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ORCIDBriefings in Bioinformatics, Volume 15
Volume 15, Number 1, January 2014
- Bing Liu, Jiuyong Li
, Murray J. Cairns:
Identifying miRNAs, targets and functions. 1-19 - Yongxin Liu, Tianfu Yang, Hongwang Li, Runqing Yang:
Iteratively reweighted LASSO for mapping multiple quantitative trait loci. 20-29 - Zhong Wang, Yaqun Wang, Ningtao Wang, Jianxin Wang, Zuoheng Wang, C. Eduardo Vallejos, Rongling Wu:
Towards a comprehensive picture of the genetic landscape of complex traits. 30-42 - Chunfa Tong, Lianying Shen, Yafei Lv, Zhong Wang, Xiaoling Wang, Sisi Feng, Xin Li, Yihan Sui, Xiaoming Pang, Rongling Wu:
Structural mapping: how to study the genetic architecture of a phenotypic trait through its formation mechanism. 43-53 - Weiqiang Zhou, Hong Yan:
Alpha shape and Delaunay triangulation in studies of protein-related interactions. 54-64 - Wasco Wruck, Martin Peuker, Christian R. A. Regenbrecht:
Data management strategies for multinational large-scale systems biology projects. 65-78 - Pascal Lapierre, Erica Lasek-Nesselquist, Johann Peter Gogarten:
The impact of HGT on phylogenomic reconstruction methods. 79-90 - Thomas Dandekar, Astrid Fieselmann, Saman Majeed, Zeeshan Ahmed:
Software applications toward quantitative metabolic flux analysis and modeling. 91-107 - Meiyappan Lakshmanan, Geoffrey Koh, Bevan Chung, Dong-Yup Lee:
Software applications for flux balance analysis. 108-122 - Thomas Bernard, Alan J. Bridge, Anne Morgat, Sébastien Moretti, Ioannis Xenarios, Marco Pagni:
Reconciliation of metabolites and biochemical reactions for metabolic networks. 123-135
Volume 15, Number 2, March 2014
- Paul Horton:
Next-generation Bioinformatics: connecting bases to genes, networks and disease. 137
- Anish Man Singh Shrestha, Martin C. Frith, Paul Horton:
A bioinformatician's guide to the forefront of suffix array construction algorithms. 138-154 - M. Michael Gromiha, Yu-Yen Ou:
Bioinformatics approaches for functional annotation of membrane proteins. 155-168 - Thom Vreven, Howook Hwang, Brian G. Pierce, Zhiping Weng:
Evaluating template-based and template-free protein-protein complex structure prediction. 169-176 - Bolin Chen, Weiwei Fan, Juan Liu, Fang-Xiang Wu:
Identifying protein complexes and functional modules - from static PPI networks to dynamic PPI networks. 177-194 - Stefan Maetschke, Piyush B. Madhamshettiwar, Melissa J. Davis, Mark A. Ragan:
Supervised, semi-supervised and unsupervised inference of gene regulatory networks. 195-211 - Yongsoo Kim, Seungmin Han, Seungjin Choi, Daehee Hwang:
Inference of dynamic networks using time-course data. 212-228 - Meiyi Li, Tao Zeng, Rui Liu, Luonan Chen:
Detecting tissue-specific early warning signals for complex diseases based on dynamical network biomarkers: study of type 2 diabetes by cross-tissue analysis. 229-243 - Jing Zhang, Jie Liu, Jianbo Sun, Chen Chen, Gregory Foltz, Biaoyang Lin:
Identifying driver mutations from sequencing data of heterogeneous tumors in the era of personalized genome sequencing. 244-255 - Stephan Pabinger, Andreas Dander, Maria Fischer, René Snajder, Michael Sperk, Mirjana Efremova, Birgit Krabichler, Michael R. Speicher, Johannes Zschocke, Zlatko Trajanoski:
A survey of tools for variant analysis of next-generation genome sequencing data. 256-278 - Cen Wu, Yuehua Cui:
Boosting signals in gene-based association studies via efficient SNP selection. 279-291 - Qi Liu, Han Zhou, Ruixin Zhu, Ying Xu, Zhiwei Cao:
Reconsideration of in silico siRNA design from a perspective of heterogeneous data integration: problems and solutions. 292-305 - Yanru Zeng, Wei Hou, Shuang Song, Sisi Feng, Lin Shen, Guohua Xia, Rongling Wu:
A statistical design for testing apomictic diversification through linkage analysis. 306-318 - Yihan Sui, Weimiao Wu, Zhong Wang, Jianxin Wang, Zuoheng Wang, Rongling Wu:
A case-control design for testing and estimating epigenetic effects on complex diseases. 319-326 - Mariana L. Neves, Ulf Leser:
A survey on annotation tools for the biomedical literature. 327-340
Volume 15, Number 3, May 2014
- Susana Vinga:
Editorial: Alignment-free methods in computational biology. 341-342
- Kai Song, Jie Ren, Gesine Reinert, Minghua Deng, Michael S. Waterman, Fengzhu Sun:
New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. 343-353 - Isabel Schwende, Tuan D. Pham:
Pattern recognition and probabilistic measures in alignment-free sequence analysis. 354-368 - Jonas S. Almeida:
Sequence analysis by iterated maps, a review. 369-375 - Susana Vinga:
Information theory applications for biological sequence analysis. 376-389 - Raffaele Giancarlo, Simona E. Rombo, Filippo Utro:
Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies. 390-406 - Bernhard Haubold:
Alignment-free phylogenetics and population genetics. 407-418 - Luca Pinello, Giosuè Lo Bosco, Guo-Cheng Yuan:
Applications of alignment-free methods in epigenomics. 419-430 - Melanie Schirmer, William T. Sloan, Christopher Quince:
Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes. 431-442 - Vasilis J. Promponas, Christos A. Ouzounis, Ioannis Iliopoulos:
Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. 443-454 - Miranda D. Stobbe, Gerbert A. Jansen, Perry D. Moerland, Antoine H. C. van Kampen:
Knowledge representation in metabolic pathway databases. 455-470
Volume 15, Number 4, July 2014
- Thomas Triplet, Gregory Butler:
A review of genomic data warehousing systems. 471-483 - Ralf Stefan Neumann, Surendra Kumar, Kamran Shalchian-Tabrizi:
BLAST output visualization in the new sequencing era. 484-503 - Henryk Maciejewski:
Gene set analysis methods: statistical models and methodological differences. 504-518 - Maria Rodrigo-Domingo, Rasmus Waagepetersen, Julie Støve Bødker, Steffen Falgreen, Malene Krag Kjeldsen, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted:
Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor. 519-533 - Ningtao Wang, Yaqun Wang, Han Hao, Luojun Wang, Zhong Wang, Jianxin Wang, Rongling Wu:
A bi-Poisson model for clustering gene expression profiles by RNA-seq. 534-541 - Feng-Chi Chen:
Are all of the human exons alternatively spliced? 542-551 - Huijiang Gao, Yang Wu, Jiahan Li, Hongwang Li, Junya Li, Runqing Yang:
Forward LASSO analysis for high-order interactions in genome-wide association study. 552-561 - Zhongwen Huang, Chunfa Tong, Wenhao Bo, Xiaoming Pang, Zhong Wang, Jichen Xu, Junyi Gai, Rongling Wu:
An allometric model for mapping seed development in plants. 562-570 - Wenhao Bo, Zhong Wang, Fang Xu, Guifang Fu, Yihan Sui, Weimiao Wu, Xuli Zhu, Danni Yin, Qin Yan, Rongling Wu:
Shape mapping: genetic mapping meets geometric morphometrics. 571-581 - Hong Luo, Harm Nijveen:
Understanding and identifying amino acid repeats. 582-591 - José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry:
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. 592-611 - Janine Roy, Christof Winter, Zerrin Isik, Michael Schroeder:
Network information improves cancer outcome prediction. 612-625 - James Christopher Bare, Nitin S. Baliga:
Architecture for interoperable software in biology. 626-636 - Quan Zou, Xu-Bin Li, Wen-Rui Jiang, Ziyu Lin, Gui-Lin Li, Ke Chen:
Survey of MapReduce frame operation in bioinformatics. 637-647 - Jakob Lewin Rukov, Roni Wilentzik, Ishai Jaffe, Jeppe Vinther, Noam Shomron:
Pharmaco-miR: linking microRNAs and drug effects. 648-659 - Wenhao Bo, Guifang Fu, Zhong Wang, Fang Xu, Yong Shen, Jichen Xu, Zhongwen Huang, Junyi Gai, C. Eduardo Vallejos, Rongling Wu:
Systems mapping: how to map genes for biomass allocation toward an ideotype. 660-669
Volume 15, Number 5, September 2014
- Xingjie Shi, Shihao Shen, Jin Liu, Jian Huang, Yong Zhou, Shuangge Ma:
Similarity of markers identified from cancer gene expression studies: observations from GEO. 671-684 - Xiaotu Ma, Ting Chen, Fengzhu Sun:
Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. 685-698 - Hiroyuki Kurata, Kazuhiro Maeda, Toshikazu Onaka, Takenori Takata:
BioFNet: biological functional network database for analysis and synthesis of biological systems. 699-709 - Chao Huang, Chunli Zheng, Yan Li, Yonghua Wang, Aiping Lu, Ling Yang:
Systems pharmacology in drug discovery and therapeutic insight for herbal medicines. 710-733 - Hao Ding, Ichigaku Takigawa, Hiroshi Mamitsuka, Shanfeng Zhu:
Similarity-based machine learning methods for predicting drug-target interactions: a brief review. 734-747 - Michiaki Hamada:
Fighting against uncertainty: an essential issue in bioinformatics. 748-767 - Robert Smith, Dan Ventura, John T. Prince:
Controlling for confounding variables in MS-omics protocol: why modularity matters. 768-770 - Maria Secrier, Reinhard Schneider:
Visualizing time-related data in biology, a review. 771-782 - A. Murat Eren, Hilary G. Morrison, Susan M. Huse, Mitchell L. Sogin:
DRISEE overestimates errors in metagenomic sequencing data. 783-787 - Daniel Glez-Peña, Anália Lourenço, Hugo López-Fernández, Miguel Reboiro-Jato, Florentino Fdez-Riverola:
Web scraping technologies in an API world. 788-797 - Marco Aldinucci, Massimo Torquati, Concetto Spampinato, Maurizio Drocco, Claudia Misale, Cristina Calcagno, Mario Coppo:
Parallel stochastic systems biology in the cloud. 798-813 - Runqing Yang, Hongwang Li, Lina Fu, Yongxin Liu:
An efficient approach to large-scale genotype-phenotype association analyses. 814-822 - Mingyu Shao, Yi Yang, Jihong Guan, Shuigeng Zhou:
Choosing appropriate models for protein-protein interaction networks: a comparison study. 823-838 - Haipeng Gong, Xiaoqing Liu, Jun Wu, Zengyou He:
Data construction for phosphorylation site prediction. 839-855 - Chen Li, Maria Liakata, Dietrich Rebholz-Schuhmann:
Biological network extraction from scientific literature: state of the art and challenges. 856-877
Volume 15, Number 6, November 2014
- Yan Guo, Fei Ye, Quanghu Sheng, Travis Clark, David C. Samuels:
Three-stage quality control strategies for DNA re-sequencing data. 879-889 - Oliver Bonham-Carter, Joe Steele, Dhundy Bastola:
Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. 890-905 - Suzana de Siqueira Santos, Daniel Yasumasa Takahashi, Asuka Nakata, André Fujita:
A comparative study of statistical methods used to identify dependencies between gene expression signals. 906-918 - Subhajyoti De, Brent S. Pedersen, Katerina J. Kechris:
The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. 919-928 - Sarah Dedeurwaerder, Matthieu Defrance, Martin Bizet, Emilie Calonne, Gianluca Bontempi, François Fuks:
A comprehensive overview of Infinium HumanMethylation450 data processing. 929-941 - Irene Kouskoumvekaki, Nour Shublaq, Søren Brunak:
Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. 942-952 - Catherine Ching Han Chang, Jiangning Song, Beng Ti Tey, Ramakrishnan Nagasundara Ramanan:
Bioinformatics approaches for improved recombinant protein production in Escherichia coli: protein solubility prediction. 953-962 - Tingting Li, Boyan Song, Zheng Wu, Ming Lu, Wei-Guo Zhu:
Systematic identification of Class I HDAC substrates. 963-972 - Liam G. Fearnley, Melissa J. Davis, Mark A. Ragan, Lars Keld Nielsen:
Extracting reaction networks from databases-opening Pandora's box. 973-983 - Peiqin Gu, Huajun Chen:
Modern bioinformatics meets traditional Chinese medicine. 984-1003 - Jingchu Luo:
Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course. 1004-1013 - Hui Liu, Ruichang Zhang, Wei Xiong, Jihong Guan, Ziheng Zhuang, Shuigeng Zhou:
A comparative evaluation on prediction methods of nucleosome positioning. 1014-1027 - Fang Wang, Shaojun Zhang, Yanhua Wen, Yanjun Wei, Haidan Yan, Hongbo Liu, Jianzhong Su, Yan Zhang, Jianhua Che:
Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. 1028-1043 - Fang Xu, Yafei Lyu, Chunfa Tong, Weimiao Wu, Xuli Zhu, Danni Yin, Qin Yan, Jian Zhang, Xiaoming Pang, Christian M. Tobias, Rongling Wu:
A statistical model for QTL mapping in polysomic autotetraploids underlying double reduction. 1044-1056 - Jiahan Li, Jun Dan, Chunlei Li, Rongling Wu:
A model-free approach for detecting interactions in genetic association studies. 1057-1068 - Xin Li, Yihan Sui, Tian Liu, Jianxin Wang, Yongci Li, Zhenwu Lin, John Hegarty, Walter A. Koltun, Zuoheng Wang, Rongling Wu:
A model for family-based case-control studies of genetic imprinting and epistasis. 1069-1079
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