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BMC Bioinformatics

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https://www.readbyqxmd.com/read/29224068/hi-plex-for-simple-accurate-and-cost-effective-amplicon-based-targeted-dna-sequencing
#1
Bernard J Pope, Fleur Hammet, Tu Nguyen-Dumont, Daniel J Park
Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28984189/the-international-conference-on-intelligent-biology-and-medicine-icibm-2016-from-big-data-to-big-analytical-tools
#2
EDITORIAL
Zhandong Liu, W Jim Zheng, Genevera I Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao
The 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held on December 8-10, 2016 in Houston, Texas, USA. ICIBM included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics on 3D genomics structural analysis, next generation sequencing (NGS) analysis, computational drug discovery, medical informatics, cancer genomics, and systems biology. Here, we present a summary of the nine research articles selected from ICIBM 2016 program for publishing in BMC Bioinformatics...
October 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28931551/emc10-endoplasmic-reticulum-membrane-protein-complex-subunit-10-is-a-bone-marrow-derived-angiogenic-growth-factor-promoting-tissue-repair-after-myocardial-infarction
#3
Marc R Reboll, Mortimer Korf-Klingebiel, Stefanie Klede, Felix Polten, Eva Brinkmann, Ines Reimann, Hans-Joachim Schönfeld, Maria Bobadilla, Jan Faix, George Kensah, Ina Gruh, Michael Klintschar, Matthias Gaestel, Hans W Niessen, Andreas Pich, Johann Bauersachs, Joseph A Gogos, Yong Wang, Kai C Wollert
BACKGROUND: Clinical trials of bone marrow cell-based therapies after acute myocardial infarction (MI) have produced mostly neutral results. Treatment with specific bone marrow cell-derived secreted proteins may provide an alternative biological approach to improving tissue repair and heart function after MI. We recently performed a bioinformatic secretome analysis in bone marrow cells from patients with acute MI and discovered a poorly characterized secreted protein, EMC10 (endoplasmic reticulum membrane protein complex subunit 10), showing activity in an angiogenic screen...
November 7, 2017: Circulation
https://www.readbyqxmd.com/read/28841820/a-weighted-string-kernel-for-protein-fold-recognition
#4
Saghi Nojoomi, Patrice Koehl
BACKGROUND: Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done before those methods provide reliable fold recognition for proteins whose sequences share little similarity. We have recently proposed an alignment-free method based on the concept of string kernels, SeqKernel (Nojoomi and Koehl, BMC Bioinformatics, 2017, 18:137). In this previous study, we have shown that while Seqkernel performs better than standard alignment-based methods, its applications are potentially limited, because of biases due mostly to sequence length effects...
August 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28720122/enhance-the-performance-of-current-scoring-functions-with-the-aid-of-3d-protein-ligand-interaction-fingerprints
#5
Jie Liu, Minyi Su, Zhihai Liu, Jie Li, Yan Li, Renxiao Wang
BACKGROUND: In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling this problem, but this approach is also associated with certain technical difficulties. We previously reported the Knowledge-Guided Scoring (KGS) method as an alternative approach (BMC Bioinformatics, 2010, 11, 193-208). The key idea is to compute the binding affinity of a given protein-ligand complex based on the known binding data of an appropriate reference complex, so the error in binding affinity prediction can be reduced effectively...
July 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28494756/solving-the-master-equation-for-indels
#6
EDITORIAL
Ian H Holmes
BACKGROUND: Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that are as tractable as the analogous models for substitution events. MAIN TEXT: This paper discusses progress in the area of insertion-deletion models, in view of recent work by Ezawa (BMC Bioinformatics 17:304, 2016); (BMC Bioinformatics 17:397, 2016); (BMC Bioinformatics 17:457, 2016) on the calculation of time-dependent gap length distributions in pairwise alignments, and current approaches for extending these approaches from ancestor-descendant pairs to phylogenetic trees...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28419380/%C3%AE-carboxysome-bioinformatics-identification-and-evolution-of-new-bacterial-microcompartment-protein-gene-classes-and-core-locus-constraints
#7
Manuel Sommer, Fei Cai, Matthew Melnicki, Cheryl A Kerfeld
Carboxysomes are bacterial microcompartments (BMCs) that enhance CO2 fixation in all cyanobacteria. Structurally, carboxysome shell proteins are classified according to the type of oligomer formed: hexameric (BMC-H), trimeric (BMC-T) and pentameric (BMC-P) proteins. To understand the forces driving the evolution of the carboxysome shell, we conducted a bioinformatic study of genes encoding β-carboxysome shell proteins, taking advantage of the recent large increase in sequenced cyanobacterial genomes. In addition to the four well-established BMC-H (CcmK1-4) classes, our analysis reveals two new CcmK classes, which we name CcmK5 and CcmK6...
June 1, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28407038/emmaw-computing-minimal-absent-words-in-external-memory
#8
Alice Héliou, Solon P Pissis, Simon J Puglisi
Motivation: The biological significance of minimal absent words has been investigated in genomes of organisms from all domains of life. For instance, three minimal absent words of the human genome were found in Ebola virus genomes. There exists an O(n) -time and O(n) -space algorithm for computing all minimal absent words of a sequence of length n on a fixed-sized alphabet based on suffix arrays. A standard implementation of this algorithm, when applied to a large sequence of length n , requires more than 20 n  bytes of RAM...
September 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28361713/the-joint-nettab-integrative-bioinformatics-2015-meeting-aims-topics-and-outcomes
#9
EDITORIAL
Paolo Romano, Ralf Hofestädt, Matthias Lange, Domenica D'Elia
The 15(th) International NETTAB workshop and the 11(th) Integrative Bioinformatics Symposium were held together in Bari, on October 14-16, 2016, as Joint NETTAB/IB 2015 Meeting. A special topic for the meeting was "Bioinformatics for ncRNA", but the traditional topics of both meetings series were also included in the event.About 60 scientific contributions were presented, including six keynote lectures, one special guest lecture, and many oral communications and posters. A "Two-Day Hands-on Tutorial" event was organised before the workshop...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28289437/best-hits-of-11110110111-model-free-selection-and-parameter-free-sensitivity-calculation-of-spaced-seeds
#10
Laurent Noé
BACKGROUND: Spaced seeds, also named gapped q-grams, gapped k-mers, spaced q-grams, have been proven to be more sensitive than contiguous seeds (contiguous q-grams, contiguous k-mers) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities and to anchor sequence alignments, spaced seeds have more recently been applied in several alignment-free related methods. Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28155668/bioinformatics-and-systems-biology-research-update-from-the-15-th-international-conference-on-bioinformatics-incob2016
#11
Christian Schönbach, Chandra Verma, Peter J Bond, Shoba Ranganathan
The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20-22, 2017.
December 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28155656/2016-update-on-apbionet-s-annual-international-conference-on-bioinformatics-incob
#12
EDITORIAL
Christian Schönbach, Chandra Verma, Lawrence Jin Kiat Wee, Peter John Bond, Shoba Ranganathan
InCoB became since its inception in 2002 one of the largest annual bioinformatics conferences in the Asia-Pacific region with attendance ranging between 150 and 250 delegates depending on the venue location. InCoB 2016 in Singapore was attended by almost 220 delegates. This year, sessions on structural bioinformatics, sequence and sequencing, and next-generation sequencing fielded the highest number of oral presentation. Forty-four out 96 oral presentations were associated with an accepted manuscript in supplemental issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics or BMC Systems Biology...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27822515/open-source-sequence-clustering-methods-improve-the-state-of-the-art
#13
Evguenia Kopylova, Jose A Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Hong-Wei Zhou, Torbjørn Rognes, J Gregory Caporaso, Rob Knight
Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE...
January 2016: MSystems
https://www.readbyqxmd.com/read/27587087/advancing-systems-biology-in-the-international-conference-on-intelligent-biology-and-medicine-icibm-2015
#14
Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang, Jianhua Ruan
The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13-15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial sessions, one poster session, and four keynote presentations that covered the frontier research in broad areas related to bioinformatics, systems biology, big data science, biomedical informatics, pharmacogenomics, and intelligent computing. Here, we present a summary of the 10 research articles that were selected from ICIBM 2015 and included in the supplement to BMC Systems Biology...
August 26, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27556805/read-split-run-an-improved-bioinformatics-pipeline-for-identification-of-genome-wide-non-canonical-spliced-regions-using-rna-seq-data
#15
Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin R Hassler, Randal J Kaufman
BACKGROUND: Most existing tools for detecting next-generation sequencing-based splicing events focus on generic splicing events. Consequently, special types of non-canonical splicing events of short mRNA regions (IRE1α targeted) have not yet been thoroughly addressed at a genome-wide level using bioinformatics approaches in conjunction with next-generation technologies. During endoplasmic reticulum (ER) stress, the gene encoding the RNase Ire1α is known to splice out a short 26 nt region from the mRNA of the transcription factor Xbp1 non-canonically within the cytosol...
August 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27556295/intelligent-biology-and-medicine-in-2015-advancing-interdisciplinary-education-collaboration-and-data-science
#16
Kun Huang, Yunlong Liu, Yufei Huang, Lang Li, Lee Cooper, Jianhua Ruan, Zhongming Zhao
We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected from the manuscripts submitted to ICIBM 2015. The conference was held on November 13-15, 2015 at Indianapolis, Indiana, USA. It included eight scientific sessions, three tutorials, four keynote presentations, three highlight talks, and a poster session that covered current research in bioinformatics, systems biology, computational biology, biotechnologies, and computational medicine...
August 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27532290/gender-specific-association-of-tp53-polymorphisms-ex4-215g-c-arg72pro-ivs3-40-41ins16-and-ivs6-62g-a-with-risk-of-oral-cancer-subtypes-and-overall-survival-of-the-patients
#17
Srivani L S S Nagam, Saritha Katta, Vidudala V T S Prasad
Reports on the association of TP53 polymorphisms with oral cancer are not only limited but also not specific to site and/or gender. Hence, we examined the effect of TP53 polymorphisms (EX4 215G>C, IVS3+40-41ins16 and IVS6+62G>A) on buccal mucosa cancer (BMC) and tongue cancer (TC) risk, survival of patients in relation to risk and clinical factors, gender wise (excepting for estimating hazards ratio [HR]), using Fisher's Exact Test, Kaplan-Meier analysis, and Cox-proportional hazards models. The exonic polymorphism increased BMC and TC risk in males by 2-4-fold...
March 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/27153720/pon-sol-prediction-of-effects-of-amino-acid-substitutions-on-protein-solubility
#18
Yang Yang, Abhishek Niroula, Bairong Shen, Mauno Vihinen
MOTIVATION: Solubility is one of the fundamental protein properties. It is of great interest because of its relevance to protein expression. Reduced solubility and protein aggregation are also associated with many diseases. RESULTS: We collected from literature the largest experimentally verified solubility affecting amino acid substitution (AAS) dataset and used it to train a predictor called PON-Sol. The predictor can distinguish both solubility decreasing and increasing variants from those not affecting solubility...
July 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27102907/empirical-estimation-of-sequencing-error-rates-using-smoothing-splines
#19
Xuan Zhu, Jian Wang, Bo Peng, Sanjay Shete
BACKGROUND: Next-generation sequencing has been used by investigators to address a diverse range of biological problems through, for example, polymorphism and mutation discovery and microRNA profiling. However, compared to conventional sequencing, the error rates for next-generation sequencing are often higher, which impacts the downstream genomic analysis. Recently, Wang et al. (BMC Bioinformatics 13:185, 2012) proposed a shadow regression approach to estimate the error rates for next-generation sequencing data based on the assumption of a linear relationship between the number of reads sequenced and the number of reads containing errors (denoted as shadows)...
April 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27027968/identifying-molecular-mechanisms-of-the-late-phase-asthmatic-response-by-integrating-cellular-gene-and-metabolite-levels-in-blood
#20
Amrit Singh, Casey P Shannon, Young Woong Kim, Mari L DeMarco, Gail M Gauvreau, J Mark FitzGerald, Louis-Philippe Boulet, Paul M O'Byrne, Kim-Anh Le Cao, Scott J Tebbutt
RATIONALE: Individuals with allergic asthma respond differently, but reproducibly, to allergen inhalation challenge. Some individuals develop an isolated early response (early responders) (ERs), whereas others go on to develop a late response (dual responders) (DRs). It is not understood why late responses do not develop in all sensitized individuals. OBJECTIVES: The aim of this study was to identify blood biomarkers that can discriminate ERs and DRs using cellular frequencies and gene and metabolite expression from whole blood...
March 2016: Annals of the American Thoracic Society
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