
Halenia elliptica is a popular Chinese medicinal herb that is used to treat jaundice disease and virus hepatitis, and its wild populations have been reduced significantly due to overharvesting recently. However, effective conservation could not be implemented because of the lack of genomic information and genetic markers. In this study, a de novo transcriptome of H elliptica was sequenced using the NGS Illumina, and 132 695 unigenes with the length >200 bp (base pairs) were obtained. Among them, a total of 32 109 unigenes were scanned to develop simple sequence repeats (SSRs)...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30083049/comparative-genome-analysis-of-2-mycobacterium-tuberculosis-strains-from-pakistan-insights-globally-into-drug-resistance-virulence-and-niche-adaptation
#7
Asma Muhammad Yar, Ghanva Zaman, Annam Hussain, Yan Changhui, Azhar Rasul, Abrar Hussain, Zhu Bo, Habib Bokhari, Muhammad Ibrahim
Multidrug-resistant Mycobacterium tuberculosis is a global threat particularly in developing countries like Pakistan. In this study, we identified 2 M tuberculosis strains, mnpk and swlpk, by 16S RNA genes, sequenced their draft genome, and compared the 2 genomes with reference strain H37Rv and gene expression analysis of selected virulent genes. Phylogenetic analysis of M tuberculosis strains, mnpk and swlpk, using 16S RNA genes revealed that the strains are closely related with reference strain H37Rv. The draft genome sequence of mnpk and swlpk contains 4305 and 4295 protein-coding genes, respectively, having 99...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30046236/-bhlh13-regulates-jasmonate-mediated-defense-responses-and-growth
#8
Huang Huang, Hua Gao, Bei Liu, Meng Fan, Jiaojiao Wang, Cuili Wang, Haixia Tian, Lanxiang Wang, Chengyuan Xie, Dewei Wu, Liangyu Liu, Jianbin Yan, Tiancong Qi, Susheng Song
Jasmonates (JAs) regulate plant growth and defense responses. On perception of bioactive JAs, the JA receptor CORONATINE INSENSITIVE1 (COI1) recruits JA ZIM-domain (JAZ) proteins for degradation, and JAZ-targeted transcription factors are released to regulate JA responses. The subgroup IIId bHLH transcriptional factors, including bHLH17, bHLH13, bHLH3, and bHLH14, interact with JAZs and repress JA responses. In this study, we show that IIId bHLH factors form dimers via the C-terminus in yeast. N-terminus of bHLH13 is essential for its transcriptional repression function...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30038485/distinguishing-species-using-gc-contents-in-mixed-dna-or-rna-sequences
#9
REVIEW
Kamran Karimi, Daniel M Wuitchik, Matthew J Oldach, Peter D Vize
With the advent of whole transcriptome and genome analysis methods, classifying samples containing multiple origins has become a significant task. Nucleotide sequences can be allocated to a genome or transcriptome by aligning sequences to multiple target sequence sets, but this approach requires extensive computational resources and also depends on target sequence sets lacking contaminants, which is often not the case. Here, we demonstrate that raw sequences can be rapidly sorted into groups, in practice corresponding to genera, by exploiting differences in nucleotide GC content...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30038484/lateral-gene-transfer-between-protozoa-related-giant-viruses-of-family-mimiviridae-and-chlamydiae
#10
Takanori Watanabe, Sumire Yamazaki, Chinatsu Maita, Mizue Matushita, Junji Matsuo, Torahiko Okubo, Hiroyuki Yamaguchi
Obligate intracellular chlamydiae diverged into pathogenic and environmental chlamydiae 0.7-1.4 billion years ago. While pathogenic chlamydiae have adapted to a wide range of vertebrates, environmental chlamydiae inhabit unicellular amoebae, the free-living Acanthamoeba . However, how and why this divergence occurred remains unclear. Meanwhile, giant viruses consisting of protozoa-related and protozoa-unrelated viruses have been discovered, with the former group being suggested to have more influenced environmental chlamydiae during their evolution while cohabiting host amoebae...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30034216/homology-inference-based-on-a-reconciliation-approach-for-the-comparative-genomics-of-protozoa
#11
Darueck A Campos, Elisa C Pereira, Rodrigo Jardim, Rafael Rc Cuadrat, Juliana S Bernardes, Alberto Mr Dávila
Protozoa parasites are responsible for several diseases in tropical countries, such as malaria, sleeping sickness, Chagas disease, leishmaniasis, amebiasis, and giardiasis, which together threaten millions of people around the world. In addition, most of the classic parasitic diseases due to protozoa are zoonotic. Understanding the biology of these organisms plays a relevant role in combating these diseases. Using homology inference and comparative genomics, this study targeted 3 protozoan species from different Phyla: Cryptosporidium muris (Apicomplexa), Entamoeba invadens (Amoebozoa), and Trypanosoma grayi (Euglenozoa)...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30022808/atypical-evolution-of-the-f-1-f-o-adenosine-triphosphate-synthase-regulatory-atp6-subunit-in-glacier-ice-worms-annelida-clitellata-mesenchytraeus
#12
Shirley A Lang, Daniel H Shain
The glacier ice worm, Mesenchytraeus solifugus , is among a few animals that reside permanently in glacier ice. Their adaptation to cold temperature has been linked to relatively high intracellular adenosine triphosphate (ATP) levels, which compensate for reductions in molecular motion at low physiological temperatures. Here, we show that ATP6-the critical regulatory subunit of the F1Fo-ATP synthase and primary target of mitochondrial disease-acquired an unprecedented histidine-rich, 18-amino acid carboxy-terminal extension, which counters the strong evolutionary trend of mitochondrial genome compaction...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/30013303/modeling-cumulative-biological-phenomena-with-suppes-bayes-causal-networks
#13
Daniele Ramazzotti, Alex Graudenzi, Giulio Caravagna, Marco Antoniotti
Several diseases related to cell proliferation are characterized by the accumulation of somatic DNA changes, with respect to wild-type conditions. Cancer and HIV are 2 common examples of such diseases, where the mutational load in the cancerous/viral population increases over time. In these cases, selective pressures are often observed along with competition, co-operation, and parasitism among distinct cellular clones. Recently, we presented a mathematical framework to model these phenomena, based on a combination of Bayesian inference and Suppes' theory of probabilistic causation, depicted in graphical structures dubbed Suppes-Bayes Causal Networks (SBCNs)...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29977111/novel-method-of-3-dimensional-graphical-representation-for-proteins-and-its-application
#14
Zhao-Hui Qi, Ke-Cheng Li, Jin-Long Ma, Yu-Hua Yao, Ling-Yun Liu
In this article, we propose a 3-dimensional graphical representation of protein sequences based on 10 physicochemical properties of 20 amino acids and the BLOSUM62 matrix. It contains evolutionary information and provides intuitive visualization. To further analyze the similarity of proteins, we extract a specific vector from the graphical representation curve. The vector is used to calculate the similarity distance between 2 protein sequences. To prove the effectiveness of our approach, we apply it to 3 real data sets...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29899660/detecting-the-population-structure-and-scanning-for-signatures-of-selection-in-horses-equus-caballus-from-whole-genome-sequencing-data
#15
Cheng Zhang, Pan Ni, Hafiz Ishfaq Ahmad, M Gemingguli, A Baizilaitibei, D Gulibaheti, Yaping Fang, Haiyang Wang, Akhtar Rasool Asif, Changyi Xiao, Jianhai Chen, Yunlong Ma, Xiangdong Liu, Xiaoyong Du, Shuhong Zhao
Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29899659/in-silico-study-on-molecular-sequences-for-identification-of-paphiopedilum-species
#16
Huyen-Trang Vu, Phuong Huynh, Hoang-Dung Tran, Ly Le
Our study searched all available sequences of Paphiopedilum from NCBI (National Center for Biotechnology Information) and tested for their species resolution capability in single as well as in combination forms. A total of 28 loci were applied for analyses in the study. From the nuclear genome, the highest resolution was of LFY , followed by ACO, DEF 4, and RAD 51. These 4 loci were found to be even better than the popular region ITS for Paphiopedilum identification. Among the chloroplast regions, the intergenic spacer atpB - rbc L gave the highest species resolution (76...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29899658/integrating-phylogenetic-and-network-approaches-to-study-gene-family-evolution-the-case-of-the-agamous-family-of-floral-genes
#17
Daniel S Carvalho, James C Schnable, Ana Maria R Almeida
The study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29881251/atram-2-0-an-improved-flexible-locus-assembler-for-ngs-data
#18
REVIEW
Julie M Allen, Raphael LaFrance, Ryan A Folk, Kevin P Johnson, Robert P Guralnick
Massive strides have been made in technologies for collecting genome-scale data. However, tools for efficiently and flexibly assembling raw outputs into downstream analytical workflows are still nascent. aTRAM 1.0 was designed to assemble any locus from genome sequencing data but was neither optimized for efficiency nor able to serve as a single toolkit for all assembly needs. We have completely re-implemented aTRAM and redesigned its structure for faster read retrieval while adding a number of key features to improve flexibility and functionality...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29844654/molecular-evolution-and-functional-divergence-of-the-iglon-family
#19
Norwin Kubick, Desiree Brösamle, Michel-Edwar Mickael
IgLON family is a subgroup of cell adhesion molecules which is known to have diverse roles in neuronal development. IgLONs are characterized by possessing 3 Ig-like C2 domains, which play a part in mediating various cellular interactions. Recently, IgLONs have been shown to be expressed at the blood-brain barrier (BBB). However, our understanding of the genetic divergence patterns and evolutionary rates of these proteins in relation to their functions, in general, and at the BBB, in particular, remains inadequate...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29720870/exploring-proteins-containing-amyloidogenic-regions-in-the-proteomes-of-bacteria-of-the-order-rhizobiales
#20
Kirill S Antonets, Sergey F Kliver, Anton A Nizhnikov
Amyloids are protein fibrils with a highly ordered spatial structure called cross-β. To date, amyloids were shown to be implicated in a wide range of biological processes, both pathogenic and functional. In bacteria, functional amyloids are involved in forming biofilms, storing toxins, overcoming the surface tension, and other functions. Rhizobiales represent an economically important group of Alphaproteobacteria , various species of which are not only capable of fixing nitrogen in the symbiosis with leguminous plants but also act as the causative agents of infectious diseases in animals and plants...
2018: Evolutionary Bioinformatics Online
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