BMC Bioinformatics, Volume 21 - Supplements

Volume 21-S, Number 1, December 2020

Selected articles from the 8th IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS 2018): bioinformatics

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  Daniel Ruiz-Perez, Haibin Guan, Purnima Madhivanan, Kalai Mathee, Giri Narasimhan:
  So you think you can PLS-DA? 2
• 
  Chunchun Zhao, Sartaj Sahni:
  Linear space string correction algorithm using the Damerau-Levenshtein distance. 4
• 
  Nasrin Akhter, Gopinath Chennupati, Hristo Djidjev, Amarda Shehu:
  Decoy selection for protein structure prediction via extreme gradient boosting and ranking. 189
• 
  Dina Abdelhafiz, Jinbo Bi, Reda Ammar, Clifford Yang, Sheida Nabavi:
  Convolutional neural network for automated mass segmentation in mammography. 192
• 
  Simone Ciccolella, Mauricio Soto Gomez, Murray D. Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni:
  gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. 413
• 
  L. M. Hall, Audrey E. Hendricks:
  High-throughput analysis suggests differences in journal false discovery rate by subject area and impact factor but not open access status. 564
• 
  Federico Marini, Jan Linke, Harald Binder:
  ideal: an R/Bioconductor package for interactive differential expression analysis. 565
• 
  Jieyue He, Xinxing Yang, Zhuo Gong, lbrahim Zamit:
  Hybrid attentional memory network for computational drug repositioning. 566
• 
  Kai-Yao Huang, Fang-Yu Hung, Hui-Ju Kao, Hui-Hsuan Lau, Shun-Long Weng:
  iDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features. 568
• 
  Matt Velinder, Dillon Lee, Gabor Marth:
  ped_draw: pedigree drawing with ease. 569

Volume 21-S, Number 4, July 2020

Proceedings of the 16th Annual MCBIOS Conference: bioinformatics

• 
  Tong Liu, Zheng Wang:
  MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials. 246
• 
  Yongsheng Bai, Steve Baker, Kevin Exoo, Xingqin Dai, Lizhong Ding, Naureen Aslam Khattak, Hongtao Li, Hannah Liu, Xiaoming Liu:
  MMiRNA-Viewer², a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network. 247
• 
  Hafez Eslami Manoochehri, Mehrdad Nourani:
  Drug-target interaction prediction using semi-bipartite graph model and deep learning. 248
• 
  Adam Thrash, Federico Hoffmann, Andy Perkins:
  Toward a more holistic method of genome assembly assessment. 249
• 
  Jonathan D. Wren, Yongsheng Bai, Zhaohui S. Qin, Da Yan, Ramin Homayouni:
  Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. 254
• 
  Mahmut Karakaya, Recep E. Hacisoftaoglu:
  Comparison of smartphone-based retinal imaging systems for diabetic retinopathy detection using deep learning. 259

Volume 21-S, Number 5, October 2020

Proceedings of the 13th International Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO 2019)

• 
  Myeong-Sang Yu, Jingyu Lee, Yongmin Lee, Dokyun Na:
  2-D chemical structure image-based in silico model to predict agonist activity for androgen receptor. 245
• 
  Jaehyun Lee, Doheon Lee, Kwang Hyung Lee:
  Literature mining for context-specific molecular relations using multimodal representations (COMMODAR). 250
• 
  Qing Xie, Kyoung Min Yang, Go Eun Heo, Min Song:
  Literature based discovery of alternative TCM medicine for adverse reactions to depression drugs. 405
• 
  Hyoung-Kyu Song, Ebrahim Al Alkeem, Jaewoong Yun, Tae-Ho Kim, Hyerin Yoo, Dasom Heo, Myungsu Chae, Chan Yeob Yeun:
  Correction to: Deep user identification model with multiple biometric data. 421

Volume 21-S, Number 6, November 2020

Selected articles from the 15th International Symposium on Bioinformatics Research and Applications (ISBRA-19): bioinformatics

• 
  Jin Liu, Guanxin Tan, Wei Lan, Jianxin Wang:
  Identification of early mild cognitive impairment using multi-modal data and graph convolutional networks. 123
• 
  Jianqiang Li, Guanghui Fu, Yueda Chen, Pengzhi Li, Bo Liu, Yan Pei, Hui Feng:
  A multi-label classification model for full slice brain computerised tomography image. 200
• 
  Lun Li, Renmin Han, Zhaotian Zhang, Tiande Guo, Zhiyong Liu, Fa Zhang:
  Compressed sensing improved iterative reconstruction-reprojection algorithm for electron tomography. 202
• 
  Wessam Elhefnawy, Min Li, Jianxin Wang, Yaohang Li:
  DeepFrag-k: a fragment-based deep learning approach for protein fold recognition. 203
• 
  Yuanyuan Ma, Junmin Zhao, Yingjun Ma:
  MHSNMF: multi-view hessian regularization based symmetric nonnegative matrix factorization for microbiome data analysis. 234
• 
  Nikita Alexeev, Javlon E. Isomurodov, Vladimir Sukhov, Gennady Korotkevich, Alexey A. Sergushichev:
  Markov chain Monte Carlo for active module identification problem. 261
• 
  Adrià Alcalà, Ricardo Alberich, Mercè Llabrés, Francesc Rosselló, Gabriel Valiente:
  AligNet: alignment of protein-protein interaction networks. 265
• 
  Yi-Wei Liu, Tz-Wei Hsu, Che-Yu Chang, Wen-Hung Liao, Jia-Ming Chang:
  GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms. 276
• 
  Xinyu Hu, Li Tang, Linconghua Wang, Fang-Xiang Wu, Min Li:
  MADA: a web service for analysing DNA methylation array data. 403
• 
  Sriram P. Chockalingam, Jodh Pannu, Sahar Hooshmand, Sharma V. Thankachan, Srinivas Aluru:
  An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction. 404
• 
  Mercè Llabrés, Gabriel Riera, Francesc Rosselló, Gabriel Valiente:
  Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks. 434

Volume 21-S, Number 8, September 2020

Italian Society of Bioinformatics (BITS): Annual Meeting 2019

• 
  Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo, Alfonso Urso:
  miRTissue _ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions. 199
• 
  Giorgio Bertolazzi, Panayiotis V. Benos, Michele Tumminello, Claudia Coronnello:
  An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs. 201
• 
  Nicola Prezza, Nadia Pisanti, Marinella Sciortino, Giovanna Rosone:
  Variable-order reference-free variant discovery with the Burrows-Wheeler Transform. 260
• 
  Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva:
  The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses. 262
• 
  Castrense Savojardo, Pier Luigi Martelli, Giacomo Tartari, Rita Casadio:
  Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito. 266
• 
  Veronica Guerrini, Felipe A. Louza, Giovanna Rosone:
  Metagenomic analysis through the extended Burrows-Wheeler transform. 299
• 
  Isabella Mendolia, Salvatore Contino, Ugo Perricone, Edoardo Ardizzone, Roberto Pirrone:
  Convolutional architectures for virtual screening. 310
• 
  Alessandro Stefano, Albert Comelli, Valentina Bravatà, Stefano Barone, Igor Daskalovski, Gaetano Savoca, Maria Gabriella Sabini, Massimo Ippolito, Giorgio Russo:
  A preliminary PET radiomics study of brain metastases using a fully automatic segmentation method. 325
• 
  Domenico Amato, Giosuè Lo Bosco, Riccardo Rizzo:
  CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification. 326
• 
  Paolo Castagno, Simone Pernice, Gianni Ghetti, Massimiliano Povero, Lorenzo Pradelli, Daniela Paolotti, Gianfranco Balbo, Matteo Sereno, Marco Beccuti:
  A computational framework for modeling and studying pertussis epidemiology and vaccination. 344
• 
  Alfonso Urso, Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Giosuè Lo Bosco, Riccardo Rizzo:
  BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics. 363

Volume 21-S, Number 9, December 2020

Selected Articles from the 20th International Conference on Bioinformatics & Computational Biology (BIOCOMP 2019)

• 
  Casey A. Cole, Caleb Parks, Julian Rachele, Homayoun Valafar:
  Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package. 204
• 
  Qingyang Zhang, Thy Dao:
  A distance based multisample test for high-dimensional compositional data with applications to the human microbiome. 205
• 
  Mona Maharjan, Raihanul Bari Tanvir, Kamal Chowdhury, Wenrui Duan, Ananda Mohan Mondal:
  Computational identification of biomarker genes for lung cancer considering treatment and non-treatment studies. 218
• 
  Zongtao Yu, Yuanyuan Fu, Junmei Ai, Jicai Zhang, Gang Huang, Youping Deng:
  Development of predicitve models to distinguish metals from non-metal toxicants, and individual metal from one another. 239
• 
  Rebecca M. Rodriguez, Vedbar S. Khadka, Mark Menor, Brenda Y. Hernandez, Youping Deng:
  Tissue-associated microbial detection in cancer using human sequencing data. 523
• 
  Yuanyuan Fu, Zhougui Ling, Hamid R. Arabnia, Youping Deng:
  Current trend and development in bioinformatics research. 538
• 
  Fan Zhang, Chris K. Deng, Mu Wang, Bin Deng, Robert Barber, Gang Huang:
  Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq. 541

Volume 21-S, Number 10, August 2020

Proceedings from the 13th Bioinformatics and Computational Biology International Conference - BBCC2018

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  Alessio Mancini, Leonardo Vito, Elisa Marcelli, Marco Piangerelli, Renato De Leone, Sandra Pucciarelli, Emanuela Merelli:
  Machine learning models predicting multidrug resistant urinary tract infections using "DsaaS". 347
• 
  Ludovica Liguori, Maria Monticelli, Mariateresa Allocca, Maria Vittoria Cubellis, Bruno Hay Mele:
  Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach. 348
• 
  Ichcha Manipur, Ilaria Granata, Lucia Maddalena, Mario R. Guarracino:
  Clustering analysis of tumor metabolic networks. 349
• 
  Angelo Ciaramella, Davide Nardone, Antonino Staiano:
  Data integration by fuzzy similarity-based hierarchical clustering. 350
• 
  Luisa Cutillo, Alexis Boukouvalas, Elli Marinopoulou, Nancy Papalopulu, Magnus Rattray:
  OscoNet: inferring oscillatory gene networks. 351
• 
  Tiziana Castrignanò, Silvia Gioiosa, Tiziano Flati, Mirko Cestari, Ernesto Picardi, Matteo Chiara, Maddalena Fratelli, Stefano Amente, Marco Cirilli, Marco Antonio Tangaro, Giovanni Chillemi, Graziano Pesole, Federico Zambelli:
  ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community. 352
• 
  Tiziano Flati, Silvia Gioiosa, Nicola Spallanzani, Ilario Tagliaferri, Maria Angela Diroma, Graziano Pesole, Giovanni Chillemi, Ernesto Picardi, Tiziana Castrignanò:
  HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis. 353
• 
  Irene Righetto, Francesco Filippini:
  Normal modes analysis and surface electrostatics of haemagglutinin proteins as fingerprints for high pathogenic type A influenza viruses. 354

Volume 21-S, Number 11, September 2020

Selected Topics in "Systems Biology and Bioinformatics" - 2019: bioinformatics

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  Timofey V. Ivanisenko, Olga V. Saik, Pavel S. Demenkov, Nikita V. Ivanisenko, Alexander N. Savostianov, Vladimir A. Ivanisenko:
  ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature. 228
• 
  Vitali A. Likhoshvai, Vladimir P. Golubyatnikov, Tamara M. Khlebodarova:
  Limit cycles in models of circular gene networks regulated by negative feedback loops. 255
• 
  Tamara M. Khlebodarova, Vladislav V. Kogai, Vitali A. Likhoshvai:
  On the dynamical aspects of local translation at the activated synapse. 258
• 
  Mila Efimenko, Alexander Ignatev, Konstantin Koshechkin:
  Review of medical image recognition technologies to detect melanomas using neural networks. 270
• 
  Anastasia A. Anashkina, Yuri M. Poluektov, Vladimir A. Dmitriev, Eugene N. Kuznetsov, Vladimir A. Mitkevich, Alexander A. Makarov, Irina Yu. Petrushanko:
  A novel approach for predicting protein S-glutathionylation. 282
• 
  Valery Polyanovsky, Alexander Lifanov, Natalia G. Esipova, Vladimir G. Tumanyan:
  The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion. 294
• 
  Yuriy L. Orlov, Elvira R. Galieva, Tatiana V. Tatarinova:
  Bioinformatics research at SBB-2019. 366

Volume 21-S, Number 12, July 2020

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

• 
  Andrey D. Prjibelski, Giuseppe D. Puglia, Dmitry Antipov, Elena Bushmanova, Daniela Giordano, Alla Mikheenko, Domenico Vitale, Alla L. Lapidus:
  Extending rnaSPAdes functionality for hybrid transcriptome assembly. 302
• 
  Yulia Kondratenko, Anton I. Korobeynikov, Alla L. Lapidus:
  CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities. 303
• 
  Gennady V. Khvorykh, Andrey V. Khrunin:
  imputeqc: an R package for assessing imputation quality of genotypes and optimizing imputation parameters. 304
• 
  Maria A. Daugavet, Sergey V. Shabelnikov, Olga I. Podgornaya:
  Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer. 305
• 
  Tatiana Dvorkina, Dmitry Antipov, Anton I. Korobeynikov, Sergey Nurk:
  SPAligner: alignment of long diverged molecular sequences to assembly graphs. 306

Volume 21-S, Number 13, September 2020

Selected articles from the 18th Asia Pacific Bioinformatics Conference (APBC 2020): bioinformatics

• 
  Jinling Liu, Xiaojun Ma, Gregory F. Cooper, Xinghua Lu:
  Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks. 379
• 
  Jian Wang, Mengying Li, Qishuai Diao, Hongfei Lin, Zhihao Yang, Yi-Jia Zhang:
  Biomedical document triage using a hierarchical attention-based capsule network. 380
• 
  Ke Li, Sijia Zhang, Di Yan, Yannan Bin, Junfeng Xia:
  Prediction of hot spots in protein-DNA binding interfaces based on supervised isometric feature mapping and extreme gradient boosting. 381
• 
  Sangwoo Lee, Eun Kyung Choe, So Yeon Kim, Hua Sun Kim, Kyu Joo Park, Dokyoon Kim:
  Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan. 382
• 
  Yujie You, Xufang Ru, Wanjing Lei, Tingting Li, Ming Xiao, Huiru Zheng, Yujie Chen, Le Zhang:
  Developing the novel bioinformatics algorithms to systematically investigate the connections among survival time, key genes and proteins for Glioblastoma multiforme. 383
• 
  Yuliang Pan, Shuigeng Zhou, Jihong Guan:
  Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach. 384
• 
  Yuanke Zhong, Jing Li, Junhao He, Yiqun Gao, Jie Liu, Jingru Wang, Xuequn Shang, Jialu Hu:
  Twadn: an efficient alignment algorithm based on time warping for pairwise dynamic networks. 385
• 
  Sudipta Acharya, Laizhong Cui, Yi Pan:
  A consensus multi-view multi-objective gene selection approach for improved sample classification. 386
• 
  Renyi Zhou, Zhangli Lu, Huimin Luo, Ju Xiang, Min Zeng, Min Li:
  NEDD: a network embedding based method for predicting drug-disease associations. 387
• 
  Nauman Ahmed, Tong Dong Qiu, Koen Bertels, Zaid Al-Ars:
  GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads. 388
• 
  Yang-Chi-Dung Lin, Hsi-Yuan Huang, Sirjana Shrestha, Chih-Hung Chou, Yen-Hua Chen, Chi-Ru Chen, Hsiao-Chin Hong, Jing Li, Yi-An Chang, Men-Yee Chiew, Ya-Rong Huang, Siang-Jyun Tu, Ting-Hsuan Sun, Shun-Long Weng, Ching-Ping Tseng, Hsien-Da Huang:
  Multi-omics profiling reveals microRNA-mediated insulin signaling networks. 389
• 
  Benjamin Albrecht, Caner Bagci, Daniel H. Huson:
  MAIRA- real-time taxonomic and functional analysis of long reads on a laptop. 390
• 
  Yongchun Lü, Xiangrui Zeng, Xinhui Tian, Xiao Shi, Hui Wang, Xiaohui Zheng, Xiaodong Liu, Xiaofang Zhao, Xin Gao, Min Xu:
  Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation. 391
• 
  Xiaoyang Chen, Shengquan Chen, Rui Jiang:
  EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes. 392
• 
  Ko Abe, Kodai Minoura, Yuka Maeda, Hiroyoshi Nishikawa, Teppei Shimamura:
  Model-based clustering for flow and mass cytometry data with clinical information. 393
• 
  Jiajie Peng, Jingyi Li, Xuequn Shang:
  A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network. 394

Volume 21-S, Number 14, September 2020

Selected original articles from the Sixth International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2019): bioinformatics

• 
  Nahim Adnan, Chengwei Lei, Jianhua Ruan:
  Robust edge-based biomarker discovery improves prediction of breast cancer metastasis. 359
• 
  Evan A. Clayton, Toyya A. Pujol, John F. McDonald, Peng Qiu:
  Leveraging TCGA gene expression data to build predictive models for cancer drug response. 364
• 
  Md. Abid Hasan, Stefano Lonardi:
  DeeplyEssential: a deep neural network for predicting essential genes in microbes. 367
• 
  Talip Zengin, Tugba Onal Suzek:
  Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma. 368
• 
  Chanaka Bulathsinghalage, Lu Liu:
  Network-based method for regions with statistically frequent interchromosomal interactions at single-cell resolution. 369
• 
  Chunrui Xu, Bronson R. Weston, John J. Tyson, Yang Cao:
  Cell cycle control and environmental response by second messengers in Caulobacter crescentus. 408

Volume 21-S, Number 16, December 2020

Selected articles from the Biological Ontologies and Knowledge bases workshop 2019

• 
  Guangjie Zhou, Jun Wang, Xiangliang Zhang, Maozu Guo, Guoxian Yu:
  Predicting functions of maize proteins using graph convolutional network. 420
• 
  Huijuan Xu, Hairong Wang, Chenshan Yuan, Qinghua Zhai, Xufeng Tian, Lei Wu, Yuanyuan Mi:
  Identifying diseases that cause psychological trauma and social avoidance by GCN-Xgboost. 504
• 
  Leilei Liu, Xianglei Zhu, Yi Ma, Haiyin Piao, Yaodong Yang, Xiaotian Hao, Yue Fu, Li Wang, Jiajie Peng:
  Combining sequence and network information to enhance protein-protein interaction prediction. 537
• 
  Ruiyu Xiao, Guoshan Lu, Wanqian Guo, Shuilin Jin:
  NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data. 540
• 
  Rui Xing, Jie Luo, Tengwei Song:
  BioRel: towards large-scale biomedical relation extraction. 543
• 
  Yongzhuang Liu, Jian Liu, Yadong Wang:
  Filtering de novo indels in parent-offspring trios. 547
• 
  Tianyi Zhao, Yang Hu, Tianyi Zang:
  DRACP: a novel method for identification of anticancer peptides. 559
• 
  Xiaoshi Zhong, Jagath C. Rajapakse:
  Graph embeddings on gene ontology annotations for protein-protein interaction prediction. 560

Volume 21-S, Number 17, December 2020

Selected papers from the 3rd International Workshop on Computational Methods for the Immune System Function (CMISF 2019)

• 
  Miguel A. Juárez, Marzio Pennisi, Giulia Russo, Dimitrios Kiagias, Cristina Curreli, Marco Viceconti, Francesco Pappalardo:
  Generation of digital patients for the simulation of tuberculosis with UISS-TB. 449
• 
  Giulia Russo, Giuseppe Sgroi, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Miguel A. Juárez, Pere-Joan Cardona, Santo Motta, Kenneth B. Walker, Epifanio Fichera, Marco Viceconti, Francesco Pappalardo:
  Moving forward through the in silico modeling of tuberculosis: a further step with UISS-TB. 458
• 
  Ping Zhang, Tegan Roberts, Brent Richards, Luke J. Haseler:
  Utilizing heart rate variability to predict ICU patient outcome in traumatic brain injury. 481
• 
  Marta Gomez-Perosanz, Alvaro Ras-Carmona, Esther M. Lafuente, Pedro A. Reche:
  Identification of CD8⁺ T cell epitopes through proteasome cleavage site predictions. 484
• 
  Paola Stolfi, Ilaria Valentini, Maria Concetta Palumbo, Paolo Tieri, Andrea Grignolio, Filippo Castiglione:
  Potential predictors of type-2 diabetes risk: machine learning, synthetic data and wearable health devices. 508
• 
  Giulia Russo, Marzio Pennisi, Epifanio Fichera, Santo Motta, Giuseppina Raciti, Marco Viceconti, Francesco Pappalardo:
  In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform. 527
• 
  Francesco Pappalardo, Giulia Russo, Pedro A. Reche:
  Toward computational modelling on immune system function. 546
• 
  Simone Pernice, Laura Follia, Alessandro Maglione, Marzio Pennisi, Francesco Pappalardo, Francesco Novelli, Marinella Clerico, Marco Beccuti, Francesca Cordero, Simona Rolla:
  Computational modeling of the immune response in multiple sclerosis using epimod framework. 550
• 
  Carla Rezende Barbosa Bonin, Guilherme Côrtes Fernandes, Reinaldo de Menezes Martins, Luiz Antonio Bastos Camacho, Andréa Teixeira-Carvalho, Lícia Maria Henrique da Mota, Sheila Maria Barbosa de Lima, Ana Carolina Campi-Azevedo, Olindo Assis Martins-Filho, Rodrigo Weber dos Santos, Marcelo Lobosco:
  Validation of a yellow fever vaccine model using data from primary vaccination in children and adults, re-vaccination and dose-response in adults and studies with immunocompromised individuals. 551
• 
  Bernhard Roither, Chris Oostenbrink, Wolfgang Schreiner:
  Molecular dynamics of the immune checkpoint programmed cell death protein I, PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab. 557

Volume 21-S, Number 18, December 2020

• 
  David S. Campo, Yury Khudyakov:
  Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences. 482
• 
  Sudipta Acharya, Laizhong Cui, Yi Pan:
  Multi-view feature selection for identifying gene markers: a diversified biological data driven approach. 483
• 
  Dhara Shah, Christopher Freas, Irene T. Weber, Robert W. Harrison:
  Evolution of drug resistance in HIV protease. 497
• 
  Elham Sherafat, Jordan Force, Ion I. Mandoiu:
  Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy. 498
• 
  Deeptanshu Jha, Rahul Singh:
  Analysis of associations between emotions and activities of drug users and their addiction recovery tendencies from social media posts using structural equation modeling. 554
• 
  Noel-Marie Plonski, Emily Johnson, Madeline Frederick, Heather Mercer, Gail Fraizer, Richard Meindl, Gemma Casadesus, Helen Piontkivska:
  Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data. 578

Volume 21-S, Number 19, December 2020

Proceedings from the Joint NETTAB/BBCC 2019 Conference

• 
  Maciej Rybinski, Sarvnaz Karimi, Vincent Nguyen, Cécile Paris:
  A2A: a platform for research in biomedical literature search. 572
• 
  Yasaman Karami, Paul Saighi, Rémy Vanderhaegen, Denis Gerlier, Sonia Longhi, Elodie Laine, Alessandra Carbone:
  Predicting substitutions to modulate disorder and stability in coiled-coils. 573
• 
  Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini, Maria Paola Martelli:
  ARPIR: automatic RNA-Seq pipelines with interactive report. 574
• 
  Munira Alballa, Gregory Butler:
  Integrative approach for detecting membrane proteins. 575

Volume 21-S, Number 20, December 2020

Selected abstracts of Bioinformatics: from Algorithms to Applications 2020 conference

•