BMC Bioinformatics, Volume 20 - Supplements

Volume 20-S, Number 1, February 2019

Selected articles from BGRS\SB-2018: bioinformatics

• 
  Vladimir 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. 5-15
• 
  Ranajit Das, Priyanka Upadhyai:
  Application of the geographic population structure (GPS) algorithm for biogeographical analyses of wild and captive gorillas. 17-26
• 
  Fedor 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. 27-34
• 
  Tatiana V. Tatarinova, Ming Chen, Yuriy L. Orlov:
  Bioinformatics research at BGRS-2018. 33:1-33:3
• 
  Dmitry 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). 35-46
• 
  Eugeniya I. Bondar, Julia A. Putintseva, Nataliya V. Oreshkova, Konstantin V. Krutovsky:
  Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers. 47-52

Volume 20-S, Number 2, March 2019

Proceedings of the 15th Annual MCBIOS Conference

• 
  Philip 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. 7-16
• 
  Bohu 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. 17-29
• 
  Sujoy Roy, Kazi I. Zaman, Robert W. Williams, Ramin Homayouni:
  Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion. 31-43
• 
  Visanu 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. 45-57
• 
  Aleksandra 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. 59-71
• 
  Norbert Bokros, Sorina C. Popescu, George V. Popescu:
  Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions. 73-85
• 
  Mustafa Bayraktar, Sinan Kockara, Tansel Halic, Mutlu Mete, Henry K. Wong, Kamran Iqbal:
  Local edge-enhanced active contour for accurate skin lesion border detection. 87-97
• 
  Jonathan D. Wren, Robert J. Doerksen, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar:
  Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. 95:1-95:5
• 
  Doga Demirel, Berk Cetinsaya, Tansel Halic, Sinan Kockara, Shahryar Ahmadi:
  Partition-based optimization model for generative anatomy modeling language (POM-GAML). 99-114
• 
  Joseph Luttrell IV, Tong Liu, Chaoyang Zhang, Zheng Wang:
  Predicting protein residue-residue contacts using random forests and deep networks. 115-127
• 
  Leihong 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. 129-139
• 
  Adam 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. 141-149

Volume 20-S, Number 3, March 2019

Selected articles from the 17th Asia Pacific Bioinformatics Conference (APBC 2019): bioinformatics

• 
  Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, Jun Sese:
  reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction. 15-24
• 
  Jayoung 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. 25-36
• 
  Safa Jammali, Jean-David Aguilar, Esaie Kuitche, Aïda Ouangraoua:
  SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. 37-52
• 
  Audrey Legendre, Eric Angel, Fariza Tahi:
  RCPred: RNA complex prediction as a constrained maximum weight clique problem. 53-62
• 
  Xiujuan Lei, Ming Fang, Ling Guo, Fang-Xiang Wu:
  Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks. 63-74
• 
  Ran Li, Xiangrui Zeng, Stephanie E. Sigmund, Ruogu Lin, Bo Zhou, Chang Liu, Kaiwen Wang, Rui Jiang, Zachary Freyberg, Hairong Lv, Min Xu:
  Automatic localization and identification of mitochondria in cellular electron cryo-tomography using faster-RCNN. 75-85
• 
  Nayang Shan, Zuoheng Wang, Lin Hou:
  Identification of trans-eQTLs using mediation analysis with multiple mediators. 87-97
• 
  Chao 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. 99-108
• 
  Quan Chen, Jun Zhu:
  Detecting virus-specific effects on post-infection temporal gene expression. 109-118

Volume 20-S, Number 4, April 2019

Methods, tools and platforms for Personalized Medicine in the Big Data Era (NETTAB 2017)

• 
  Alessandro Zandonà, Rosario Vasta, Adriano Chiò, Barbara Di Camillo:
  A Dynamic Bayesian Network model for the simulation of Amyotrophic Lateral Sclerosis progression. 118:1-118:11
• 
  Alexander 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. 119:1-119:20
• 
  Giovanni 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. 120:1-120:13
• 
  Fabio 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. 124:1-124:7
• 
  Paolo Romano, 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. 125:1-125:9
• 
  Umberto 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. 138:1-138:14
• 
  Pierre 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. 139:1-139:16
• 
  Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Yu. Zinovyev, Inna Kuperstein:
  Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer. 140:1-140:14
• 
  Hamed Khakzad, Johan Malmström, Lars Malmström:
  Greedy de novo motif discovery to construct motif repositories for bacterial proteomes. 141:1-141:10
• 
  Ismael 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. 150:1-150:11
• 
  Sandra Krüger, Rosario M. Piro:
  decompTumor2Sig: identification of mutational signatures active in individual tumors. 152:1-152:15
• 
  Michela Quadrini, Luca Tesei, Emanuela Merelli:
  An algebraic language for RNA pseudoknots comparison. 161:1-161:18
• 
  Ilaria 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. 162:1-162:11
• 
  Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind, Mario Rosario Guarracino:
  From trash to treasure: detecting unexpected contamination in unmapped NGS data. 168:1-168:12
• 
  Andrea 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. 172:1-172:14
• 
  David R. Gilbert, Monika Heiner, Leila Ghanbar, Jacek Chodak:
  Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking. 173:1-173:23

Volume 20-S, Number 5, April 2019

Selected articles from the Second International Workshop on Cells in ExperimentaL Life Sciences (CELLS-2018) at the 2018 International Conference on Biological Ontology (ICBO-2018)

• 
  Sirarat Sarntivijai, Yongqun He, Alexander D. Diehl:
  Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies. 227-230
• 
  Lucas M. Serra, William D. Duncan, Alexander D. Diehl:
  An ontology for representing hematologic malignancies: the cancer cell ontology. 231-236
• 
  Yongqun He, William D. Duncan, Daniel J. Cooper, Jens Hansen, Ravi Iyengar, Edison Ong, Kendal Walker, Omar Tibi, Sam Smith, Lucas M. Serra, Jie Zheng, 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. 237-247
• 
  Hongjie 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. 249-258
• 
  James 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. 259-264

Volume 20-S, Number 6, December 2019

Towards computational modeling on immune system function

• 
  Ping Zhang, 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. 413
• 
  Alva Presbitero, Emiliano Mancini, Filippo Castiglione, Valeria V. Krzhizhanovskaya, Rick Quax:
  Game of neutrophils: modeling the balance between apoptosis and necrosis. 475
• 
  Monica J. Quinzo, Esther M. Lafuente, Pilar Zuluaga, Darren R. Flower, Pedro A. Reche:
  Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy. 476
• 
  Pin-Yen Chen, Allan Cripps, Nicholas P. West, Amanda J. Cox, Ping Zhang:
  A correlation-based network for biomarker discovery in obesity with metabolic syndrome. 477
• 
  Marzio 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:
  Predicting the artificial immunity induced by RUTI® vaccine against tuberculosis using universal immune system simulator (UISS). 504
• 
  Ruy 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. 532
• 
  Mozhgan Kabiri Chimeh, Peter Heywood, Marzio Pennisi, Francesco Pappalardo, Paul Richmond:
  Parallelisation strategies for agent based simulation of immune systems. 579
• 
  Francesco Pappalardo, Marzio Pennisi, Pedro A. Reche, Giulia Russo:
  Toward computational modelling on immune system function. 622
• 
  Simone Pernice, Marzio Pennisi, Greta Romano, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Gianfranco Balbo, Marco Beccuti, Francesca Cordero, Raffaele A. Calogero:
  A computational approach based on the colored Petri net formalism for studying multiple sclerosis. 623

Volume 20-S, Number 7, May 2019

Selected papers from the 12th International Conference on Computational Systems Biology (ISB 2018)

• 
  Yance Feng, Sheng Zhang, Liang Li, Lei M. Li:
  The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation. 5-15
• 
  Tongxin Wang, Jie Zhang, Kun Huang:
  Generalized gene co-expression analysis via subspace clustering using low-rank representation. 17-27
• 
  Yang Hao, Daixi Li, Yong Xu, Jian Ouyang, Yongkun Wang, Yuqi Zhang, Baoguo Li, Lu Xie, Guangrong Qin:
  Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data. 29-39
• 
  Jialu Hu, Jingru Wang, Jianan Lin, Tianwei Liu, Yuanke Zhong, Jie Liu, Yan Zheng, Yiqun Gao, Junhao He, Xuequn Shang:
  MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites. 41-48
• 
  Tao-Chuan Shih, Li-Ping Ho, Jen-Leih Wu, Hsin-Yiu Chou, Tun-Wen Pai:
  A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family. 49-58
• 
  Weishan Liang, Yongjiang Zheng, Ji Zhang, Xiaoqiang Sun:
  Multiscale modeling reveals angiogenesis-induced drug resistance in brain tumors and predicts a synergistic drug combination targeting EGFR and VEGFR pathways. 59-71
• 
  Junhua Xu, Min Wu, Shanshan Zhu, Jinzhi Lei, Jie Gao:
  Detecting the stable point of therapeutic effect of chronic myeloid leukemia based on dynamic network biomarkers. 73-81
• 
  Xuemeng Fan, Yaolai Wang, Xu-Qing Tang:
  Extracting predictors for lung adenocarcinoma based on Granger causality test and stepwise character selection. 83-96
• 
  Chaima Aouiche, Bolin Chen, Xuequn Shang:
  Predicting stage-specific cancer related genes and their dynamic modules by integrating multiple datasets. 97-107
• 
  Le Zhang, Jin Li, Kaikai Yin, Zhouyang Jiang, Tingting Li, Rong Hu, Zheng Yu, Hua Feng, Yujie Chen:
  Computed tomography angiography-based analysis of high-risk intracerebral haemorrhage patients by employing a mathematical model. 109-116
• 
  Hong Yu, Solomiya Nysak, Noemi Garg, Edison Ong, Xianwei Ye, Xiangyan Zhang, Yongqun He:
  ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. 117-128
• 
  Min Luo, Jianfeng Jiao, Ruiqi Wang:
  Screening drug target combinations in disease-related molecular networks. 129-138
• 
  Shengquan Chen, Kui Hua, Hongfei Cui, Rui Jiang:
  VPAC: Variational projection for accurate clustering of single-cell transcriptomic data. 139-151
• 
  Yong Wang, Xiang-Sun Zhang, Luonan Chen:
  Systems biology intertwines with single cell and AI. 204:1-204:3

Volume 20-S, Number 8, June 2019

Decipher computational analytics in digital health and precision medicine

• 
  Junyi 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. 283:1-283:7
• 
  Jiajie Peng, Xiaoyu Wang, Xuequn Shang:
  Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data. 284:1-284:12
• 
  Yanan Wang, Qi Lv, Yingying Zhang, Luhui Wang, Yafei Dong:
  Probe computing model based on small molecular switch. 285:1-285:7
• 
  Henry Han, Wenbin Liu:
  Preface. 286:1
• 
  Zhen 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. 287:1-287:13
• 
  Xiaoli Qiang, Zheng Kou:
  Scoring amino acid mutation to predict pandemic risk of avian influenza virus. 288:1-288:11
• 
  Fei Han, 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. 289:1-289:13
• 
  Hui Huang, 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. 290:1-290:14
• 
  Yuan Lin, Yinyin Cai, Juan Liu, Chen Lin, Xiangrong Liu:
  An advanced approach to identify antimicrobial peptides and their function types for penaeus through machine learning strategies. 291:1-291:10

Volume 20-S, Number 9, November 2019

Italian Society of Bioinformatics (BITS): Annual Meeting 2018

• 
  Yoshihiro Shibuya, Matteo Comin:
  Better quality score compression through sequence-based quality smoothing. 302:1-302:11
• 
  Luis 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. 337:1-337:12
• 
  Valeria Boscaino, Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo, Alfonso Urso:
  MiRNA therapeutics based on logic circuits of biological pathways. 344:1-344:22
• 
  Mattia Dalsass, Margherita Bodini, Christophe G. 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. 347:1-347:8
• 
  Salvatore Alaimo, Antonio Di Maria, Dennis E. Shasha, Alfredo Ferro, Alfredo Pulvirenti:
  TACITuS: transcriptomic data collector, integrator, and selector on big data platform. 366:1-366:11
• 
  Jia Qian, Matteo Comin:
  MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage. 367:1-367:12
• 
  Damiano 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. 390:1-390:13
• 
  Mainá Bitar, Stefanie Kuiper, Elizabeth A. O'Brien, Guy Barry:
  Genes with human-specific features are primarily involved with brain, immune and metabolic evolution. 406:1-406:12
• 
  Ilaria Patuzzi, Giacomo Baruzzo, Carmen Losasso, Antonia Ricci, Barbara Di Camillo:
  metaSPARSim: a 16S rRNA gene sequencing count data simulator. 416:1-416:13
• 
  Federico Ansaloni, Margherita Scarpato, Elia Di Schiavi, Stefano Gustincich, Remo Sanges:
  Exploratory analysis of transposable elements expression in the C. elegans early embryo. 484:1-484:13
• 
  Giovanni Spirito, Damiano Mangoni, Remo Sanges, Stefano Gustincich:
  Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data. 495:1-495:13
• 
  Francesca Cordero, Raffaele A. Calogero, Michele Caselle:
  BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics. 562:1-562:4

Volume 20-S, Number 10, May 2019

Proceedings of the 12th International Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO 2018)

• 
  Jihoon 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. 13-21
• 
  João D. Ferreira, Francisco M. Couto:
  Multi-domain semantic similarity in biomedical research. 23-31
• 
  Eunyoung Kim, A.-Sol Choi, Hojung Nam:
  Drug repositioning of herbal compounds via a machine-learning approach. 33-43
• 
  Mijin Kwon, Soorin Yim, Gwangmin Kim, Saehwan Lee, Chungsun Jeong, Doheon Lee:
  CODA-ML: context-specific biological knowledge representation for systemic physiology analysis. 45-53
• 
  Wonjin Yoon, Chan Ho So, Jinhyuk Lee, Jaewoo Kang:
  CollaboNet: collaboration of deep neural networks for biomedical named entity recognition. 55-65
• 
  Hyang-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. 67-73
• 
  Judita Preiss:
  Is automatic detection of hidden knowledge an anomaly? 75-80
• 
  Zolzaya Dashdorj, Min Song:
  An application of convolutional neural networks with salient features for relation classification. 244:1-244:12

Volume 20-S, Number 11, June 2019

Selected articles from the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017): bioinformatics

• 
  Douglas 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. 275:1-275:6
• 
  Cuncong Zhong, Youngik Yang, Shibu Yooseph:
  GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data. 276:1-276:12
• 
  Chunchun Zhao, Sartaj Sahni:
  String correction using the Damerau-Levenshtein distance. 277:1-277:28
• 
  Trevor Cickovski, Vanessa Aguiar-Pulido, Giri Narasimhan:
  MATria: a unified centrality algorithm. 278:1-278:9
• 
  Ardalan Naseri, Degui Zhi, Shaojie Zhang:
  Multi-allelic positional Burrows-Wheeler transform. 279:1-279:8
• 
  David Morris, Tatiana Maximova, Erion Plaku, Amarda Shehu:
  Attenuating dependence on structural data in computing protein energy landscapes. 280:1-280:10
• 
  Dina Abdelhafiz, Clifford Yang, Reda Ammar, Sheida Nabavi:
  Deep convolutional neural networks for mammography: advances, challenges and applications. 281:1-281:20
• 
  Hosein Toosi, Ali Moeini, Iman Hajirasouliha:
  BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples. 282:1-282:9

Volume 20-S, Number 12, June 2019

Selected original research articles from the Fifth International Workshop on Computational Network Biology: Modeling, Analysis and Control (CNB-MAC 2018): Bioinformatics

• 
  Miriam Bern, Alexander King, Derek A. Applewhite, Anna M. Ritz:
  Network-based prediction of polygenic disease genes involved in cell motility. 313:1-313:13
• 
  Chieh Lo, Radu Marculescu:
  MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks. 314:1-314:14
• 
  Minghan Chen, Yang Cao:
  Analysis and remedy of negativity problem in hybrid stochastic simulation algorithm and its application. 315:1-315:16
• 
  Byung-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). 316:1-316:3
• 
  Saugato Rahman Dhruba, Aminur Rahman, Raziur Rahman, Souparno Ghosh, Ranadip Pal:
  Recursive model for dose-time responses in pharmacological studies. 317:1-317:12
• 
  Yuanfang Ren, Ahmet Ay, Alin Dobra, Tamer Kahveci:
  Characterizing building blocks of resource constrained biological networks. 318:1-318:14
• 
  Mohammed Alokshiya, Saeed Salem, Fidaa Abed:
  A linear delay algorithm for enumerating all connected induced subgraphs. 319:1-319:11
• 
  Dalia Elmansy, Mehmet Koyutürk:
  Cross-population analysis for functional characterization of type II diabetes variants. 320:1-320:17
• 
  Shahin Boluki, Siamak Zamani Dadaneh, Xiaoning Qian, Edward R. Dougherty:
  Optimal clustering with missing values. 321:1-321:10
• 
  Mansooreh Ahmadian, John J. Tyson, Yang Cao:
  A stochastic model of size control in the budding yeast cell cycle. 322:1-322:13

Volume 20-S, Number 13, July 2019

Selected articles from the 8th Translational Bioinformatics Conference: Bioinformatics

• 
  Yongsub Lim, In-Jae Yu, Dongmin Seo, U Kang, Lee Sael:
  PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks. 381:1-381:12
• 
  Chi-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. 382:1-382:10
• 
  Yonghyun Nam, Myungjun Kim, Hang-Seok Chang, Hyunjung Shin:
  Drug repurposing with network reinforcement. 383:1-383:10
• 
  Jungmin 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. 384:1-384:7

Volume 20-S, Number 14, July 2019

Proceedings of VarI-COSI 2018: identification and annotation of genetic variants in the context of structure, function, and disease: bioinformatics

• 
  Ludovica 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. 335:1-335:10

Volume 20-S, Number 15, December 2019

Selected articles from the 14th International Symposium on Bioinformatics Research and Applications (ISBRA-18): bioinformatics

• 
  Prapaporn Techa-angkoon, Kevin L. Childs, Yanni Sun:
  GPRED-GC: a Gene PREDiction model accounting for 5 ^′- 3^′ GC gradient. 482
• 
  Fei 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. 483
• 
  Yuping Lu, Charles A. Phillips, Michael A. Langston:
  A robustness metric for biological data clustering algorithms. 503
• 
  Jin-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. 535
• 
  Neo Christopher Chung, Blazej Miasojedow, Michal Startek, Anna Gambin:
  Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data. 644
• 
  Liyuan Liu, Bingchen Yu, Meng Han, Shanshan Yuan, Na Wang:
  Mild cognitive impairment understanding: an empirical study by data-driven approach. 481
• 
  Jianwei Lu, Yao Lu, Yusheng Ding, Qingyang Xiao, Linqing Liu, Qingpo Cai, Yunchuan Kong, Yun Bai, Tianwei Yu:
  DNLC: differential network local consistency analysis. 489
• 
  Min Li, Li Tang, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
  CSA: a web service for the complete process of ChIP-Seq analysis. 515
• 
  Cheng Yan, Guihua Duan, Yi Pan, Fang-Xiang Wu, Jianxin Wang:
  DDIGIP: predicting drug-drug interactions based on Gaussian interaction profile kernels. 538
• 
  Yuehui Wang, Maozu Guo, Yazhou Ren, Lianyin Jia, Guoxian Yu:
  Drug repositioning based on individual bi-random walks on a heterogeneous network. 547
• 
  Hongda Bu, Jiaqi Hao, Yanglan Gan, Shuigeng Zhou, Jihong Guan:
  DEEPSEN: a convolutional neural network based method for super-enhancer prediction. 598

Volume 20-S, Number 16, December 2019

Selected articles from the IEEE BIBM International Conference on Bioinformatics & Biomedicine (BIBM) 2018: bioinformatics and systems biology

• 
  Canlin Zhang, Daniel Bis, Xiuwen Liu, Zhe He:
  Biomedical word sense disambiguation with bidirectional long short-term memory and attention-based neural networks. 502:1-502:15
• 
  Ibrahim Youssef, Jeffrey N. Law, Anna M. Ritz:
  Integrating protein localization with automated signaling pathway reconstruction. 505:1-505:15
• 
  Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li, Yi Pan:
  DeepEP: a deep learning framework for identifying essential proteins. 506:1-506:10
• 
  Da Zhang, Mansur R. Kabuka:
  Multimodal deep representation learning for protein interaction identification and protein family classification. 531:1-531:14
• 
  Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang:
  LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets. 582:1-582:11
• 
  Xusheng Li, Chengcheng Fu, Ran Zhong, Duo Zhong, Tingting He, Xingpeng Jiang:
  A hybrid deep learning framework for bacterial named entity recognition with domain features. 583:1-583:9
• 
  Slim Karkar, Lauren E. Alfonse, Catherine M. Grgicak, Desmond S. Lun:
  Statistical modeling of STR capillary electrophoresis signal. 584:1-584:12
• 
  Joyce 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. 585:1-585:13
• 
  Ye Yuan, Kebin Jia, Fenglong Ma, Guangxu Xun, Yaqing Wang, Lu Su, Aidong Zhang:
  A hybrid self-attention deep learning framework for multivariate sleep stage classification. 586:1-586:10
• 
  Lei Chen, Hong Song, Chi Wang, Yutao Cui, Jian Yang, Xiaohua Hu, Le Zhang:
  Liver tumor segmentation in CT volumes using an adversarial densely connected network. 587:1-587:13
• 
  Hongryul 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. 588:1-588:14
• 
  Han Zhang, Xueting Huo, Xia Guo, Xin Su, Xiongwen Quan, Chen Jin:
  A disease-related gene mining method based on weakly supervised learning model. 589:1-589:11
• 
  Bo Xu, Hongfei Lin, Liang Yang, Kan Xu, Yi-Jia Zhang, Dongyu Zhang, Zhihao Yang, Jian Wang, Yuan Lin, Fuliang Yin:
  A supervised term ranking model for diversity enhanced biomedical information retrieval. 590:1-590:11
• 
  Satoshi 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. 591:1-591:10
• 
  Tong Liu, Zheng Wang:
  Exploring the 2D and 3D structural properties of topologically associating domains. 592:1-592:10
• 
  Kefei Liu, Li Shen, Hui Jiang:
  Joint between-sample normalization and differential expression detection through ℓ 0-regularized regression. 593:1-593:16
• 
  Dan Liu, Yingjun Ma, Xingpeng Jiang, Tingting He:
  Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion. 594:1-594:10

Volume 20-S, Number 17, November 2019

Selected abstracts and papers of Bioinformatics: from Algorithms to Applications 2019 conference

• 
  Third international conference "Bioinformatics: from Algorithms to Applications" (BiATA 2019) - Saint Petersburg, Russia. 20-22 June 2019. 516:1-516:11

Volume 20-S, Number 18, December 2019

• 
  Wenxiang Zhang, Xiujuan Lei, Chen Bian:
  Identifying Cancer genes by combining two-rounds RWR based on multiple biological data. 518:1-518:12
• 
  Qianlong Liu, Kangenbei Liao, Kelvin Kam-fai Tsoi, Zhongyu Wei:
  Acceptance Prediction for Answers on Online Health-care Community. 567:1-567:8
• 
  Zhenxing Wang, Yadong Wang:
  Extracting a biologically latent space of lung cancer epigenetics with variational autoencoders. 568:1-568:7
• 
  Jialu Hu, Yiqun Gao, Jing Li, Yan Zheng, Jingru Wang, Xuequn Shang:
  A novel algorithm based on bi-random walks to identify disease-related lncRNAs. 569:1-569:11
• 
  Tianyi Zhao, Yang Hu, Tianyi Zang, Liang Cheng:
  Identifying Alzheimer's disease-related proteins by LRRGD. 570:1-570:9
• 
  Hanxu Hou, Tian Gan, Yaodong Yang, Xianglei Zhu, Sen Liu, Weiming Guo, Jianye Hao:
  Using deep reinforcement learning to speed up collective cell migration. 571:1-571:10
• 
  Jiajie 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. 572:1-572:7
• 
  Qing 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. 573:1-573:10
• 
  Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang:
  Prioritizing candidate diseases-related metabolites based on literature and functional similarity. 574:1-574:11
• 
  Xianglei 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. 575:1-575:10

Volume 20-S, Number 19, December 2019

18th International Conference on Bioinformatics

• 
  Jiang Huang, Min Wu, Fan Lu, Le Ou-Yang, Zexuan Zhu:
  Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization. 657
• 
  Yi 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. 661
• 
  Lei Deng, Guolun Zhong, Chenzhe Liu, Judong Luo, Hui Liu:
  MADOKA: an ultra-fast approach for large-scale protein structure similarity searching. 662
• 
  Yue Cao, Yingxin Lin, John T. Ormerod, Pengyi Yang, Jean Yee Hwa Yang, Kitty K. Lo:
  scDC: single cell differential composition analysis. 721
• 
  Bee Guan Teo, Sarinder Kaur Dhillon:
  An automated 3D modeling pipeline for constructing 3D models of MONOGENEAN HARDPART using machine learning techniques. 658
• 
  Sean 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. 659
• 
  Thomas 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. 660
• 
  Hsin-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. 703

Volume 20-S, Number 20, December 2019

Proceedings of the 17th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop: Bioinformatics

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

Volume 20-S, Number 21, December 2019

Selected articles from the 7th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2018)

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

Volume 20-S, Number 22, December 2019

Decipher computational analytics in digital health and precision medicine

• 
  Henry Han, Wenbin Liu:
  The coming era of artificial intelligence in biological data science. 712
• 
  Hang 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. 713
• 
  Shudong 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. 714
• 
  Ying Xiong, Qing-Hua Ling, Fei Han, Qing-Hua Liu:
  An efficient gene selection method for microarray data based on LASSO and BPSO. 715
• 
  Chun-Mei Feng, Yong Xu, 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. 716
• 
  Guimin Qin, Luqiong Yang, Yuying Ma, Jiayan Liu, Qiuyan Huo:
  The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma. 717
• 
  Juan Wang, 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. 718
• 
  Yuhua Yao, Yaping Lv, Ling Li, Huimin Xu, Binbin Ji, Jing Chen, Chun Li, Bo Liao, Xu-Ying Nan:
  Protein sequence information extraction and subcellular localization prediction with gapped k-Mer method. 719
• 
  Mingzhao 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. 720

Volume 20-S, Number 23, December 2019

Proceedings of the Joint International GIW & ABACBS-2019 Conference: bioinformatics

• 
  Juris 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. 618
• 
  Tzu-Hsien Yang:
  Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast. 630
• 
  Kodai Minoura, Ko Abe, Yuka Maeda, Hiroyoshi Nishikawa, Teppei Shimamura:
  Model-based cell clustering and population tracking for time-series flow cytometry data. 633
• 
  Binh 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. 634
• 
  Xubo Tang, Yanni Sun:
  Fast and accurate microRNA search using CNN. 646
• 
  Cesar Augusto Nieto-Acuna, Cesar Augusto Vargas Garcia, Abhyudai Singh, Juan Manuel Pedraza:
  Efficient computation of stochastic cell-size transient dynamics. 647
• 
  Lingxi Chen, Jiao Xu, Shuai Cheng Li:
  DeepMF: deciphering the latent patterns in omics profiles with a deep learning method. 648
• 
  Cheng Yan, Guihua Duan, Fang-Xiang Wu, Jianxin Wang:
  IILLS: predicting virus-receptor interactions based on similarity and semi-supervised learning. 651
• 
  Ruohan Wang, Zishuai Wang, Jianping Wang, Shuaicheng Li:
  SpliceFinder: ab initio prediction of splice sites using convolutional neural network. 652
• 
  Haohan 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. 656
• 
  Benjamin 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. 667
• 
  Chen Li, Yiqi Jiang, Shuaicheng Li:
  LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics. 702
• 
  Junpeng Zhang, Vu Viet Hoang Pham, Lin Liu, Taosheng Xu, Buu Minh Thanh Truong, Jiuyong Li, Nini Rao, Thuc Duy Le:
  Identifying miRNA synergism using multiple-intervention causal inference. 613
• 
  Yi Zheng, Hui Peng, Xiaocai Zhang, Zhixun Zhao, Xiaoying Gao, Jinyan Li:
  Old drug repositioning and new drug discovery through similarity learning from drug-target joint feature spaces. 605
• 
  Shifu 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. 606
• 
  Mehwish Noureen, Ipputa Tada, Takeshi Kawashima, Masanori Arita:
  Rearrangement analysis of multiple bacterial genomes. 631

Volume 20-S, Number 24, December 2019

The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: Bioinformatics methods and applications for human diseases

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

Volume 20-S, Number 25, December 2019

Proceedings of the 2018 International Conference on Intelligent Computing (ICIC 2018) and Intelligent Computing and Biomedical Informatics (ICBI) 2018 conference: bioinformatics

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

Volume 20, Number 26, December 2019

• 
  Ran Wang, Shuai Li, Lixin Cheng, Man Hon Wong, Kwong-Sak Leung:
  Predicting associations among drugs, targets and diseases by tensor decomposition for drug repositioning. 628