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Briefings in Bioinformatics, Volume 18
Volume 18, Number 1, January 2017
- Katrin Sameith
, Juliana G. Roscito
Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly. 1-8
- Sohiya Yotsukura
Computational recognition for long non-coding RNA (lncRNA): Software and databases. 9-27
- Xin Sheng, Jiayan Wu
MTD: a mammalian transcriptomic database to explore gene expression and regulation. 28-36 - Xun Gu, Wenda Tang:
Model parameters of molecular evolution explain genomic correlations. 37-42 - Clément Frainay
Computational methods to identify metabolic sub-networks based on metabolomic profiles. 43-56 - Yingying Zhang, Zhong Wang, Yongyan Wang:
Multi-hierarchical profiling: an emerging and quantitative approach to characterizing diverse biological networks. 57-68 - Oliver Bonham-Carter, Ishwor Thapa, Steven G. From, Dhundy Bastola:
A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays. 69-84 - Wei Ma
An analysis of human microbe-disease associations. 85-97 - Weiyang Bai, Wen Yang, Wenjing Wang, Yang Wang, Can Liu, Qinghua Jiang, Jinlian Hua, Mingzhi Liao
GED: a manually curated comprehensive resource for epigenetic modification of gametogenesis. 98-104 - Khader Shameer, Marcus A. Badgeley
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. 105-124 - Tianyi Qiu, Jingxuan Qiu, Jun Feng, Dingfeng Wu, Yiyan Yang, Kailin Tang
The recent progress in proteochemometric modelling: focusing on target descriptors, cross-term descriptors and application scope. 125-136 - Qin Yan, Xuli Zhu, Libo Jiang, Meixia Ye, Lidan Sun, John S. Terblanche
A computing platform to map ecological metabolism by integrating functional mapping and the metabolic theory of ecology. 137-144 - Yossy Machluf
Making authentic science accessible - the benefits and challenges of integrating bioinformatics into a high-school science curriculum. 145-159 - Yuan Luo
Bridging semantics and syntax with graph algorithms - state-of-the-art of extracting biomedical relations. 160-178
Volume 18, Number 2, March 2017
- Walter Pirovano, Marten Boetzer, Martijn F. L. Derks, Sandra Smit
NCBI-compliant genome submissions: tips and tricks to save time and money. 179-182
- Idoia Ochoa
Effect of lossy compression of quality scores on variant calling. 183-194 - Soyoun Lee, Jie Yang, Jiayu Huang, Hao Chen, Wei Hou, Song Wu:
Multi-marker linkage disequilibrium mapping of quantitative trait loci. 195-204 - Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi
A benchmark of gene expression tissue-specificity metrics. 205-214 - Pasquale Di Salle, Guido Incerti
Gene co-expression analyses: an overview from microarray collections in Arabidopsis thaliana. 215-225 - Tyler Weirick
Resolving the problem of multiple accessions of the same transcript deposited across various public databases. 226-235 - Jinyuan Xu, Jing Bai, Xinxin Zhang, Yanling Lv, Yonghui Gong, Ling Liu, Hongying Zhao, Fulong Yu
A comprehensive overview of lncRNA annotation resources. 236-249 - Kirk Gosik, Lan Kong, Vernon M. Chinchilli, Rongling Wu:
iFORM/eQTL: an ultrahigh-dimensional platform for inferring the global genetic architecture of gene transcripts. 250-259 - Matthew Dapas
Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms. 260-269 - Kuan Li, Chaoqun Xu, Jian Huang, Wei Liu
Prediction and identification of the effectors of heterotrimeric G proteins in rice (Oryza sativa L.). 270-278 - Ryuichiro Nakato
Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. 279-290 - Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen
A comprehensive study of RNA secondary structure alignment algorithms. 291-305 - Benedikt Löwes, Cédric Chauve
The BRaliBase dent - a tale of benchmark design and interpretation. 306-311 - Sandra L. Taylor
Effects of imputation on correlation: implications for analysis of mass spectrometry data from multiple biological matrices. 312-320 - Jinan Wang, Zihu Guo
Weak-binding molecules are not drugs? - toward a systematic strategy for finding effective weak-binding drugs. 321-332 - Zengrui Wu, Feixiong Cheng
SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning. 333-347 - Nathan S. Watson-Haigh
Towards an open, collaborative, reusable framework for sharing hands-on bioinformatics training workshops. 348-355
Volume 18, Number 3, May 2017
- Wen Wei, Feng Gao
Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties. 357-366 - Vahid Jalili
MuSERA: Multiple Sample Enriched Region Assessment. 367-381 - Jing Wang
A high-dimensional linkage analysis model for characterizing crossover interference. 382-393 - Cheikh Loucoubar, Audrey V. Grant, Jean-François Bureau, Isabelle Casademont, Ndjido Ardo Bar, Avner Bar-Hen, Mamadou Diop, Joseph Faye, Fatoumata Diene Sarr, Abdoulaye Badiane, Adama Tall, Jean-François Trape, Freddy Cliquet, Benno Schwikowski
Detecting multi-way epistasis in family-based association studies. 394-402 - Eugenia Galeota
Ontology-based annotations and semantic relations in large-scale (epi)genomics data. 403-412 - Peilin Jia, Zhongming Zhao:
Impacts of somatic mutations on gene expression: an association perspective. 413-425 - Yanhua Wen, Yanjun Wei
Cell subpopulation deconvolution reveals breast cancer heterogeneity based on DNA methylation signature. 426-440 - Reuben Thomas, Sean Thomas, Alisha K. Holloway, Katherine S. Pollard:
Features that define the best ChIP-seq peak calling algorithms. 441-450 - Stephen A. Smith
Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny. 451-457 - Li C. Xue, João P. G. L. M. Rodrigues, Drena Dobbs
Template-based protein-protein docking exploiting pairwise interfacial residue restraints. 458-466
- Sandeep Kumar Dhanda
Novel in silico tools for designing peptide-based subunit vaccines and immunotherapeutics. 467-478
- Christian R. Bauer
Interdisciplinary approach towards a systems medicine toolbox using the example of inflammatory diseases. 479-487 - Hsih-te Yang
Literature-based discovery of new candidates for drug repurposing. 488-497
- Alice Cambiaghi, Manuela Ferrario, Marco Masseroli:
Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration. 498-510
- Yuan Luo
Tensor factorization toward precision medicine. 511-514
- Ning Zhao
Optimization of cell lines as tumour models by integrating multi-omics data. 515-529 - Jeremy Leipzig
A review of bioinformatic pipeline frameworks. 530-536 - Jerico Nico De Leon Revote, Nathan S. Watson-Haigh
Development of a cloud-based Bioinformatics Training Platform. 537-544
- Ning Zhao, Yongjing Liu, Yunzhen Wei, Zichuang Yan, Qiang Zhang, Wu Cheng, Zhi-qiang Chang, Yan Xu:
Optimization of cell lines as tumour models by integrating multi-omics data. 545
Volume 18, Number 4, July 2017
- Xianwen Meng, Xue Li, Peijing Zhang, Jingjing Wang, Yincong Zhou, Ming Chen
Circular RNA: an emerging key player in RNA world. 547-557 - Xing Chen, Chenggang Clarence Yan, Xu Zhang, Zhu-Hong You
Long non-coding RNAs and complex diseases: from experimental results to computational models. 558-576 - Thuc Duy Le
Computational methods for identifying miRNA sponge interactions. 577-590 - Haitao Yang, Shaoyu Li, Hongyan Cao, Chichen Zhang, Yuehua Cui:
Predicting disease trait with genomic data: a composite kernel approach. 591-601 - Umaporn Siangphoe, Kellie J. Archer
Estimation of random effects and identifying heterogeneous genes in meta-analysis of gene expression studies. 602-618 - Sohiya Yotsukura
Exploring phenotype patterns of breast cancer within somatic mutations: a modicum in the intrinsic code. 619-633 - Gerald Li, Peter Bankhead
Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned. 634-646 - Wankun Deng
Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins. 647-658 - Luciano A. Abriata:
Structural database resources for biological macromolecules. 659-669 - Santiago Vilar, George Hripcsak:
The role of drug profiles as similarity metrics: applications to repurposing, adverse effects detection and drug-drug interactions. 670-681 - Feixiong Cheng, Huixiao Hong
Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era. 682-697 - Vinita Periwal
A comprehensive overview of computational resources to aid in precision genome editing with engineered nucleases. 698-711 - Dongxue Che, Yang Wang, Weiyang Bai, Leijie Li, Guiyou Liu, Liangcai Zhang, Yongchun Zuo
Dynamic and modular gene regulatory networks drive the development of gametogenesis. 712-721
- Yuan Luo
Bridging semantics and syntax with graph algorithms - state-of-the-art of extracting biomedical relations. 722
Volume 18, Number 5, September 2017
- Alida Palmisano
OpenGeneMed: a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trials. 723-734 - Maria K. Jaakkola, Fatemeh Seyednasrollah, Arfa Mehmood, Laura L. Elo
Comparison of methods to detect differentially expressed genes between single-cell populations. 735-743 - Yao Zhou
Systematic bias of correlation coefficient may explain negative accuracy of genomic prediction. 744-753 - Libo Jiang, Miaomiao Zhang
Evo-Devo-EpiR: a genome-wide search platform for epistatic control on the evolution of development. 754-760 - Xiaofei Yang, Lin Gao, Shihua Zhang:
Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns. 761-773 - Silvia Salatino
BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files. 774-779 - Giuseppe Militello
Screening and validation of lncRNAs and circRNAs as miRNA sponges. 780-788 - Haitao Luo, Dechao Bu, Liang Sun, Shuangsang Fang, Zhiyong Liu, Yi Zhao
Identification and function annotation of long intervening noncoding RNAs. 789-797 - Xiaoqing Peng, Jianxin Wang, Wei Peng, Fang-Xiang Wu
Protein-protein interactions: detection, reliability assessment and applications. 798-819 - Francisco Azuaje:
Computational models for predicting drug responses in cancer research. 820-829 - Shihua Zhang
TBC2health: a database of experimentally validated health-beneficial effects of tea bioactive compounds. 830-836 - Yvonne Lichtblau, Karin Zimmermann, Berit Haldemann, Dido Lenze, Michael Hummel
Comparative assessment of differential network analysis methods. 837-850 - Seonwoo Min
Deep learning in bioinformatics. 851-869
- Marco S. Nobile
Graphics processing units in bioinformatics, computational biology and systems biology. 870-885
- Gaston K. Mazandu
Gene Ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery. 886-901
- Ron Henkel, Robert Hoehndorf
Notions of similarity for systems biology models. 902 - Aliyu Musa
A review of connectivity map and computational approaches in pharmacogenomics. 903 - Seyed Hamid Aghaee-Bakhtiari, Ehsan Arefian
miRandb: a resource of online services for miRNA research. 904
- Bohdan B. Khomtchouk, Edmund Weitz, Peter D. Karp, Claes Wahlestedt:
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications. 905 - Yang-Jun Wen, Hanwen Zhang, Yuan-Li Ni, Bo Huang, Jin Zhang, Jian-Ying Feng, Shi-Bo Wang, Jim M. Dunwell, Yuan-Ming Zhang, Rongling Wu:
Methodological implementation of mixed linear models in multi-locus genome-wide association studies. 906
Volume 18, Number 6, November 2017
- Martin J. Bishop:
Editorial. 907
- Lavanya Rishishwar
Benchmarking computational tools for polymorphic transposable element detection. 908-918 - Xuli Zhu, Huan Li, Meixia Ye, Libo Jiang, Mengmeng Sang
AlloMap6: an R package for genetic linkage analysis in allohexaploids. 919-927 - Wei Jiang
What is the probability of replicating a statistically significant association in genome-wide association studies? 928-939 - Alberto Magi
Characterization of MinION nanopore data for resequencing analyses. 940-953 - Xuefeng Wang, Zhenyu Zhang, Nathan Morris, Tianxi Cai, Seunggeun Lee, Chaolong Wang, Timothy W. Yu
Rare variant association test in family-based sequencing studies. 954-961 - Miriam Kesselmeier
Robust logistic regression to narrow down the winner's curse for rare and recessive susceptibility variants. 962-972 - Zhifu Sun
Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. 973-983 - Siyu Xia
Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes. 984-992 - David John
RNAEditor: easy detection of RNA editing events and the introduction of editing islands. 993-1001 - Juan Xu, Tingting Shao, Na Ding, Yongsheng Li
miRNA-miRNA crosstalk: from genomics to phenomics. 1002-1011
- David Roy Smith
Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline. 1012-1016
- David Alvarez-Ponce:
Recording negative results of protein-protein interaction assays: an easy way to deal with the biases and errors of interactomic data sets. 1017-1020
- K. C. Dukka B.:
Recent advances in sequence-based protein structure prediction. 1021-1032 - José D. Colbes, Rosario I. Corona, Christian Lezcano, David O. Rodríguez, Carlos A. Brizuela
Protein side-chain packing problem: is there still room for improvement? 1033-1043 - William Dunn Jr, Anita Burgun
Exploring and visualizing multidimensional data in translational research platforms. 1044-1056 - Peng Zhang
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. 1057-1070 - Davide S. Sardina
A novel computational method for inferring competing endogenous interactions. 1071-1081 - Lucia Bianchi, Pietro Liò
Opportunities for community awareness platforms in personal genomics and bioinformatics education. 1082-1090
- Javier De Las Rivas
Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures. 1091 - Huilin Wang, Liubin Feng, Geoffrey I. Webb
Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity. 1092 - Yao Zhou, M. Isabel Vales
Systematic bias of correlation coefficient may explain negative accuracy of genomic prediction. 1093
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