Journal: BMC Bioinformatics

Volume 20-S, Issue 9

0 -- 0Yoshihiro Shibuya, Matteo Comin. Better quality score compression through sequence-based quality smoothing
0 -- 0Ilaria Patuzzi, Giacomo Baruzzo, Carmen Losasso, Antonia Ricci, Barbara Di Camillo. metaSPARSim: a 16S rRNA gene sequencing count data simulator
0 -- 0Valeria Boscaino, Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo, Alfonso Urso. MiRNA therapeutics based on logic circuits of biological pathways
0 -- 0Mainá Bitar, Stefanie Kuiper, Elizabeth A. O'Brien, Guy Barry. Genes with human-specific features are primarily involved with brain, immune and metabolic evolution
0 -- 0Francesca Cordero, Raffaele A. Calogero, Michele Caselle. BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics
0 -- 0Giovanni Spirito, Damiano Mangoni, Remo Sanges, Stefano Gustincich. Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data
0 -- 0Luis Torada, Lucrezia Lorenzon, Alice Beddis, Ulas Isildak, Linda Pattini, Sara Mathieson, Matteo Fumagalli. ImaGene: a convolutional neural network to quantify natural selection from genomic data
0 -- 0Jia Qian, Matteo Comin. MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
0 -- 0Federico Ansaloni, Margherita Scarpato, Elia Di Schiavi, Stefano Gustincich, Remo Sanges. Exploratory analysis of transposable elements expression in the C. elegans early embryo
0 -- 0Mattia Dalsass, Margherita Bodini, Christophe Lambert, Marie-Cécile Mortier, Marco Romanelli, Duccio Medini, Alessandro Muzzi, Alessandro Brozzi. STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data
0 -- 0Salvatore Alaimo, Antonio Di Maria, Dennis E. Shasha, Alfredo Ferro, Alfredo Pulvirenti. TACITuS: transcriptomic data collector, integrator, and selector on big data platform
0 -- 0Damiano Verda, Stefano Parodi, Enrico Ferrari, Marco Muselli. Analyzing gene expression data for pediatric and adult cancer diagnosis using logic learning machine and standard supervised methods

Volume 20-S, Issue 8

0 -- 0Zhen Cui, Ying-Lian Gao, Jin-Xing Liu, Ling-Yun Dai, Shasha Yuan. L2, 1-GRMF: an improved graph regularized matrix factorization method to predict drug-target interactions
0 -- 0Yanan Wang, Qi Lv, Yingying Zhang, Luhui Wang, Yafei Dong. Probe computing model based on small molecular switch
0 -- 0Yuan Lin, Yinyin Cai, Juan Liu 0003, Chen Lin, Xiangrong Liu. An advanced approach to identify antimicrobial peptides and their function types for penaeus through machine learning strategies
0 -- 0Henry Han, Wenbin Liu. Preface
0 -- 0Hui Huang 0009, Xi'an Feng, Suying Zhou, Jionghui Jiang, Huiling Chen, Yuping Li, Chengye Li. A new fruit fly optimization algorithm enhanced support vector machine for diagnosis of breast cancer based on high-level features
0 -- 0Junyi Li, Li Zhang, Huinian Li, Yuan-Ping, Qingzhe Xu, Rongjie Wang, Renjie Tan, Zhen Wang, Bo Liu, Yadong Wang. Integrated entropy-based approach for analyzing exons and introns in DNA sequences
0 -- 0Jiajie Peng, Xiaoyu Wang, Xuequn Shang. Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data
0 -- 0Xiaoli Qiang, Zheng Kou. Scoring amino acid mutation to predict pandemic risk of avian influenza virus
0 -- 0Fei Han 0001, Di Tang, Yu-Wen-Tian Sun, Zhun Cheng, Jing Jiang, Qiuwei Li. A hybrid gene selection method based on gene scoring strategy and improved particle swarm optimization

Volume 20-S, Issue 6

413 -- 0Ping Zhang 0008, Nicholas P. West, Pin-Yen Chen, Mike W. C. Thang, Gareth Price, Allan Cripps, Amanda J. Cox. Selection of microbial biomarkers with genetic algorithm and principal component analysis
475 -- 0Alva Presbitero, Emiliano Mancini, Filippo Castiglione, Valeria V. Krzhizhanovskaya, Rick Quax. Game of neutrophils: modeling the balance between apoptosis and necrosis
476 -- 0Monica J. Quinzo, Esther M. Lafuente, Pilar Zuluaga, Darren R. Flower, Pedro A. Reche. Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy
477 -- 0Pin-Yen Chen, Allan Cripps, Nicholas P. West, Amanda J. Cox, Ping Zhang 0008. A correlation-based network for biomarker discovery in obesity with metabolic syndrome
504 -- 0Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Angela Bonaccorso, Giuseppe Alessandro Parasiliti Palumbo, Epifanio Fichera, Dipendra Kumar Mitra, Kenneth B. Walker, Pere Joan Cardona, Merce Amat, Marco Viceconti, Francesco Pappalardo 0001. Predicting the artificial immunity induced by RUTI® vaccine against tuberculosis using universal immune system simulator (UISS)
532 -- 0Ruy Freitas Reis, Juliano Lara Fernandes, Thaiz Ruberti Schmal, Bernardo Martins Rocha, Rodrigo Weber dos Santos, Marcelo Lobosco. A personalized computational model of edema formation in myocarditis based on long-axis biventricular MRI images
579 -- 0Mozhgan Kabiri Chimeh, Peter Heywood, Marzio Pennisi, Francesco Pappalardo 0001, Paul Richmond. Parallelisation strategies for agent based simulation of immune systems
622 -- 0Francesco Pappalardo 0001, Marzio Pennisi, Pedro A. Reche, Giulia Russo. Toward computational modelling on immune system function
623 -- 0Simone Pernice, Marzio Pennisi, Greta Romano, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo 0001, Gianfranco Balbo, Marco Beccuti, Francesca Cordero, Raffaele A. Calogero. A computational approach based on the colored Petri net formalism for studying multiple sclerosis

Volume 20-S, Issue 5

227 -- 230Sirarat Sarntivijai, Yongqun He, Alexander D. Diehl. Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies
231 -- 236Lucas M. Serra, William D. Duncan, Alexander D. Diehl. An ontology for representing hematologic malignancies: the cancer cell ontology
237 -- 247Yongqun He, William D. Duncan, Daniel J. Cooper, Jens Hansen, Ravi Iyengar, Edison Ong, Kendal Walker, Omar Tibi, Sam Smith, Lucas M. Serra, Jie Zheng 0001, Sirarat Sarntivijai, Stephan C. Schürer, K. Sue O'Shea, Alexander D. Diehl. OSCI: standardized stem cell ontology representation and use cases for stem cell investigation
249 -- 258Hongjie Pan, Xiaocui Bian, Sheng Yang, Yongqun He, Xiaolin Yang, Yuqin Liu. The cell line ontology-based representation, integration and analysis of cell lines used in China
259 -- 264James A. Overton, Randi Vita, Patrick Dunn, Julie G. Burel, Syed Ahmad Chan Bukhari, Kei-Hoi Cheung, Steven H. Kleinstein, Alexander D. Diehl, Bjoern Peters. Reporting and connecting cell type names and gating definitions through ontologies

Volume 20-S, Issue 4

0 -- 0Ilaria Granata, Enrico Troiano, Mara Sangiovanni, Mario Rosario Guarracino. Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer
0 -- 0Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind, Mario Rosario Guarracino. From trash to treasure: detecting unexpected contamination in unmapped NGS data
0 -- 0Hamed Khakzad, Johan Malmström, Lars Malmström. Greedy de novo motif discovery to construct motif repositories for bacterial proteomes
0 -- 0Ismael Navas Delgado, José García-Nieto, Esteban López-Camacho, Maciej Rybinski, Rocio Lavado-Valenzuela, Miguel Ángel Berciano Guerrero, José Francisco Aldana Montes. VIGLA-M: visual gene expression data analytics
0 -- 0Fabio Fassetti, Claudia Giallombardo, Ofelia Leone, Luigi Palopoli, Simona E. Rombo, Adolfo Saiardi. FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing
0 -- 0Michela Quadrini, Luca Tesei, Emanuela Merelli. An algebraic language for RNA pseudoknots comparison
0 -- 0Giovanni Perconti, Patrizia Rubino, Flavia Contino, Serena Bivona, Giorgio Bertolazzi, Michele Tumminello, Salvatore Feo, Agata Giallongo, Claudia Coronnello. RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets
0 -- 0Paolo Romano 0001, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia, Alfonso Urso. The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes
0 -- 0Alessandro Zandonà, Rosario Vasta, Adriano Chiò, Barbara Di Camillo. A Dynamic Bayesian Network model for the simulation of Amyotrophic Lateral Sclerosis progression
0 -- 0Sandra Krüger, Rosario M. Piro. decompTumor2Sig: identification of mutational signatures active in individual tumors
0 -- 0Pierre Monnin, Joël Legrand, Graziella Husson, Patrice Ringot, Andon Tchechmedjiev, Clément Jonquet, Amedeo Napoli, Adrien Coulet. PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison
0 -- 0Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Zinovyev, Inna Kuperstein. Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer
0 -- 0Umberto Ferraro Petrillo, Mara Sorella, Giuseppe Cattaneo, Raffaele Giancarlo, Simona E. Rombo. Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics
0 -- 0Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Pietro Liò, Ivan Merelli, Daniela Besozzi. GenHap: a novel computational method based on genetic algorithms for haplotype assembly
0 -- 0David R. Gilbert, Monika Heiner, Leila Ghanbar, Jacek Chodak. Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking
0 -- 0Alexander E. Kel, Ulyana Boyarskikh, Philip Stegmaier, Leonid S. Leskov, Andrey V. Sokolov, Ivan S. Yevshin, Nikita Mandrik, Daria Stelmashenko, Jeannette Koschmann, Olga V. Kel-Margoulis, Mathias Krull, Anna Martínez-Cardús, Sebastian Moran, Manel Esteller, Fedor A. Kolpakov, Maxim Filipenko, Edgar Wingender. Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

Volume 20-S, Issue 3

15 -- 24Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, Jun Sese. reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction
25 -- 36Jayoung Ryu, Hyun-Woong Kim, Dongchan Yang, Andrew J. Lee, Inkyung Jung. A new class of constitutively active super-enhancers is associated with fast recovery of 3D chromatin loops
37 -- 52Safa Jammali, Jean-David Aguilar, Esaie Kuitche, Aïda Ouangraoua. SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups
53 -- 62Audrey Legendre, Eric Angel, Fariza Tahi. RCPred: RNA complex prediction as a constrained maximum weight clique problem
63 -- 74Xiujuan Lei, Ming Fang, Ling Guo, Fang-Xiang Wu. Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks
75 -- 85Ran Li, Xiangrui Zeng, Stephanie E. Sigmund, Ruogu Lin, Bo Zhou, Chang Liu, Kaiwen Wang, Rui Jiang, Zachary Freyberg, Hairong Lv, Min Xu 0009. Automatic localization and identification of mitochondria in cellular electron cryo-tomography using faster-RCNN
87 -- 97Nayang Shan, Zuoheng Wang, Lin Hou. Identification of trans-eQTLs using mediation analysis with multiple mediators
99 -- 108Chao Wang, Yi Wei, Haicang Zhang, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu. Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling
109 -- 118Quan Chen, Jun Zhu. Detecting virus-specific effects on post-infection temporal gene expression

Volume 20-S, Issue 25

681 -- 0Huijuan Lu, Yige Xu, Minchao Ye, Ke Yan, Zhigang Gao, Qun Jin. Learning misclassification costs for imbalanced classification on gene expression data
682 -- 0Jie Zhao, Xiujuan Lei. Detecting overlapping protein complexes in weighted PPI network based on overlay network chain in quotient space
683 -- 0Hongjie Wu, Hongmei Huang, Weizhong Lu, Qiming Fu, Yijie Ding, Jing Qiu, Haiou Li. Ranking near-native candidate protein structures via random forest classification
684 -- 0Weizhong Lu, Ye Tang, Hongjie Wu, Hongmei Huang, Qiming Fu, Jing Qiu, Haiou Li. Predicting RNA secondary structure via adaptive deep recurrent neural networks with energy-based filter
685 -- 0Hongjie Wu, Ru Yang, Qiming Fu, Jianping Chen, Weizhong Lu, Haiou Li. Research on predicting 2D-HP protein folding using reinforcement learning with full state space
686 -- 0Zhen Cui, Jin-Xing Liu, Ying-Lian Gao, Chun-Hou Zheng, Juan Wang 0003. RCMF: a robust collaborative matrix factorization method to predict miRNA-disease associations
687 -- 0Yulian Jiao, Qiutao Hu, Yan Zhu, Longfei Zhu, Tengfei Ma, Haiyong Zeng, Qiaolu Zang, Xuan Li, Xinchun Lin. Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)
688 -- 0Qingxin Xiao, Weilu Li, Yuanzhong Kai, Peng Chen 0001, Jun Zhang, Bing Wang 0004. Occurrence prediction of pests and diseases in cotton on the basis of weather factors by long short term memory network
689 -- 0Shanshan Hu, Chenglin Zhang, Peng Chen 0001, Pengying Gu, Jun Zhang, Bing Wang 0004. Predicting drug-target interactions from drug structure and protein sequence using novel convolutional neural networks
690 -- 0Yiran Zhou, Qinghua Cui, Yuan Zhou. NmSEER V2.0: a prediction tool for 2′-O-methylation sites based on random forest and multi-encoding combination
691 -- 0Zhifa Han, Tao Wang, Rui Tian, Wenyang Zhou, Pingping Wang, Peng Ren, Jian Zong, Yang Hu 0008, Shuilin Jin, Qinghua Jiang. BIN1 rs744373 variant shows different association with Alzheimer's disease in Caucasian and Asian populations
692 -- 0Fei Luo. A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing data
693 -- 0Beiji Zou, Changlong Chen, Rongchang Zhao, Ping-Bo Ouyang, Chengzhang Zhu, Qilin Chen, Xuanchu Duan. A novel glaucomatous representation method based on Radon and wavelet transform
694 -- 0ZhengWei Li, Ru Nie, Zhuhong You, Chen Cao, Jiashu Li. Using discriminative vector machine model with 2DPCA to predict interactions among proteins
695 -- 0Yongqing Zhang, Shaojie Qiao, Rongzhao Lu, Nan Han, Dingxiang Liu, Jiliu Zhou. How to balance the bioinformatics data: pseudo-negative sampling
696 -- 0Yumeng Yan, Sheng-You Huang. Pushing the accuracy limit of shape complementarity for protein-protein docking
697 -- 0Shaoyan Sun, Xiangtian Yu, Fengnan Sun, Ying Tang, Juan Zhao, Tao Zeng. Dynamically characterizing individual clinical change by the steady state of disease-associated pathway
698 -- 0Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu. DTA-SiST: de novo transcriptome assembly by using simplified suffix trees
699 -- 0Ye Wang, Changqing Mei, Yuming Zhou, Yan Wang, Chunhou Zheng, Xiao Zhen, Yan Xiong, Peng Chen, Jun Zhang, Bing Wang 0004. Semi-supervised prediction of protein interaction sites from unlabeled sample information
700 -- 0Lei Guo, Shunfang Wang, Mingyuan Li, Zicheng Cao. Accurate classification of membrane protein types based on sequence and evolutionary information using deep learning
701 -- 0Shunfang Wang, Xiaoheng Wang. Prediction of protein structural classes by different feature expressions based on 2-D wavelet denoising and fusion

Volume 20-S, Issue 24

596 -- 0Xikang Feng, Zishuai Wang, Hechen Li, Shuai Cheng Li. MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals
668 -- 0Benjamin V. Church, Henry T. Williams, Jessica C. Mar. Investigating skewness to understand gene expression heterogeneity in large patient cohorts
669 -- 0Tara Eicher, Andrew Patt, Esko Kautto, Raghu Machiraju, Ewy Mathé, Yan Zhang. Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge
670 -- 0Venkat Sundar Gadepalli, Hatice Gulcin Ozer, Ayse Selen Yilmaz, Maciej Pietrzak, Amy Webb. BISR-RNAseq: an efficient and scalable RNAseq analysis workflow with interactive report generation
671 -- 0Yilin Liu, Jiao Xu, Miaoxia Chen, Changfa Wang, Shuaicheng Li. A unified STR profiling system across multiple species with whole genome sequencing data
672 -- 0Yu Zhang, Changlin Wan, Pengcheng Wang, Wennan Chang, Yan Huo, Jian Chen, Qin Ma, Sha Cao, Chi Zhang. M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data
673 -- 0Jasmit S. Shah, Guy N. Brock, Jeremy Gaskins. BayesMetab: treatment of missing values in metabolomic studies using a Bayesian modeling approach
674 -- 0Mohamed Ayed, Hansaim Lim, Lei Xie. Biological representation of chemicals using latent target interaction profile
675 -- 0Lianbo Yu, Jianying Zhang, Guy N. Brock, Soledad Fernandez. Fully moderated t-statistic in linear modeling of mixed effects for differential expression analysis
676 -- 0Zhongming Zhao, Yulin Dai, Chi Zhang, Ewy Mathé, Lai Wei, Kai Wang. The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases
677 -- 0Jhe-Ming Wu, Yu-Chen Liu, Darby Tien-Hao Chang. SigUNet: signal peptide recognition based on semantic segmentation
678 -- 0Hongfei Cui, Hailin Hu, Jianyang Zeng, Ting Chen. DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data
679 -- 0Zachary B. Abrams, Travis Johnson, Kun Huang 0001, Philip R. O. Payne, Kevin R. Coombes. A protocol to evaluate RNA sequencing normalization methods
680 -- 0Jon P. Klein, Zhifu Sun, Nathan P. Staff. Association between ALS and retroviruses: evidence from bioinformatics analysis

Volume 20-S, Issue 23

605 -- 0Yi Zheng, Hui Peng, Xiaocai Zhang, Zhixun Zhao, Xiaoying Gao, Jinyan Li 0001. Old drug repositioning and new drug discovery through similarity learning from drug-target joint feature spaces
606 -- 0Shifu Chen, Yanqing Zhou, Yaru Chen, Tanxiao Huang, Wenting Liao, Yun Xu, Zhicheng Li, Jia Gu. Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data
613 -- 0Junpeng Zhang, Vu Viet Hoang Pham, Lin Liu 0003, Taosheng Xu, Buu Minh Thanh Truong, Jiuyong Li, NiNi Rao, Thuc Duy Le. Identifying miRNA synergism using multiple-intervention causal inference
618 -- 0Juris Viksna, Gatis Melkus, Edgars Celms, Karlis Cerans, Karlis Freivalds, Paulis Kikusts, Lelde Lace, Martins Opmanis, Darta Rituma, Peteris Rucevskis. Topological structure analysis of chromatin interaction networks
630 -- 0Tzu-Hsien Yang. Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast
631 -- 0Mehwish Noureen, Ipputa Tada, Takeshi Kawashima, Masanori Arita. Rearrangement analysis of multiple bacterial genomes
633 -- 0Kodai Minoura, Ko Abe, Yuka Maeda, Hiroyoshi Nishikawa, Teppei Shimamura. Model-based cell clustering and population tracking for time-series flow cytometry data
634 -- 0Binh P. Nguyen, Quang H. Nguyen, Giang-Nam Doan-Ngoc, Thanh-Hoang Nguyen-Vo, Susanto Rahardja. iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks
646 -- 0Xubo Tang, Yanni Sun. Fast and accurate microRNA search using CNN
647 -- 0Cesar Augusto Nieto-Acuna, Cesar Augusto Vargas Garcia, Abhyudai Singh, Juan Manuel Pedraza. Efficient computation of stochastic cell-size transient dynamics
648 -- 0Lingxi Chen, Jiao Xu, Shuai Cheng Li. DeepMF: deciphering the latent patterns in omics profiles with a deep learning method
651 -- 0Cheng Yan, Guihua Duan, Fang-Xiang Wu, Jianxin Wang. IILLS: predicting virus-receptor interactions based on similarity and semi-supervised learning
652 -- 0Ruohan Wang, Zishuai Wang, Jianping Wang, Shuaicheng Li. SpliceFinder: ab initio prediction of splice sites using convolutional neural network
656 -- 0Haohan Wang, Tianwei Yue, Jingkang Yang, Wei Wu, Eric P. Xing. Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies
667 -- 0Benjamin Hur, Dongwon Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee, Sun Kim. Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments
702 -- 0Chen Li, Yiqi Jiang, Shuaicheng Li. LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics

Volume 20-S, Issue 22

712 -- 0Henry Han, Wenbin Liu. The coming era of artificial intelligence in biological data science
713 -- 0Hang Zhang, Ke Wang, Juan Zhou, Jianhua Chen, Yizhou Xu, Dong Wang, Xiaoqi Li, Renliang Sun, Mancang Zhang, Zhuo Wang, Yongyong Shi. VariFAST: a variant filter by automated scoring based on tagged-signatures
714 -- 0Shudong Wang, Lihua Wang, Yuanyuan Zhang, Shanchen Pang, Xinzeng Wang. PEIS: a novel approach of tumor purity estimation by identifying information sites through integrating signal based on DNA methylation data
715 -- 0Ying Xiong, Qing-Hua Ling, Fei Han 0001, Qing-Hua Liu. An efficient gene selection method for microarray data based on LASSO and BPSO
716 -- 0Chun-Mei Feng, Yong Xu 0001, Mi-Xiao Hou, Ling-Yun Dai, Junliang Shang. PCA via joint graph Laplacian and sparse constraint: Identification of differentially expressed genes and sample clustering on gene expression data
717 -- 0Guimin Qin, Luqiong Yang, Yuying Ma, Jiayan Liu, Qiuyan Huo. The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma
718 -- 0Juan Wang 0003, Cong-Hai Lu, Jin-Xing Liu, Ling-Yun Dai, Xiang-Zhen Kong. Multi-cancer samples clustering via graph regularized low-rank representation method under sparse and symmetric constraints
719 -- 0Yuhua Yao, Ya-ping Lv, Ling Li, Huimin Xu, Bin-Bin Jia, Jing Chen, Chun Li, Bo Liao, Xu-Ying Nan. Protein sequence information extraction and subcellular localization prediction with gapped k-Mer method
720 -- 0Mingzhao Wang, Linglong Ding, Meng Xu, Juanying Xie, Shengli Wu, Shengquan Xu, Yingmin Yao, Qingguang Liu. A novel method detecting the key clinic factors of portal vein system thrombosis of splenectomy & cardia devascularization patients for cirrhosis & portal hypertension

Volume 20-S, Issue 21

704 -- 0Edison Ong, Peter Sun, Kimberly Berke, Jie Zheng 0001, Guanming Wu, Yongqun He. VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions
705 -- 0Junguk Hur, Cui Tao, Yongqun He. A 2018 workshop: vaccine and drug ontology studies (VDOS 2018)
706 -- 0Muhammad Amith, Kirk Roberts, Cui Tao. Conceiving an application ontology to model patient human papillomavirus vaccine counseling for dialogue management
707 -- 0Mert Tiftikci, Arzucan Özgür, Yongqun He, Junguk Hur. Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels
708 -- 0Jonathan P. Bona, Mathias Brochhausen, William R. Hogan. Enhancing the drug ontology with semantically-rich representations of National Drug Codes and RxNorm unique concept identifiers

Volume 20-S, Issue 20

635 -- 0Yue Zhang, Chunfang Zheng, David Sankoff. Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment
636 -- 0Santi Santichaivekin, Ross Mawhorter, Ran Libeskind-Hadas. An efficient exact algorithm for computing all pairwise distances between reconciliations in the duplication-transfer-loss model
637 -- 0Guo Liang Gan, Elijah Willie, Cédric Chauve, Leonid Chindelevitch. Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework
638 -- 0Anna-Katharina Lau, Svenja Dörrer, Chris-André Leimeister, Christoph Bleidorn, Burkhard Morgenstern. Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
639 -- 0Ross Mawhorter, Nuo Liu, Ran Libeskind-Hadas, Yi-Chieh Wu. Inferring Pareto-optimal reconciliations across multiple event costs under the duplication-loss-coalescence model
640 -- 0Esaie Kuitche, Safa Jammali, Aïda Ouangraoua. SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution
641 -- 0Sergey Aganezov, Ilya Zban, Vitaly Aksenov, Nikita Alexeev, Michael C. Schatz. Recovering rearranged cancer chromosomes from karyotype graphs
642 -- 0Louxin Zhang. Generating normal networks via leaf insertion and nearest neighbor interchange

Volume 20-S, Issue 2

0 -- 0Jonathan D. Wren, Robert J. Doerkson, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar. Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference
7 -- 16Philip Berg, Evan W. McConnell, Leslie M. Hicks, Sorina C. Popescu, George V. Popescu. Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics
17 -- 29Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong. Similarities and differences between variants called with human reference genome HG19 or HG38
31 -- 43Sujoy Roy, Kazi I. Zaman, Robert W. Williams, Ramin Homayouni. Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion
45 -- 57Visanu Wanchai, Jing Jin, Emine Bircan, Charis Eng, Mohammed Orloff. Genome-wide tracts of homozygosity and exome analyses reveal repetitive elements with Barrets esophagus/esophageal adenocarcinoma risk
59 -- 71Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren. MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations
73 -- 85Norbert Bokros, Sorina C. Popescu, George V. Popescu. Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions
87 -- 97Mustafa Bayraktar, Sinan Kockara, Tansel Halic, Mutlu Mete, Henry K. Wong, Kamran Iqbal. Local edge-enhanced active contour for accurate skin lesion border detection
99 -- 114Doga Demirel, Berk Cetinsaya, Tansel Halic, Sinan Kockara, Shahryar Ahmadi. Partition-based optimization model for generative anatomy modeling language (POM-GAML)
115 -- 127Joseph Luttrell IV, Tong Liu, Chaoyang Zhang, Zheng Wang. Predicting protein residue-residue contacts using random forests and deep networks
129 -- 139Leihong Wu, Taylor Ingle, Zhichao Liu, Anna Zhao-Wong, Stephen C. Harris, Shraddha Thakkar, GuangXu Zhou, Junshuang Yang, Joshua Xu, Darshan Mehta, Weigong Ge, Weida Tong, Hong Fang. Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA
141 -- 149Adam Thrash, Mark Arick II, Robyn A. Barbato, Robert M. Jones, Thomas A. Douglas, Julie Esdale, Edward J. Perkins, Natàlia Garcia-Reyero. Keanu: a novel visualization tool to explore biodiversity in metagenomes

Volume 20-S, Issue 19

657 -- 0Jiang Huang, Min Wu 0008, Fan Lu, Le Ou-Yang, Zexuan Zhu. Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization
658 -- 0Bee Guan Teo, Sarinder Kaur Dhillon. An automated 3D modeling pipeline for constructing 3D models of MONOGENEAN HARDPART using machine learning techniques
659 -- 0Sean Chun-Chang Chen, Chung-Ming Lo, Shih-Hua Wang, Emily Chia-Yu Su. RNA editing-based classification of diffuse gliomas: predicting isocitrate dehydrogenase mutation and chromosome 1p/19q codeletion
660 -- 0Thomas Andrew Geddes, Taiyun Kim, Lihao Nan, James G. Burchfield, Jean Yee Hwa Yang, Dacheng Tao, Pengyi Yang. Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis
661 -- 0Yi Zheng, Hui Peng, Xiaocai Zhang, Zhixun Zhao, Xiaoying Gao, Jinyan Li. DDI-PULearn: a positive-unlabeled learning method for large-scale prediction of drug-drug interactions
662 -- 0Lei Deng, Guolun Zhong, Chenzhe Liu, Judong Luo, Hui Liu. MADOKA: an ultra-fast approach for large-scale protein structure similarity searching
703 -- 0Hsin-Yao Wang, Wen-Chi Li, Kai-Yao Huang, Chia-Ru Chung, Jorng-Tzong Horng, Jen-Fu Hsu, Jang-Jih Lu, Tzong-Yi Lee. Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques
721 -- 0Yue Cao, Yingxin Lin, John T. Ormerod, Pengyi Yang, Jean Y. H. Yang, Kitty K. Lo. scDC: single cell differential composition analysis

Volume 20-S, Issue 18

0 -- 0Wenxiang Zhang, Xiujuan Lei, Chen Bian. Identifying Cancer genes by combining two-rounds RWR based on multiple biological data
0 -- 0Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang. Prioritizing candidate diseases-related metabolites based on literature and functional similarity
0 -- 0Jiajie Peng, Guilin Lu, Hansheng Xue, Tao Wang, Xuequn Shang. TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology
0 -- 0Qing Zhan, Nan Wang, Shuilin Jin, Renjie Tan, Qinghua Jiang, Yadong Wang. ProbPFP: a multiple sequence alignment algorithm combining hidden Markov model optimized by particle swarm optimization with partition function
0 -- 0Hanxu Hou, Tian Gan, Yaodong Yang, Xianglei Zhu, Sen Liu, Weiming Guo, Jianye Hao. Using deep reinforcement learning to speed up collective cell migration
0 -- 0Xianglei Zhu, Bofeng Fu, Yaodong Yang, Yu Ma, Jianye Hao, Siqi Chen, Shuang Liu, Tiegang Li, Sen Liu, Weiming Guo, Zhenyu Liao. Attention-based recurrent neural network for influenza epidemic prediction
0 -- 0Qianlong Liu, Kangenbei Liao, Kelvin Kam-fai Tsoi, Zhongyu Wei. Acceptance Prediction for Answers on Online Health-care Community
0 -- 0Jialu Hu, Yiqun Gao, Jing Li, Yan Zheng, Jingru Wang, Xuequn Shang. A novel algorithm based on bi-random walks to identify disease-related lncRNAs
0 -- 0Tianyi Zhao, Yang Hu 0008, Tianyi Zang, Liang Cheng 0006. Identifying Alzheimer's disease-related proteins by LRRGD
0 -- 0Zhenxing Wang, Yadong Wang. Extracting a biologically latent space of lung cancer epigenetics with variational autoencoders

Volume 20-S, Issue 17

0 -- 0. Third international conference "Bioinformatics: from Algorithms to Applications" (BiATA 2019) - Saint Petersburg, Russia. 20-22 June 2019

Volume 20-S, Issue 16

0 -- 0Bo Xu 0009, Hongfei Lin, Liang Yang 0003, Kan Xu, Yi-Jia Zhang 0001, Dongyu Zhang, Zhihao Yang, Jian Wang 0021, Yuan Lin 0001, Fuliang Yin. A supervised term ranking model for diversity enhanced biomedical information retrieval
0 -- 0Xusheng Li, Chengcheng Fu, Ran Zhong, Duo Zhong, Tingting He, Xingpeng Jiang. A hybrid deep learning framework for bacterial named entity recognition with domain features
0 -- 0Slim Karkar, Lauren E. Alfonse, Catherine M. Grgicak, Desmond S. Lun. Statistical modeling of STR capillary electrophoresis signal
0 -- 0Tong Liu, Zheng Wang. Exploring the 2D and 3D structural properties of topologically associating domains
0 -- 0Da Zhang, Mansur R. Kabuka. Multimodal deep representation learning for protein interaction identification and protein family classification
0 -- 0Ye Yuan 0006, Kebin Jia, Fenglong Ma, Guangxu Xun, Yaqing Wang, Lu Su, Aidong Zhang. A hybrid self-attention deep learning framework for multivariate sleep stage classification
0 -- 0Ibrahim Youssef, Jeffrey Law, Anna M. Ritz. Integrating protein localization with automated signaling pathway reconstruction
0 -- 0Lei Chen, Hong Song, Chi Wang, Yutao Cui, Jian Yang 0009, Xiaohua Hu, Le Zhang. Liver tumor segmentation in CT volumes using an adversarial densely connected network
0 -- 0Joyce Kang, Benjamin Siranosian, Eli Moss, Niaz Banaei, Tessa Andermann, Ami Bhatt. Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly
0 -- 0Dan Liu, Yingjun Ma, Xingpeng Jiang, Tingting He. Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion
0 -- 0Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang. LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets
0 -- 0Min Zeng, Min Li 0007, Fang-Xiang Wu, Yaohang Li, Yi Pan 0001. DeepEP: a deep learning framework for identifying essential proteins
0 -- 0Han Zhang, Xueting Huo, Xia Guo, Xin Su, Xiongwen Quan, Chen Jin. A disease-related gene mining method based on weakly supervised learning model
0 -- 0Hongryul Ahn, Inuk Jung, Heejoon Chae, Dongwon Kang, Woosuk Jung, Sun Kim. HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis
0 -- 0Canlin Zhang, Daniel Bis, Xiuwen Liu, Zhe He 0001. Biomedical word sense disambiguation with bidirectional long short-term memory and attention-based neural networks
0 -- 0Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano. Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers
0 -- 0Kefei Liu 0001, Li Shen 0001, Hui Jiang 0002. Joint between-sample normalization and differential expression detection through ℓ 0-regularized regression

Volume 20-S, Issue 15

481 -- 0Liyuan Liu, Bingchen Yu, Meng Han, Shanshan Yuan, Na Wang. Mild cognitive impairment understanding: an empirical study by data-driven approach
482 -- 0Prapaporn Techa-angkoon, Kevin L. Childs, Yanni Sun. ′ GC gradient
483 -- 0Fei Guo, Quan Zou, Guang Yang, Dan Wang, Jijun Tang, Junhai Xu. Identifying protein-protein interface via a novel multi-scale local sequence and structural representation
489 -- 0Jianwei Lu, Yao Lu, Yusheng Ding, Qingyang Xiao, Linqing Liu, Qingpo Cai, Yunchuan Kong, Yun Bai, Tianwei Yu. DNLC: differential network local consistency analysis
503 -- 0Yuping Lu, Charles A. Phillips, Michael A. Langston. A robustness metric for biological data clustering algorithms
515 -- 0Min Li 0007, Li Tang, Fang-Xiang Wu, Yi Pan 0001, Jianxin Wang 0001. CSA: a web service for the complete process of ChIP-Seq analysis
535 -- 0Jin-Hong Shi, Yan Yan, Matthew G. Links, Longhai Li, Jo-Anne R. Dillon, Michael Horsch, Anthony J. Kusalik. Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection
538 -- 0Cheng Yan, Guihua Duan, Yi Pan 0001, Fang-Xiang Wu, Jianxin Wang 0001. DDIGIP: predicting drug-drug interactions based on Gaussian interaction profile kernels
547 -- 0Yuehui Wang, Maozu Guo 0001, Yazhou Ren 0001, Lianyin Jia, Guoxian Yu. Drug repositioning based on individual bi-random walks on a heterogeneous network
598 -- 0Hongda Bu, Jiaqi Hao, Yanglan Gan, Shuigeng Zhou, Jihong Guan. DEEPSEN: a convolutional neural network based method for super-enhancer prediction
644 -- 0Neo Christopher Chung, Blazej Miasojedow, Michal Startek, Anna Gambin. Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data

Volume 20-S, Issue 14

0 -- 0Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal, Piero Fariselli. DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations

Volume 20-S, Issue 13

0 -- 0Yonghyun Nam, Myungjun Kim, Hang-Seok Chang, Hyunjung Shin. Drug repurposing with network reinforcement
0 -- 0Yongsub Lim, Injae Yu, Dongmin Seo, U. Kang, Lee Sael. PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks
0 -- 0Jungmin Ha, Ho Hwi Jeon, Dong U. Woo, Yejin Lee, Halim Park, Joohyeong Lee, Yang Jae Kang. Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection
0 -- 0Chi-Ching Lee, Po-Jung Huang, Yuan-Ming Yeh, Sin-You Chen, Cheng-Hsun Chiu, Wei-Hung Cheng, Petrus Tang. Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins

Volume 20-S, Issue 12

0 -- 0Saugato Rahman Dhruba, Aminur Rahman, Raziur Rahman, Souparno Ghosh, Ranadip Pal. Recursive model for dose-time responses in pharmacological studies
0 -- 0Mansooreh Ahmadian, John J. Tyson, Yang Cao 0001. A stochastic model of size control in the budding yeast cell cycle
0 -- 0Yuanfang Ren, Ahmet Ay, Alin Dobra, Tamer Kahveci. Characterizing building blocks of resource constrained biological networks
0 -- 0Shahin Boluki, Siamak Zamani Dadaneh, Xiaoning Qian, Edward R. Dougherty. Optimal clustering with missing values
0 -- 0Dalia Elmansy, Mehmet Koyutürk. Cross-population analysis for functional characterization of type II diabetes variants
0 -- 0Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci, Ranadip Pal. Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)
0 -- 0Miriam Bern, Alexander King, Derek A. Applewhite, Anna M. Ritz. Network-based prediction of polygenic disease genes involved in cell motility
0 -- 0Minghan Chen, Yang Cao 0001. Analysis and remedy of negativity problem in hybrid stochastic simulation algorithm and its application
0 -- 0Mohammed Alokshiya, Saeed Salem, Fidaa Abed. A linear delay algorithm for enumerating all connected induced subgraphs
0 -- 0Chieh Lo, Radu Marculescu. MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks

Volume 20-S, Issue 11

0 -- 0Dina Abdelhafiz, Clifford Yang, Reda Ammar, Sheida Nabavi. Deep convolutional neural networks for mammography: advances, challenges and applications
0 -- 0Hosein Toosi, Ali Moeini, Iman Hajirasouliha. BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples
0 -- 0Chunchun Zhao, Sartaj Sahni. String correction using the Damerau-Levenshtein distance
0 -- 0David Morris, Tatiana Maximova, Erion Plaku, Amarda Shehu. Attenuating dependence on structural data in computing protein energy landscapes
0 -- 0Douglas Abrams, Parveen Kumar, R. Krishna Murthy Karuturi, Joshy George. A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification
0 -- 0Cuncong Zhong, Youngik Yang, Shibu Yooseph. GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data
0 -- 0Trevor Cickovski, Vanessa Aguiar-Pulido, Giri Narasimhan. MATria: a unified centrality algorithm
0 -- 0Ardalan Naseri, Degui Zhi, Shaojie Zhang. Multi-allelic positional Burrows-Wheeler transform

Volume 20-S, Issue 10

0 -- 0Zolzaya Dashdorj, Min Song. An application of convolutional neural networks with salient features for relation classification
13 -- 21Jihoon Jo, Sunkyung Choi, Joo-Seong Oh, Sung Gwon Lee, Song-yi Choi, Kee K. Kim, Chungoo Park. Conventionally used reference genes are not outstanding for normalization of gene expression in human cancer research
23 -- 31João D. Ferreira, Francisco M. Couto. Multi-domain semantic similarity in biomedical research
33 -- 43Eunyoung Kim, A.-Sol Choi, Hojung Nam. Drug repositioning of herbal compounds via a machine-learning approach
45 -- 53Mijin Kwon, Soorin Yim, Gwangmin Kim, Saehwan Lee, Chungsun Jeong, Doheon Lee. CODA-ML: context-specific biological knowledge representation for systemic physiology analysis
55 -- 65Wonjin Yoon, Chan Ho So, Jinhyuk Lee, Jaewoo Kang. CollaboNet: collaboration of deep neural networks for biomedical named entity recognition
67 -- 73Hyang-Mi Lee, Myeong-Sang Yu, Sayada Reemsha Kazmi, Seong Yun Oh, Ki-Hyeong Rhee, Myung-Ae Bae, Byung Ho Lee, Dae-Seop Shin, Kwang-Seok Oh, Hyithaek Ceong, Donghyun Lee, Dokyun Na. Computational determination of hERG-related cardiotoxicity of drug candidates
75 -- 80Judita Preiss. Is automatic detection of hidden knowledge an anomaly?

Volume 20-S, Issue 1

0 -- 0Tatiana Tatarinova, Ming Chen, Yuriy L. Orlov. Bioinformatics research at BGRS-2018
5 -- 15Vladimir A. Ivanisenko, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena L. Mishchenko, Olga V. Saik. A new version of the ANDSystem tool for automatic extraction of knowledge from scientific publications with expanded functionality for reconstruction of associative gene networks by considering tissue-specific gene expression
17 -- 26Ranajit Das, Priyanka Upadhyai. Application of the geographic population structure (GPS) algorithm for biogeographical analyses of wild and captive gorillas
27 -- 34Fedor V. Kazantsev, Ekaterina S. Skolotneva, Vasiliy N. Kelbin, Elena A. Salina, Sergey A. Lashin. MIGREW: database on molecular identification of genes for resistance in wheat
35 -- 46Dmitry A. Kuzmin, Sergey I. Feranchuk, Vadim V. Sharov, Alexander N. Cybin, Stepan V. Makolov, Julia A. Putintseva, Natalya V. Oreshkova, Konstantin V. Krutovsky. Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)
47 -- 52Eugeniya I. Bondar, Julia A. Putintseva, Nataliya V. Oreshkova, Konstantin V. Krutovsky. Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers