BMC Bioinformatics, Volume 19 - Supplements

Volume 19-S, Number 1, February 2018

• 
  Maryam Etemadi, Mehri Bagherian, Zhi-Zhong Chen, Lusheng Wang:
  Better ILP models for haplotype assembly. 11-21
• 
  Seowon Choi, Jin-Wu Nam:
  TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association. 23-31
• 
  Hajime Suzuki, Masahiro Kasahara:
  Introducing difference recurrence relations for faster semi-global alignment of long sequences. 33-47
• 
  In Seok Yang, Sangwoo Kim:
  Isoform specific gene expression analysis of KRAS in the prognosis of lung adenocarcinoma patients. 40:1-40:10
• 
  Taehoon Lee, Sungmin Lee, Woo Young Sim, Yu Mi Jung, Sunmi Han, Joong-Ho Won, Hyeyoung Min, Sungroh Yoon:
  HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment. 49-61
• 
  Inyoung Kim, Saemi Choi, Sun Kim:
  BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways. 63-72
• 
  Peiying Ruan, Morihiro Hayashida, Tatsuya Akutsu, Jean-Philippe Vert:
  Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. 73-84
• 
  Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori, Kiyoshi Asai:
  Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities. 85-95
• 
  Gunhwan Ko, Pan-Gyu Kim, Jongcheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byungwook Lee:
  Closha: bioinformatics workflow system for the analysis of massive sequencing data. 97-104

Volume 19-S, Number 2, March 2018

Proceedings of Bringing Maths to Life (BMTL) 2017

• 
  Lokmane Chebouba, Bertrand Miannay, Dalila Boughaci, Carito Guziolowski:
  Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming. 15-26
• 
  Kumar Parijat Tripathi, Marina Piccirillo, Mario Rosario Guarracino:
  An integrated approach to infer cross-talks between intracellular protein transport and signaling pathways. 27-40
• 
  Maurizio Giordano, Kumar Parijat Tripathi, Mario Rosario Guarracino:
  Ensemble of rankers for efficient gene signature extraction in smoke exposure classification. 41-54
• 
  Diego Fioravanti, Ylenia Giarratano, Valerio Maggio, Claudio Agostinelli, Marco Chierici, Giuseppe Jurman, Cesare Furlanello:
  Phylogenetic convolutional neural networks in metagenomics. 49:1-49:13

Volume 19-S, Number 3, March 2018

Selected original research articles from the Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2017): bioinformatics

• 
  Ali Foroughi Pour, Lori A. Dalton:
  Heuristic algorithms for feature selection under Bayesian models with block-diagonal covariance structure. 5-19
• 
  Kevin Matlock, Carlos De Niz, Raziur Rahman, Souparno Ghosh, Ranadip Pal:
  Investigation of model stacking for drug sensitivity prediction. 21-33
• 
  Ahmad Al Kawam, Mustafa Alshawaqfeh, James J. Cai, Erchin Serpedin, Aniruddha Datta:
  Simulating variance heterogeneity in quantitative genome wide association studies. 35-44
• 
  Ashish Katiyar, Anwoy Kumar Mohanty, Jianping Hua, Chao Sima, Rosana Lopes, Aniruddha Datta, Michael L. Bittner:
  A Bayesian approach to determine the composition of heterogeneous cancer tissue. 45-58
• 
  Yang Ni, Peter Müller, Lin Wei, Yuan Ji:
  Bayesian graphical models for computational network biology. 59-69
• 
  Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci, Ranadip Pal:
  Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). 69:1-69:4

Volume 19-S, Number 4, May 2018

• 
  Shu-Hwa Chen, Wen-Yu Kuo, Sheng-Yao Su, Wei-Chun Chung, Jen-Ming Ho, Henry Horng-Shing Lu, Chung-Yen Lin:
  A gene profiling deconvolution approach to estimating immune cell composition from complex tissues. 15-23
• 
  Yongkang Kim, Sungyoung Lee, Sungkyoung Choi, Jin-Young Jang, Taesung Park:
  Hierarchical structural component modeling of microRNA-mRNA integration analysis. 25-34
• 
  Shunyun Yang, Runxin Guo, Rui Liu, Xiangke Liao, Quan Zou, Benyun Shi, Shaoliang Peng:
  cmFSM: a scalable CPU-MIC coordinated drug-finding tool by frequent subgraph mining. 35-47
• 
  Yoichi Takenaka, Kazuma Mikami, Shigeto Seno, Hideo Matsuda:
  Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. 49-59
• 
  Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama:
  MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. 61-72
• 
  Yujuan Gao, Sheng Wang, Minghua Deng, Jinbo Xu:
  RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning. 73-84
• 
  Sungyoung Lee, Yongkang Kim, Sungkyoung Choi, Heungsun Hwang, Taesung Park:
  Pathway-based approach using hierarchical components of rare variants to analyze multiple phenotypes. 85-97
• 
  Jiyun Zhou, Hongpeng Wang, Zhishan Zhao, Ruifeng Xu, Qin Lu:
  CNNH_PSS: protein 8-class secondary structure prediction by convolutional neural network with highway. 99-109
• 
  Y-h. Taguchi:
  Tensor decomposition-based and principal-component-analysis-based unsupervised feature extraction applied to the gene expression and methylation profiles in the brains of social insects with multiple castes. 99:1-99:13
• 
  Xiaofeng Gong, Jianping Jiang, Zhongqu Duan, Hui Lu:
  A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology. 111-119

Volume 19-S, Number 5, April 2018

Selected articles from the Biological Ontologies and Knowledge bases workshop 2017

• 
  Zhenxing Wang, Xiaoliang Wu, Yadong Wang:
  A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip. 15-22
• 
  Xiaotian Hao, Jianye Hao, Wang Li, Hanxu Hou:
  Effective norm emergence in cell systems under limited communication. 23-35
• 
  Yang Hu, Tianyi Zhao, Ningyi Zhang, Tianyi Zang, Jun Zhang, Liang Cheng:
  Identifying diseases-related metabolites using random walk. 37-46
• 
  Shiquan Sun, Xifang Sun, Yan Zheng:
  Higher-order partial least squares for predicting gene expression levels from chromatin states. 47-54
• 
  Huaixiao Tou, Lu Yao, Zhongyu Wei, Xiahai Zhuang, Bo Zhang:
  Automatic infection detection based on electronic medical records. 55-63
• 
  Jiajie Peng, Weiwei Hui, Xuequn Shang:
  Measuring phenotype-phenotype similarity through the interactome. 65-77
• 
  Yan-Shuo Chu, Mingxiang Teng, Yadong Wang:
  Modeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferring. 79-87
• 
  Yang Guo, Shuhui Liu, Zhanhuai Li, Xuequn Shang:
  BCDForest: a boosting cascade deep forest model towards the classification of cancer subtypes based on gene expression data. 118:1-118:13

Volume 19-S, Number 6, May 2018

Proceedings of the 15th Annual Research in Computational Molecular Biology (RECOMB) Com$ bioinformatics

• 
  Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab:
  ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. 15-30
• 
  Diego P. Rubert, Edna Ayako Hoshino, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez:
  Computing the family-free DCJ similarity. 31-42
• 
  Leonid Chindelevitch, João Paulo Pereira Zanetti, João Meidanis:
  On the rank-distance median of 3 permutations. 43-62
• 
  Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Zohar Zafrir, Shimshi Atar, Tahel Altman, Justin Julander, Tamir Tuller:
  Generation and comparative genomics of synthetic dengue viruses. 140:1-140:14

Volume 19-S, Number 7, July 2018

12th and 13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2015/16)

• 
  Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre:
  NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability. 3-12
• 
  Susana Conde, Xiaoguang Xu, Hui Guo, Markus Perola, Teresa Fazia, Luisa Bernardinelli, Carlo Berzuini:
  Mendelian randomisation analysis of clustered causal effects of body mass on cardiometabolic biomarkers. 13-22
• 
  Marco Fornili, Patrizia Boracchi, Federico Ambrogi, Elia Biganzoli:
  Modeling the covariates effects on the hazard function by piecewise exponential artificial neural networks: an application to a controlled clinical trial on renal carcinoma. 23-29
• 
  Chiara Gigliarano, Alessandro Nonis, Alberto Briganti, Marco Bonetti, Clelia Di Serio:
  Effect of the number of removed lymph nodes on prostate cancer recurrence and survival: evidence from an observational study. 31-44
• 
  Riccardo Colombo, Chiara Damiani, David R. Gilbert, Monika Heiner, Giancarlo Mauri, Dario Pescini:
  Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. 45-59
• 
  Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Giosuè Lo Bosco, Giovanni Renda, Riccardo Rizzo, Salvatore Gaglio, Alfonso Urso:
  Deep learning models for bacteria taxonomic classification of metagenomic data. 61-76
• 
  Davide S. Sardina, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno:
  INBIA: a boosting methodology for proteomic network inference. 77-88
• 
  Régis Garnier, Christophe Guyeux, Jean-François Couchot, Michel Salomon, Bashar Al-Nuaimi, Bassam AlKindy:
  Comparison of metaheuristics to measure gene effects on phylogenetic supports and topologies. 89-107
• 
  Kirsty L. Hassall, Andrew Mead:
  Beyond the one-way ANOVA for 'omics data. 109-126
• 
  Igor Saggese, Elisa Bona, Maxwell Conway, Francesco Favero, Marco Ladetto, Pietro Liò, Giovanni Manzini, Flavio Mignone:
  STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow. 127-137
• 
  Francesco Bardozzo, Pietro Liò, Roberto Tagliaferri:
  A study on multi-omic oscillations in Escherichia coli metabolic networks. 139-154
• 
  Claudia Angelini, Andrea Bracciali, David Gilbert, Riccardo Rizzo:
  Preface to the BMC-CIBB 2015-16 special issue. 201:1-201:2

Volume 19-S, Number 8, June 2018

Proceedings of the 11th International Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO 2017)

• 
  Ingoo Lee, Hojung Nam:
  Identification of drug-target interaction by a random walk with restart method on an interactome network. 9-18
• 
  Yousang Jo, Sanghyeon Kim, Doheon Lee:
  Identification of common coexpression modules based on quantitative network comparison. 19-28
• 
  Myeong-Sang Yu, Hyang-Mi Lee, Aaron Park, Chungoo Park, Hyithaek Ceong, Ki-Hyeong Rhee, Dokyun Na:
  In silico prediction of potential chemical reactions mediated by human enzymes. 29-37
• 
  Víctor Suárez-Paniagua, Isabel Segura-Bedmar:
  Evaluation of pooling operations in convolutional architectures for drug-drug interaction extraction. 39-47
• 
  Kyungrin Noh, Sunyong Yoo, Doheon Lee:
  A systematic approach to identify therapeutic effects of natural products based on human metabolite information. 49-55
• 
  Reilly Grant, David Kucher, Ana M. Leon, Jonathan Gemmell, Daniela Stan Raicu, Samah J. Fodeh:
  Automatic extraction of informal topics from online suicidal ideation. 57-66
• 
  Keyuan Jiang, Shichao Feng, Qunhao Song, Ricardo A. Calix, Matrika Gupta, Gordon R. Bernard:
  Identifying tweets of personal health experience through word embedding and LSTM neural network. 67-74
• 
  Munui Kim, Seung Han Baek, Min Song:
  Relation extraction for biological pathway construction using node2vec. 75-84
• 
  Shashank Gupta, Sachin Pawar, Nitin Ramrakhiyani, Girish Keshav Palshikar, Vasudeva Varma:
  Semi-Supervised Recurrent Neural Network for Adverse Drug Reaction mention extraction. 212:1-212:7

Volume 19-S, Number 9, August 2018

Selected articles from the 13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017): bioinformatics

• 
  Balaji Veeramani, John W. Raymond, Pritam Chanda:
  DeepSort: deep convolutional networks for sorting haploid maize seeds. 85-93
• 
  Dan Wang, Lusheng Wang:
  GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences. 95-103
• 
  Soumya Kundu, Mukul S. Bansal:
  On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation. 105-115
• 
  Sungtae Kim, Sungkyoung Choi, Jung-Hwan Yoon, Youngsoo Kim, Seungyeoun Lee, Taesung Park:
  Drug response prediction model using a hierarchical structural component modeling method. 117-128
• 
  Jianliang Gao, Bo Song, Xiaohua Hu, Fengxia Yan, Jianxin Wang:
  ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species. 129-135
• 
  Tun-Wen Pai, Kuan-Hung Li, Cing-Han Yang, Chin-Hwa Hu, Han-Jia Lin, Wen-Der Wang, Yet-Ran Chen:
  Multiple model species selection for transcriptomics analysis of non-model organisms. 137-150
• 
  Shengling Wang, Chenyu Wang, Shenling Wang, Liran Ma:
  Big data analysis for evaluating bioinvasion risk. 151-159
• 
  Kaiyuan Zhu, Xiaowen Liu:
  A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra. 161-168
• 
  Jianyu Shi, Hua Huang, Yan-Ning Zhang, Jiang-Bo Cao, Siu-Ming Yiu:
  BMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion. 169-176
• 
  Lishuang Li, Jia Wan, Jieqiong Zheng, Jian Wang:
  Biomedical event extraction based on GRU integrating attention mechanism. 177-184
• 
  Shaoliang Peng, Minxia Cheng, Kaiwen Huang, Yingbo Cui, Zhiqiang Zhang, Runxin Guo, Xiaoyu Zhang, Shunyun Yang, Xiangke Liao, Yutong Lu, Quan Zou, Benyun Shi:
  Efficient computation of motif discovery on Intel Many Integrated Core (MIC) Architecture. 185-194
• 
  Hsin-Yi Tsao, Pei-Ying S. Chan, Emily Chia-Yu Su:
  Predicting diabetic retinopathy and identifying interpretable biomedical features using machine learning algorithms. 195-205

Volume 19-S, Number 10, October 2018

Italian Society of Bioinformatics (BITS): Annual Meeting 2017

• 
  Giuliano Armano, Giorgio Fotia, Andrea Manconi:
  BITS 2017: the annual meeting of the Italian Society of Bioinformatics. 207-210
• 
  Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele A. Calogero:
  Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. 211-219
• 
  Vincenzo Bonnici, Federico Busato, Stefano Aldegheri, Murodzhon Akhmedov, Luciano Cascione, Alberto Arribas Carmena, Francesco Bertoni, Nicola Bombieri, Ivo Kwee, Rosalba Giugno:
  cuRnet: an R package for graph traversing on GPU. 221-230
• 
  Vincenzo Bonnici, Giorgio De Caro, Giorgio Constantino, Sabino Liuni, Domenica D'Elia, Nicola Bombieri, Flavio Licciulli, Rosalba Giugno:
  Arena-Idb: a platform to build human non-coding RNA interaction networks. 231-244
• 
  Emanuel Weitschek, Silvia Di Lauro, Eleonora Cappelli, Paola Bertolazzi, Giovanni Felici:
  CamurWeb: a classification software and a large knowledge base for gene expression data of cancer. 245-256
• 
  Marco Moscatelli, Andrea Manconi, Mauro Pessina, Giovanni Fellegara, Stefano Rampoldi, Luciano Milanesi, Andrea Casasco, Matteo Gnocchi:
  An infrastructure for precision medicine through analysis of big data. 257-267
• 
  Marco Frasca, Giuliano Grossi, Jessica Gliozzo, Marco Mesiti, Marco Notaro, Paolo Perlasca, Alessandro Petrini, Giorgio Valentini:
  A GPU-based algorithm for fast node label learning in large and unbalanced biomolecular networks. 269-280
• 
  Elena Casiraghi, Veronica Huber, Marco Frasca, Mara Cossa, Matteo Tozzi, Licia Rivoltini, Biagio Eugenio Leone, Antonello Villa, Barbara Vergani:
  A novel computational method for automatic segmentation, quantification and comparative analysis of immunohistochemically labeled tissue sections. 281-297
• 
  A. Merlotti, Ìtalo Faria do Valle, Gastone C. Castellani, Daniel Remondini:
  Statistical modelling of CG interdistance across multiple organisms. 299-306

Volume 19-S, Number 11, October 2018

Proceedings from the 6th Workshop on Computational Advances in Molecular Epidemiology (CAME 2017)

• 
  Seth Sims, Atkinson G. Longmire, David S. Campo, Sumathi Ramachandran, Magdalena Medrzycki, Lilia Ganova-Raeva, Yulin Lin, Amanda Sue, Hong Thai, Alexander Zelikovsky, Yury Khudyakov:
  Automated quality control for a molecular surveillance system. 358:1-358:15
• 
  Blake Camp, Jaya Krishna Mandivarapu, Nagashayana Ramamurthy, James Wingo, Anu G. Bourgeois, Xiaojun Cao, Rajshekhar Sunderraman:
  A new cross-platform architecture for epi-info software suite. 359:1-359:8
• 
  Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums:
  Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants. 360:1-360:10
• 
  Fatima Zare, Abdelrahman Hosny, Sheida Nabavi:
  Noise cancellation using total variation for copy number variation detection. 361:1-361:12
• 
  Shrikant D. Pawar, Christopher Freas, Irene T. Weber, Robert W. Harrison:
  Analysis of drug resistance in HIV protease. 362:1-362:6
• 
  Finlay Campbell, Xavier Didelot, Richard G. FitzJohn, Neil M. Ferguson, Anne Cori, Thibaut Jombart:
  outbreaker2: a modular platform for outbreak reconstruction. 363:1-363:8
• 
  Kun Zhao, Elizabeth Henderson, Kelley Bullard, M. Steven Oberste, Cara Burns, Jaume Jorba:
  PoSE: visualization of patterns of sequence evolution using PAML and MATLAB. 364:1-364:7

Volume 19-S, Number 12, October 2018

Reflections on a journey: a retrospective of the ISCB Student Council Symposium series

• 
  Mehedi Hassan, Aishwarya Alex Namasivayam, Dan F. DeBlasio, Nazeefa Fatima, Benjamin Siranosian, R. Gonzalo Parra, Bart Cuypers, Sayane Shome, Alexander Miguel Monzon, Julien Fumey, Farzana Rahman:
  Reflections on a journey: a retrospective of the ISCB Student Council symposium series. 347:1-347:8

Volume 19-S, Number 13, February 2019

17th International Conference on Bioinformatics (InCoB 2018): bioinformatics

• 
  Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu, Shun-Long Weng, Tzong-Yi Lee:
  Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites. 13-25
• 
  Yoshihiro Taguchi:
  Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data. 27-42
• 
  Saverio Candido, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Valentina Di Salvatore, Massimo Libra, Francesco Pappalardo:
  EpiMethEx: a tool for large-scale integrated analysis in methylation hotspots linked to genetic regulation. 43-53
• 
  Hamendra Manhar Reddy, Alok Sharma, Abdollah Dehzangi, Daichi Shigemizu, Abel Avitesh Chandra, Tatsuhiko Tsunoda:
  GlyStruct: glycation prediction using structural properties of amino acid residues. 55-64
• 
  Arpah Abu, Chee Guan Ngo, Nur Idayu Adira Abu-Hassan, Siti Adibah Othman:
  Automated craniofacial landmarks detection on 3D image using geometry characteristics information. 65-80
• 
  Wajdi Dhifli, Júlia Puig, Aurélien Dispot, Mohamed Elati:
  Latent network-based representations for large-scale gene expression data analysis. 81-90
• 
  Yi Zheng, Hui Peng, Shameek Ghosh, Chaowang Lan, Jinyan Li:
  Inverse similarity and reliable negative samples for drug side-effect prediction. 91-104
• 
  Piyush Agrawal, Harinder Singh, Hemant Kumar Srivastava, Sandeep Singh, Gaurav Kishore, Gajendra P. S. Raghava:
  Benchmarking of different molecular docking methods for protein-peptide docking. 105-124
• 
  Rama Kaalia, Jagath C. Rajapakse:
  Functional homogeneity and specificity of topological modules in human proteome. 125-138
• 
  Nurul Aqilah Mohd Nor, Nur Aishah Taib, Marniza Saad, Hana Salwani Zaini, Zahir Ahmad, Yamin Ahmad, Sarinder Kaur Dhillon:
  Development of electronic medical records for clinical and research purposes: the breast cancer module using an implementation framework in a middle income country- Malaysia. 139-154
• 
  Ronesh Sharma, Alok Sharma, Ashwini Patil, Tatsuhiko Tsunoda:
  Discovering MoRFs by trisecting intrinsically disordered protein sequence into terminals and middle regions. 155-163
• 
  Christian Simon, Kristian Davidsen, Christina Hansen, Emily Seymour, Mike Bogetofte Barnkob, Lars Rønn Olsen:
  BioReader: a text mining tool for performing classification of biomedical literature. 165-170
• 
  Shuhaila Mat-Sharani, Mohd Firdaus Raih:
  Computational discovery and annotation of conserved small open reading frames in fungal genomes. 171-185
• 
  Ari Hardianto, Varun Khanna, Fei Liu, Shoba Ranganathan:
  Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε. 187-197
• 
  Deepak R. Bharti, Anmol Hemrom, Andrew M. Lynn:
  GCAC: galaxy workflow system for predictive model building for virtual screening. 199-206
• 
  Sapna M. Borah, Anupam Nath Jha:
  Identification and analysis of structurally critical fragments in HopS2. 207-218
• 
  Manisha Pritam, Garima Singh, Suchit Swaroop, Akhilesh Kumar Singh, Satarudra Prakash Singh:
  Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum. 219-230
• 
  Sagnik Sen, Ashmita Dey, Sourav Chowdhury, Ujjwal Maulik, Krishnananda Chattopadhyay:
  Understanding the evolutionary trend of intrinsically structural disorders in cancer relevant proteins as probed by Shannon entropy scoring and structure network analysis. 231-242
• 
  Duleepa Jayasundara, Damayanthi Herath, Damith A. Senanayake, Isaam Saeed, Cheng-Yu Yang, Yuan Sun, Bill C. Chang, Sen-Lin Tang, Saman K. Halgamuge:
  ENVirT: inference of ecological characteristics of viruses from metagenomic data. 377:1-377:12

Volume 19-S, Number 14, November 2018

Selected articles from the 5th International Work-Conference on Bioinformatics and Biomedical Engineering: bioinformatics

• 
  Yixun Li, Mina Maleki, Nicholas J. Carruthers, Paul M. Stemmer, Alioune Ngom, Luis Rueda:
  The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins. 13-25
• 
  Jian-Yu Shi, Hua Huang, Jia-Xin Li, Peng Lei, Yan-Ning Zhang, Kai Dong, Siu-Ming Yiu:
  TMFUF: a triple matrix factorization-based unified framework for predicting comprehensive drug-drug interactions of new drugs. 27-37
• 
  V. Bleu Knight, Elba E. Serrano:
  Expression analysis of RNA sequencing data from human neural and glial cell lines depends on technical replication and normalization methods. 39-51
• 
  Seyed Ziaeddin Alborzi, David W. Ritchie, Marie-Dominique Devignes:
  Computational discovery of direct associations between GO terms and protein domains. 53-66
• 
  Eleftheria Polychronidou, Ilias Kalamaras, Andreas Agathangelidis, Lesley Ann Sutton, Xiao-Jie Yan, Vasilis Bikos, Anna Vardi, Konstantinos Mochament, Nicholas Chiorazzi, Chrysoula Belessi, Richard Rosenquist, Paolo Ghia, Kostas Stamatopoulos, Panayiotis M. Vlamos, Anna Chailyan, Nanna Overby, Paolo Marcatili, Anastasia Hatzidimitriou, Dimitrios Tzovaras:
  Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia. 67-81
• 
  Elisabeth Yaneske, Claudio Angione:
  The poly-omics of ageing through individual-based metabolic modelling. 83-96
• 
  Pedro Seoane, Marina Espigares, Rosario Carmona, Álvaro Polonio, Julia Quintana, Enrico Cretazzo, Josefina Bota, Alejandro Pérez-García, Juan de Dios Alché, Luis Gómez, M. Gonzalo Claros:
  TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms. 97-114
• 
  Paolo Boldi, Marco Frasca, Dario Malchiodi:
  Evaluating the impact of topological protein features on the negative examples selection. 115-126
• 
  Mattia Antonino Di Gangi, Giosuè Lo Bosco, Riccardo Rizzo:
  Deep learning architectures for prediction of nucleosome positioning from sequences data. 127-135
• 
  Mochammad Arfin Fardiansyah Nasution, Erwin Prasetya Toepak, Ahmad Husein Alkaff, Usman Sumo Friend Tambunan:
  Flexible docking-based molecular dynamics simulation of natural product compounds and Ebola virus Nucleocapsid (EBOV NP): a computational approach to discover new drug for combating Ebola. 137-149
• 
  Diogo Manuel Carvalho Leite, Xavier Brochet, Grégory Resch, Yok-Ai Que, Aitana Neves, Carlos A. Peña-Reyes:
  Computational prediction of inter-species relationships through omics data analysis and machine learning. 151-159
• 
  Jesús Pérez Serrano, Edans F. de O. Sandes, Alba Cristina Magalhaes Alves de Melo, Manuel Ujaldón:
  DNA sequences alignment in multi-GPUs: acceleration and energy payoff. 161-176
• 
  Guillaume Devailly, Anagha Joshi:
  Insights into mammalian transcription control by systematic analysis of ChIP sequencing data. 409:1-409:11

Volume 19-S, Number 17, December 2018

• 
  Yong He, Jiadong Ji, Lei Xie, Xinsheng Zhang, Fuzhong Xue:
  A new insight into underlying disease mechanism through semi-parametric latent differential network model. 5-19
• 
  Ziwei Li, Bo He, Qiang Kou, Zhe Wang, Si Wu, Yunlong Liu, Weixing Feng, Xiaowen Liu:
  Evaluation of top-down mass spectral identification with homologous protein sequences. 21-28
• 
  Junhui Shen, Suhas V. Vasaikar, Bing Zhang:
  DLAD4U: deriving and prioritizing disease lists from PubMed literature. 29-37
• 
  Tong Liu, Zheng Wang:
  Reconstructing high-resolution chromosome three-dimensional structures by Hi-C complex networks. 39-50
• 
  Saugato Rahman Dhruba, Raziur Rahman, Kevin Matlock, Souparno Ghosh, Ranadip Pal:
  Application of transfer learning for cancer drug sensitivity prediction. 51-63
• 
  Zexian Zeng, Sasa Espino, Ankita Roy, Xiaoyu Li, Seema A. Khan, Susan E. Clare, Xia Jiang, Richard E. Neapolitan, Yuan Luo:
  Using natural language processing and machine learning to identify breast cancer local recurrence. 65-74
• 
  Shanta Chowdhury, Xishuang Dong, Lijun Qian, Xiangfang Li, Yi Guan, Jinfeng Yang, Qiubin Yu:
  A multitask bi-directional RNN model for named entity recognition on Chinese electronic medical records. 75-84
• 
  Chunlei Zheng, Rong Xu:
  Large-scale mining disease comorbidity relationships from post-market drug adverse events surveillance data. 85-93
• 
  Atlas Khan, Qian Liu, Kai Wang:
  iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes. 95-107
• 
  Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan, Degui Zhi:
  The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. 492:1-492:3

Volume 19-S, Number 18, December 2018

Selected Articles from the Computational Approaches for Cancer at SC17 workshop

• 
  Nicolas W. Hengartner, Leticia Cuellar, Xiao-Cheng Wu, Georgia D. Tourassi, John X. Qiu, James Blair Christian, Tanmoy Bhattacharya:
  CAT: computer aided triage improving upon the Bayes risk through ε-refusal triage rules. 3-8
• 
  Will Fischer, Sanketh S. Moudgalya, Judith D. Cohn, Nga T. T. Nguyen, Garrett T. Kenyon:
  Sparse coding of pathology slides compared to transfer learning with deep neural networks. 9-17
• 
  Ahmed Sanaullah, Chen Yang, Yuri Alexeev, Kazutomo Yoshii, Martin C. Herbordt:
  Real-time data analysis for medical diagnosis using FPGA-accelerated neural networks. 19-31
• 
  Jumana Dakka, Matteo Turilli, David W. Wright, Stefan J. Zasada, Vivek Balasubramanian, Shunzhou Wan, Peter V. Coveney, Shantenu Jha:
  High-throughput binding affinity calculations at extreme scales. 33-45
• 
  Debsindhu Bhowmik, Shang Gao, Michael T. Young, Arvind Ramanathan:
  Deep clustering of protein folding simulations. 47-58
• 
  Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson T. Collier, John Bauer, Fangfang Xia, Thomas S. Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia-Cardona, Brian Van Essen, Matthew Baughman:
  CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research. 59-69
• 
  Fangfang Xia, Maulik Shukla, Thomas S. Brettin, Cristina Garcia-Cardona, Judith D. Cohn, Jonathan E. Allen, Sergei Maslov, Susan L. Holbeck, James H. Doroshow, Yvonne A. Evrard, Eric A. Stahlberg, Rick L. Stevens:
  Predicting tumor cell line response to drug pairs with deep learning. 71-79
• 
  Jonathan Ozik, Nicholson T. Collier, Justin M. Wozniak, Charles M. Macal, Chase Cockrell, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Randy W. Heiland, Gary An, Paul Macklin:
  High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. 81-97
• 
  John X. Qiu, Hong-Jun Yoon, Kshitij Srivastava, Thomas P. Watson, James Blair Christian, Arvind Ramanathan, Xiao-Cheng Wu, Paul A. Fearn, Georgia D. Tourassi:
  Scalable deep text comprehension for Cancer surveillance on high-performance computing. 99-110
• 
  Sunita Chandrasekaran, Eric Stahlberg:
  Computational approaches for Cancer 2017 workshop overview. 487:1-487:2

Volume 19-S, Number 19, December 2018

Proceedings of the 29th International Conference on Genome Informatics (GIW 2018): bioinformatics

• 
  Zhoujian Xiao, Yuwei Zhang, Runsheng Yu, Yin Chen, Xiaosen Jiang, Ziwei Wang, Shuaicheng Li:
  In silico design of MHC class I high binding affinity peptides through motifs activation map. 13-24
• 
  Yuanlin Ma, Zu-Guo Yu, Guo-Sheng Han, Jinyan Li, Vo Anh:
  Identification of pre-microRNAs by characterizing their sequence order evolution information and secondary structure graphs. 25-35
• 
  Lichun Ma, Jie Zheng:
  Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes. 37-48
• 
  Yi Zheng, Hui Peng, Xiaocai Zhang, Zhixun Zhao, Jie Yin, Jinyan Li:
  Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases. 49-59
• 
  Weijia Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li:
  Estimating heterogeneous treatment effect by balancing heterogeneity and fitness. 61-72
• 
  Cheng Yan, Jianxin Wang, Fang-Xiang Wu:
  DWNN-RLS: regularized least squares method for predicting circRNA-disease associations. 73-81
• 
  Maya Hirohara, Yutaka Saito, Yuki Koda, Kengo Sato, Yasubumi Sakakibara:
  Convolutional neural network based on SMILES representation of compounds for detecting chemical motif. 83-94
• 
  Yingying Wang, Hongyan Wu, Yunpeng Cai:
  A benchmark study of sequence alignment methods for protein clustering. 95-104
• 
  Long Zhang, Guoxian Yu, Maozu Guo, Jun Wang:
  Predicting protein-protein interactions using high-quality non-interacting pairs. 105-124
• 
  Xi Yang, Zhuo Song, Chengkun Wu, Wei Wang, Gen Li, Wei Zhang, Lingqian Wu, Kai Lu:
  Constructing a database for the relations between CNV and human genetic diseases via systematic text mining. 125-134
• 
  Lei Deng, Juan Pan, Xiaojie Xu, Wenyi Yang, Chuyao Liu, Hui Liu:
  PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine. 135-145
• 
  Shengbing Pei, Jihong Guan, Shuigeng Zhou:
  Classifying early and late mild cognitive impairment stages of Alzheimer's disease by fusing default mode networks extracted with multiple seeds. 147-155
• 
  Takashi Tajimi, Naoki Wakui, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama:
  Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques. 157-170
• 
  Ko Abe, Masaaki Hirayama, Kinji Ohno, Teppei Shimamura:
  A latent allocation model for the analysis of microbial composition and disease. 171-177
• 
  Taosheng Xu, Ning Su, Lin Liu, Junpeng Zhang, Hongqiang Wang, Weijia Zhang, Jie Gui, Kui Yu, Jiuyong Li, Thuc Duy Le:
  miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase. 179-188
• 
  Yiqian Zhang, Michiaki Hamada:
  DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning. 524:1-524:11

Volume 19-S, Number 20, December 2018

Selected articles from the IEEE BIBM International Conference on Bioinformatics & Biomedicine (BIBM) 2017: bioinformatics

• 
  Guifeng Tang, Jingwen Shi, Wenjian Wu, Xiang Yue, Wen Zhang:
  Sequence-based bacterial small RNAs prediction using ensemble learning strategies. 13-23
• 
  Nhat Tran, Vinay Abhyankar, Kytai Nguyen, Jon Weidanz, Jean Gao:
  MicroRNA dysregulational synergistic network: discovering microRNA dysregulatory modules across subtypes in non-small cell lung cancers. 25-36
• 
  Xianchao Zhu, Xianjun Shen, Xingpeng Jiang, Kaiping Wei, Tingting He, Yuanyuan Ma, Jiaqi Liu, Xiaohua Hu:
  Nonlinear expression and visualization of nonmetric relationships in genetic diseases and microbiome data. 37-48
• 
  Rosario I. Corona, Sanjana Sudarshan, Srinivas Aluru, Jun-tao Guo:
  An SVM-based method for assessment of transcription factor-DNA complex models. 49-57
• 
  Yan Wang, Jian Wang, Hongfei Lin, Xiwei Tang, Shaowu Zhang, Lishuang Li:
  Bidirectional long short-term memory with CRF for detecting biomedical event trigger in FastText semantic space. 59-66
• 
  Zachary Stephens, Chen Wang, Ravishankar K. Iyer, Jean-Pierre A. Kocher:
  Detection and visualization of complex structural variants from long reads. 67-77
• 
  Timothy Chappell, Shlomo Geva, James M. Hogan, Flavia Huygens, Irani U. Rathnayake, Stephen Rudd, Wayne Kelly, Dimitri Perrin:
  Rapid analysis of metagenomic data using signature-based clustering. 79-93
• 
  Yongping Du, Yunpeng Pan, Chencheng Wang, Junzhong Ji:
  Biomedical semantic indexing by deep neural network with multi-task learning. 502:1-502:11

Volume 19-S, Number 21, December 2018

Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics part 2

• 
  Sanjoy Dey, Heng Luo, Achille Fokoue, Jianying Hu, Ping Zhang:
  Predicting adverse drug reactions through interpretable deep learning framework. 476:1-476:13