Journal: BMC Bioinformatics

Volume 12, Issue S-1

0 -- 0Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon. PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach
0 -- 0Ashish V. Tendulkar, Pramod P. Wangikar. Characterization and sequence prediction of structural variations in α
0 -- 0Euna Jeong, Masao Nagasaki, Kazuko Ueno, Satoru Miyano. Ontology-based instance data validation for high-quality curated biological pathways
0 -- 0Giltae Song, Chih-Hao Hsu, Cathy Riemer, Webb Miller. Evaluation of methods for detecting conversion events in gene clusters
0 -- 0Laxmi Parida, Pier Palamara, Asif Javed. A minimal descriptor of an ancestral recombinations graph
0 -- 0Chunfang Zheng, David Sankoff. On the PATHGROUPS approach to rapid small phylogeny
0 -- 0Pengyi Yang, Joshua W. K. Ho, Jean Yee Hwa Yang, Bing Bing Zhou. Gene-gene interaction filtering with ensemble of filters
0 -- 0Zengyou He, Can Yang, Guangyu Guo, Ning Li, Weichuan Yu. Motif-All: discovering all phosphorylation motifs
0 -- 0Yi-Ping Chen, Kwang-Hyun Cho. The Ninth Asia Pacific Bioinformatics Conference (APBC2011)
0 -- 0Cho-Yi Chen, Shui-Tein Chen, Chiou-Shann Fuh, Hsueh-Fen Juan, Hsuan-Cheng Huang. Coregulation of transcription factors and microRNAs in human transcriptional regulatory network
0 -- 0William Murad, Rahul Singh, Ten-Yang Yen. An efficient algorithmic approach for mass spectrometry-based disulfide connectivity determination using multi-ion analysis
0 -- 0Fei Xia, Yong Dou, Guo-Qing Lei, Yusong Tan. FPGA accelerator for protein secondary structure prediction based on the GOR algorithm
0 -- 0Jhang-Wei Huang, Jinn-Moon Yang. Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses
0 -- 0Anita Sarkar, Sonu Kumar, Durai Sundar. The G protein-coupled receptors in the pufferfish Takifugu rubripes
0 -- 0Che-Wei Chang, Ping-Chiang Lyu, Masanori Arita. Reconstructing phylogeny from metabolic substrate-product relationships
0 -- 0Joo Yoon, Jeonghun Yeom, Heebum Lee, Kyutae Kim, Seungjin Na, Kunsoo Park, Eunok Paek, Cheolju Lee. High-throughput peptide quantification using mTRAQ reagent triplex
0 -- 0Suparna Mitra, Paul Rupek, Daniel C. Richter, Tim Urich, Jack A. Gilbert, Folker Meyer, Andreas Wilke, Daniel H. Huson. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
0 -- 0Christine Lo, Ali Bashir, Vikas Bansal, Vineet Bafna. Strobe sequence design for haplotype assembly
0 -- 0Keunwan Park, Dongsup Kim. Modeling allosteric signal propagation using protein structure networks
0 -- 0Nung Kion Lee, Dianhui Wang. SOMEA: self-organizing map based extraction algorithm for DNA motif identification with heterogeneous model
0 -- 0Pawel Górecki, J. Gordon Burleigh, Oliver Eulenstein. Maximum likelihood models and algorithms for gene tree evolution with duplications and losses
0 -- 0Young-Soo Song, Chan Hee Park, Hee-Joon Chung, Hyunjung Shin, Jihun Kim, Ju Han Kim. Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases
0 -- 0Yutaka Saito, Kengo Sato, Yasubumi Sakakibara. Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures
0 -- 0Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Li, Wei-Mou Zheng, Dongbo Bu. Incorporating Ab Initio energy into threading approaches for protein structure prediction
0 -- 0Zengyou He, Hongyu Zhao, Weichuan Yu. Score regularization for peptide identification
0 -- 0Wen-Chieh Chang 0002, J. Gordon Burleigh, David Fernández-Baca, Oliver Eulenstein. An ILP solution for the gene duplication problem
0 -- 0Yong Chen, Fenglou Mao, Guojun Li, Ying Xu. Genome-wide discovery of missing genes in biological pathways of prokaryotes
0 -- 0Hui Zhao, Lore Cloots, Tim Van den Bulcke, Yan Wu, Riet De Smet, Valerie Storms, Pieter Meysman, Kristof Engelen, Kathleen Marchal. Query-based biclustering of gene expression data using Probabilistic Relational Models
0 -- 0Gang Su, Charles F. Burant, Christopher W. Beecher, Brian D. Athey, Fan Meng. Integrated metabolome and transcriptome analysis of the NCI60 dataset
0 -- 0Sung-Joon Park, Kenta Nakai. A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns
0 -- 0Henry Han, Xiao-Li Li. Multi-resolution independent component analysis for high-performance tumor classification and biomarker discovery
0 -- 0Sung-Chou Li, Wen-Ching Chan, Chun-Hung Lai, Kuo-Wang Tsai, Chun-Nan Hsu, Yuh-Shan Jou, Hua-Chien Chen, Chun-hong Chen, Wen-Chang Lin. UMARS: Un-MAppable Reads Solution
0 -- 0Yi-Zhong Weng, Darby Tien-Hao Chang, Yu-Feng Huang, Chih-Wei Lin. A study on the flexibility of enzyme active sites
0 -- 0Hiroyuki Monji, Satoshi Koizumi, Tomonobu Ozaki, Takenao Ohkawa. Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks
0 -- 0Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu. A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures
0 -- 0Abhinav Grover, Ashutosh Shandilya, Vibhuti Agrawal, Piyush Pratik, Divya Bhasme, Virendra S. Bisaria, Durai Sundar. Hsp90/Cdc37 Chaperone/co-chaperone complex, a novel junction anticancer target elucidated by the mode of action of herbal drug Withaferin A
0 -- 0Byung-Jun Yoon. Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics
0 -- 0Chu Kang, Yung-Jen Chuang, Kai Che Tung, Chun Chao, Chuan Yi Tang, Shih Chi Peng, David Wong. A genetic algorithm-based boolean delay model of intracellular signal transduction in inflammation
0 -- 0Wangshu Zhang, Fengzhu Sun, Rui Jiang. Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach
0 -- 0Xiaoning Qian, Byung-Jun Yoon. Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception
0 -- 0Kai-Cheng Hsu, Yen-Fu Chen, Shen-Rong Lin, Jinn-Moon Yang. iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis
0 -- 0Maxim Totrov. Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
0 -- 0Riku Kyogoku, Ryo Fujimoto, Tomonobu Ozaki, Takenao Ohkawa. A method for supporting retrieval of articles on protein structure analysis considering users' intention
0 -- 0Yongjin Park, Joel S. Bader. Resolving the structure of interactomes with hierarchical agglomerative clustering
0 -- 0Xiao Yang, Srinivas Aluru, Karin S. Dorman. Repeat-aware modeling and correction of short read errors
0 -- 0Christina Boucher, Bin Ma. Closest string with outliers
0 -- 0Tsuyoshi Kato, Nozomi Nagano. Discriminative structural approaches for enzyme active-site prediction
0 -- 0Shalini John, Sundarapandian Thangapandian, Sugunadevi Sakkiah, Keun Lee. Potent bace-1 inhibitor design using pharmacophore modeling, in silico screening and molecular docking studies
0 -- 0Igor Chikalov, Peggy Yao, Mikhail Moshkov, Jean-Claude Latombe. Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories
0 -- 0Sanmin Liu, Lantao Liu, Ugur Uzuner, Xin Zhou, Manxi Gu, Weibing Shi, Yixiang Zhang, Susie Y. Dai, Joshua S. Yuan. HDX-Analyzer: a novel package for statistical analysis of protein structure dynamics
0 -- 0Jorge Duitama, Justin Kennedy, Sanjiv Dinakar, Yözen Hernández, Yufeng Wu, Ion I. Mandoiu. Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads
0 -- 0Yu Rang Park, Jihun Kim, Hye-Won Lee, Young Jo Yoon, Ju Han Kim. GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products
0 -- 0Can Yang, Xiang Wan, Zengyou He, Qiang Yang, Hong Xue, Weichuan Yu. The choice of null distributions for detecting gene-gene interactions in genome-wide association studies
0 -- 0Hui-Ling Huang, I.-Che Lin, Yi-Fan Liou, Chia-Ta Tsai, Kai-Ti Hsu, Wen-Lin Huang, Shinn-Jang Ho, Shinn-Ying Ho. Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties
0 -- 0Kyoohyoung Rho, Bumjin Kim, Youngjun Jang, Sanghyun Lee, Taejeong Bae, Jihae Seo, Chae Hwa Seo, Ji-Hyun Lee, Hyunjung Kang, Ungsik Yu, Sunghoon Kim, Sanghyuk Lee, Wan Kyu Kim. GARNET - gene set analysis with exploration of annotation relations
0 -- 0Ivan G. Costa, Helge G. Roider, Thais G. do Rego, Francisco de A. T. de Carvalho. Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models