


Остановите войну!
for scientists:


default search action
BMC Bioinformatics, Volume 21 - Supplements
Volume 21-S, Number 1, December 2020
- 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 4, July 2020
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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