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A Protein Classification Benchmark collection for Machine Learning
Nucleic Acids Research. 2006.
Kertesz-Farkas A., Pongor S.
Keywords: bioinformatics
Matveeva O. V., Nechipurenko Y. D., Chikako R. et al., Bioinformatics 2016 Vol. 32 No. 17 P. i552-i558
Motivation: Target-specific hybridization depends on oligo-probe characteristics that improve hybridization specificity and minimize genome-wide cross-hybridization. Interplay between specific hybridization and genome-wide cross-hybridization has been insufficiently studied, despite its crucial role in efficient probe design and in data analysis.
Results: In this study, we defined hybridization specificity as a ratio between oligo target-specific hybridization and oligo genome-wide cross-hybridization. A ...
Added: October 14, 2016
Cheloshkina K., Poptsova M., PLoS Computational Biology 2021 Vol. 17 No. 3 Article e1008749
Understanding mechanisms of cancer breakpoint mutagenesis is a difficult task and predictive models of cancer breakpoint formation have to this time failed to achieve even moderate predictive power. Here we take advantage of a machine learning approach that can gather important features from big data and quantify contribution of different factors. We performed comprehensive analysis ...
Added: March 18, 2021
Shugay M., Bagaev D., Turchaninova M. et al., PLoS Computational Biology 2015 Vol. 11 No. 11 P. e1004503
Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on ...
Added: February 17, 2016
Kertesz-Farkas A., Pongor S., Journal of Biochemical and Biophysical Methods 2008
Added: January 19, 2021
Nazipova N. N., Isaev E., Kornilov V. et al., Mathematical Biology and Bioinformatics 2018 No. 13 P. t1-t16
Sequencing of the human genome began in 1994. It took 10 years of work by many scientific teams to get a rough sequence of human DNA. Modern sequencing technologies allow you to get the genome of a specific person in a few days. We discuss the success of modern bioinformatics associated with the emergence of ...
Added: October 5, 2018
М. : ИБХ РАН, 2015
Сборник тезисов конференции. ...
Added: February 14, 2015
M. : Park Media Ltd, 2014
Added: September 15, 2014
Isaev E., Kornilov V., Математическая биология и биоинформатика 2013 Т. 8 № 1 С. 49-65
Today we have the problem of big science data. The information collecting in science experiments, especially in bioinformatics and astrophysics grows in amazing rate. In this paper we consider special program techniques and computer technologies used for work with superlarge volumes of data. Also, we discuss the state of affairs with the big data in ...
Added: March 3, 2013
Nikolenko S. I., Korobeynikov A., Alekseyev M., BMC Genomics 2013 Vol. 14 No. Suppl. 1 P. S7
Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data usually come up short in single-cell sequencing projects, algorithms actually used for single-cell error correction have been so far very simplistic.
We introduce several novel algorithms based ...
Added: February 13, 2013
Kertesz-Farkas A., Nikitin D., Gene 2018 Vol. 660 P. 8-12
ype II restriction endonucleases and modification DNA-methyltransferases are key instruments of genetic engineering. Recently the number of proteins assigned to this group exceeds 8500. Subtype IIC organizes bifunctional endonuclease-methyltransferase enzymes and currently consists of 16 described members. Here we present phylogenetic tree of 22 new potential bifunctional endonucleases. The majority of them are thought to ...
Added: October 10, 2018
M. : IITP RAS, 2021
10th Moscow Conference on Computational Molecular Biology MCCMB'21
ISBN 978-5-901158-32-6 ...
Added: September 10, 2021
Kertesz-Farkas A., Pongor S., Bioinformatics 2006
Added: January 19, 2021
Bukley G., St. Petersburg : Федеральное государственное автономное образовательное учреждение высшего образования "Санкт-Петербургский политехнический университет Петра Великого", 2021
Bioinformatics Institute 2020/21. Project abstracts. Bioinformatics Summer School 2021. Abstracts. ...
Added: August 14, 2021
Springer, 2014
This book constitutes the refereed proceedings of the 10th International Conference on Machine Learning and Data Mining in Pattern Recognition, MLDM 2014, held in St. Petersburg, Russia in July 2014. The 40 full papers presented were carefully reviewed and selected from 128 submissions. The topics range from theoretical topics for classification, clustering, association rule and ...
Added: September 30, 2014
Kertesz-Farkas A., Pongor S., Journal of Biochemical and Biophysical Methods 2008
Added: January 19, 2021
St. Petersburg : Федеральное государственное автономное образовательное учреждение высшего образования "Санкт-Петербургский политехнический университет Петра Великого", 2021
Bioinformatics Institute 2020/21. Project abstracts. Bioinformatics Summer School 2021. Abstracts. ...
Added: August 9, 2021
Nazarov V. I., Новые информационные технологии в автоматизированных системах 2015 С. 270-280
В данной статье дается обзор существующих методов анализа данных репертуаров иммунных рецепторов - фундамента адаптивного иммунитета млекопитающих. ...
Added: April 18, 2015
Novosibirsk : Publishing House SB RAS, 2014
Abstracts of the Ninth International Conference on Bioinformatics of Genome Regulation and Structure\Systems Biology. Printed without editing ...
Added: November 5, 2014
Kertesz-Farkas A., Kajan L., Pongor S., Bioinformatics 2006
Added: January 19, 2021
Kertesz-Farkas A., Dombi J., Journal of Computational Biology 2009
Added: January 19, 2021
Kertesz-Farkas A., Pongor S., Current Protein and Peptide Science 2010
Added: January 19, 2021
Nazarov V. I., Minervina A. A., Komkov A. Y. et al., Bone Marrow Transplantation 2016 Vol. 1 No. 3
Detection of minimal residual disease (MRD) is a powerful prognostic tool in many hematological malignancies including ALL.1 Several groups of markers are widely used to monitor the concentration of a malignant clone including the detection of 'clonal B-cell (BCR) or T-cell (TCR) gene receptor rearrangements2 in ALL. Identification of a clonal rearrangement specific for the ...
Added: June 14, 2016
Kertesz-Farkas A., Bauwens B. F., Filatov G., Bioinformatics 2018 Vol. 34 No. 19 P. 3281-3288
Motivation
Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis.
Results
Here, we present a new convolutional kernel function for protein sequences called the Lempel-Ziv-Welch (LZW)-Kernel. It is based on code words identified with the LZW universal text compressor. The LZW-Kernel is an alignment-free method, it is always ...
Added: October 10, 2018