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

• 
  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 N. 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, Ibrahim 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 2, March 2020

• 
  Xin Guan, George Runger, Li Liu:
  Dynamic incorporation of prior knowledge from multiple domains in biomarker discovery. 77
• 
  Yixuan Wang, Xuanping Zhang, Xiao Xiao, Fei-Ran Zhang, Xinxing Yan, Xuan Feng, Zhongmeng Zhao, Yanfang Guan, Jiayin Wang:
  Accurately estimating the length distributions of genomic micro-satellites by tumor purity deconvolution. 82
• 
  Michael G. Sadovsky, Masha Yu. Senashova, Andrew Malyshev:
  Amazing symmetrical clustering in chloroplast genomes. 83
• 
  Sara Nasiri, Julien Helsper, Matthias Jung, Madjid Fathi:
  DePicT Melanoma Deep-CLASS: a deep convolutional neural networks approach to classify skin lesion images. 84
• 
  Renzo Angles, Mauricio Arenas-Salinas, Roberto García, José Antonio Reyes-Suárez, Ehmke Pohl:
  GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns. 85
• 
  Hayman Saddik, Riad Nasr, Antonio Pinti, Eric Watelain, Ibrahim Fayad, Rafic Baddoura, Abdel-Jalil Berro, Nathalie Al Rassy, Eric Lespessailles, Hechmi Toumi, Rawad El Hage:
  Sarcopenia negatively affects hip structure analysis variables in a group of Lebanese postmenopausal women. 86
• 
  Galina V. Zhikhareva, Mikhail N. Kramm, Oleg N. Bodin, Ralf Seepold, Natividad Martínez Madrid, Anton I. Chernikov, Yana A. Kupriyanova, Natalija A. Zhuravleva:
  Conversion from electrocardiosignals to equivalent electrical sources on heart surface. 87
• 
  Ayca Kirimtat, Ondrej Krejcar, Ali Selamat, Enrique Herrera-Viedma:
  FLIR vs SEEK thermal cameras in biomedicine: comparative diagnosis through infrared thermography. 88
• 
  Ana Cernea, Juan Luis Fernández Martínez, Enrique J. deAndrés-Galiana, Francisco Javier Fernández-Ovies, Óscar Álvarez-Machancoses, Zulima Fernández-Muñiz, Leorey N. Saligan, Stephen T. Sonis:
  Robust pathway sampling in phenotype prediction. Application to triple negative breast cancer. 89
• 
  Hynek Bachratý, Katarína Bachratá, Michal Chovanec, Iveta Jancigová, Monika Smiesková, Kristína Kovalcíková:
  Applications of machine learning for simulations of red blood cells in microfluidic devices. 90
• 
  Annarita Fanizzi, Teresa M. A. Basile, Liliana Losurdo, Roberto Bellotti, Ubaldo Bottigli, Rosalba Dentamaro, Vittorio Didonna, Alfonso Fausto, Raffaella Massafra, Marco Moschetta, Ondina Popescu, Pasquale Tamborra, Sabina Tangaro, Daniele La Forgia:
  A machine learning approach on multiscale texture analysis for breast microcalcification diagnosis. 91
• 
  Cristina Soguero-Ruíz, Inmaculada Mora-Jiménez, Miguel A. Mohedano-Munoz, Manuel Rubio-Sánchez, Pablo de Miguel-Bohoyo, Alberto Sánchez:
  Visually guided classification trees for analyzing chronic patients. 92
• 
  Ping Luo, Li-Ping Tian, Bolin Chen, Qianghua Xiao, Fang-Xiang Wu:
  Ensemble disease gene prediction by clinical sample-based networks. 79

Volume 21-S, Number 3, April 2020

• 
  Munira Alballa, Gregory Butler:
  TooT-T: discrimination of transport proteins from non-transport proteins. 25
• 
  Niraj Thapa, Meenal Chaudhari, Sean McManus, Kaushik Roy, Robert H. Newman, Hiroto Saigo, Dukka B. KC:
  DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction. 63
• 
  Shonosuke Harada, Hirotaka Akita, Masashi Tsubaki, Yukino Baba, Ichigaku Takigawa, Yoshihiro Yamanishi, Hisashi Kashima:
  Dual graph convolutional neural network for predicting chemical networks. 94
• 
  Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi:
  Nanopore basecalling from a perspective of instance segmentation. 136

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 D. 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 7, May 2020

• 
  Wenting Wu, Lei Song, Yongtao Yang, Jianxin Wang, Hongtu Liu, Le Zhang:
  Exploring the dynamics and interplay of human papillomavirus and cervical tumorigenesis by integrating biological data into a mathematical model. 152
• 
  Olga Valenzuela, Fernando Rojas, Ignacio Rojas, Peter Glösekötter:
  Main findings and advances in bioinformatics and biomedical engineering- IWBBIO 2018. 153

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

• 
  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

• 
  Timofey V. Ivanisenko, Olga V. Saik, Pavel S. Demenkov, Nikita V. Ivanisenko, Alexander N. Savostyanov, 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 Önal Süzek:
  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

• 
  Selected abstracts of "Bioinformatics: from Algorithms to Applications 2020" conference. 567

Volume 21-S, Number 21, December 2020

• 
  Taeho Jo, Kwangsik Nho, Shannon L. Risacher, Andrew J. Saykin:
  Deep learning detection of informative features in tau PET for Alzheimer's disease classification. 496
• 
  Monalisa Mandal, Sanjeeb Kumar Sahoo, Priyadarsan Patra, Saurav Mallik, Zhongming Zhao:
  In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells. 499
• 
  Yanglin Tu, Zengwei Yao, Jiao Xu, Yilin Liu, Zhe Zhang:
  Fingerprint restoration using cubic Bezier curve. 514
• 
  Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng:
  Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. 534
• 
  Jin Li, Chenyuan Bian, Dandan Chen, Xianglian Meng, Haoran Luo, Hong Liang, Li Shen:
  Effect of APOE ε4 on multimodal brain connectomic traits: a persistent homology study. 535
• 
  Qian Liu, Yao Tong, Kai Wang:
  Genome-wide detection of short tandem repeat expansions by long-read sequencing. 542
• 
  Laurence de Torrenté, Samuel E. Zimmerman, Masako Suzuki, Maximilian Christopeit, John M. Greally, Jessica Cara Mar:
  The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data. 562
• 
  Yan Guo, Li Shen, Xinghua Shi, Kai Wang, Yulin Dai, Zhongming Zhao:
  Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020. 563
• 
  Zicheng Zhao, Yingxiao Zhou, Shuai Wang, Xiuqing Zhang, Changfa Wang, Shuai Cheng Li:
  LDscaff: LD-based scaffolding of de novo genome assemblies. 570
• 
  Min Jin Ha, Junghi Kim, Jessica Galloway-Pena, Kim-Anh Do, Christine B. Peterson:
  Compositional zero-inflated network estimation for microbiome data. 581

Volume 21-S, Number 23, December 2020

Recent Progresses with BioNLP Open Shared Tasks - Part 1

• 
  Arnaud Ferré, Louise Deléger, Robert Bossy, Pierre Zweigenbaum, Claire Nédellec:
  C-Norm: a neural approach to few-shot entity normalization. 579
• 
  Jenna Kanerva, Filip Ginter, Sampo Pyysalo:
  Dependency parsing of biomedical text with BERT. 580