Bioinformatics Research and Applications: 16th International Symposium, ISBRA 2020, Moscow, Russia, December 1–4, 2020, Proceedings

430 Pages·2020·43.816 MB·English

by  Zhipeng Cai, Ion Mandoiu, Giri Narasimhan, Pavel Skums, Xuan Guo

Zhipeng Cai · Ion Mandoiu ·
Giri Narasimhan · Pavel Skums ·
Xuan Guo (Eds.)
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16th International Symposium, ISBRA 2020
Moscow, Russia, December 1–4, 2020
Proceedings
123
Lecture Notes in Bioinformatics 12304
Subseries of Lecture Notes in Computer Science
Series Editors
Sorin Istrail
Brown University, Providence, RI, USA
Pavel Pevzner
University of California, San Diego, CA, USA
Michael Waterman
University of Southern California, Los Angeles, CA, USA
Editorial Board Members
Søren Brunak
Technical University of Denmark, Kongens Lyngby, Denmark
Mikhail S. Gelfand
IITP, Research and Training Center on Bioinformatics, Moscow, Russia
Thomas Lengauer
Max Planck Institute for Informatics, Saarbrücken, Germany
Satoru Miyano
University of Tokyo, Tokyo, Japan
Eugene Myers
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden,
Germany
Marie-France Sagot
Université Lyon 1, Villeurbanne, France
David Sankoff
University of Ottawa, Ottawa, Canada
Ron Shamir
Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
Terry Speed
WalterandElizaHallInstituteofMedicalResearch,Melbourne,VIC,Australia
Martin Vingron
Max Planck Institute for Molecular Genetics, Berlin, Germany
W. Eric Wong
University of Texas at Dallas, Richardson, TX, USA
More information about this series at http://www.springer.com/series/5381
Zhipeng Cai Ion Mandoiu
(cid:129) (cid:129)
Giri Narasimhan Pavel Skums
(cid:129) (cid:129)
Xuan Guo (Eds.)
Bioinformatics Research
and Applications
16th International Symposium, ISBRA 2020
–
Moscow, Russia, December 1 4, 2020
Proceedings
123
Editors
Zhipeng Cai Ion Mandoiu
Department ofComputer Science University of Connecticut
Georgia State University Storrs Mansfield, CT,USA
Atlanta, GA,USA
PavelSkums
Giri Narasimhan Georgia State University
Florida International University Atlanta, GA,USA
Miami, FL,USA
Xuan Guo
University of NorthTexas
Denton,TX, USA
ISSN 0302-9743 ISSN 1611-3349 (electronic)
Lecture Notesin Bioinformatics
ISBN 978-3-030-57820-6 ISBN978-3-030-57821-3 (eBook)
https://doi.org/10.1007/978-3-030-57821-3
LNCSSublibrary:SL8–Bioinformatics
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Preface
On behalf of the Program Committee, we would like to welcome you to the pro-
ceedings of the 16th edition of the International Symposium on Bioinformatics
Research and Applications (ISBRA 2020), held in Moscow, Russia, December 1–4,
2020. The symposium provides a forum for the exchange of ideas and results among
researchers,developers,andpractitionersworkingonallaspectsofbioinformaticsand
computational biology and their applications.
Thisyearwereceived131submissionsinresponsetothecallforextendedabstracts.
The Program Committee decided to accept 41 of them for full publication in the
proceedingsandoralpresentationatthesymposium;alistofthesecontributionscanbe
found in this front matter. The technical program also featured two keynote and three
invitedtalksgivenbyfivedistinguishedspeakers:Prof.OxanaV.Galzitskayafromthe
Russian Academy of Sciences, Russia; Prof. Phoebe Chen from La Trobe University,
Australia; Prof. Nir Ben-Tal from Tel Aviv University, Israel; Prof. Cenk Sahinalp
from National Cancer Institute, USA; and Prof. Srinivas Aluru from the Georgia
Institute of Technology, USA.
We would like to thank the Program Committee members and the additional
reviewers for volunteering their time to review and discuss symposium papers. We
wouldliketoextendspecialthankstothesteeringandgeneralchairsofthesymposium
for their leadership, and to the finance, publicity, workshops, local organization, and
publicationschairsfortheirhardworkinmakingISBRA2020asuccessfulevent.Last
but not least, we would like to thank all authors for presenting their work at the
symposium.
June 2020 Zhipeng Cai
Ion Mandoiu
Giri Narasimhan
Pavel Skums
Xuan Guo
Organization
Steering Committee
Yi Pan (Chair) Georgia State University, USA
Dan Gusfield University of California, Davis, USA
Ion Mandoiu University of Connecticut, USA
Marie-France Sagot Inria, France
Ying Xu University of Georgia, USA
Aidong Zhang University of Virginia, USA
General Chairs
Yuri Porozov Sechenov University, Russia
Dongqing Wei Shanghai Jiaotong University, China
Alex Zelikovsky Georgia State University, USA
Local Chairs
Yuri Porozov Sechenov University, Russia
Vladimir Poroikov Institute of Biomedical Chemistry, Russia
Yuri Orlov Sechenov University, Russia
Program Chairs
Zhipeng Cai Georgia State University, USA
Ion Mandoiu University of Connecticut, USA
Giri Narasimhan Florida International University, USA
Pavel Skums Georgia State University, USA
Publicity Chairs
Natalia Usova Trialogue Ltd, Russia
Natalia Rusanova Sechenov University, Russia
Jijun Tang University of South Carolina, USA
Le Zhang Sichuan University, China
Kiril Kuzmin Georgia State University, USA
Program Committee
Kamal Al Nasr Tennessee State University, USA
Max Alekseyev George Washington University, USA
Nikita Alexeev ITMO University, Russia
viii Organization
Mukul S. Bansal University of Connecticut, USA
Paola Bonizzoni Università di Milano-Bicocca, Italy
Anton Buzdin Omicsway Corp., USA
Zhipeng Cai Georgia State University, USA
Hongmin Cai South China University of Technology, China
Xing Chen China University of Mining and Technology, China
Xuefeng Cui Tsinghua University, China
Ovidiu Daescu The University of Texas at Dallas, USA
Lei Deng Central South University, China
Pufeng Du Tianjin University, China
Oliver Eulenstein Iowa State University, USA
Oxana Galzitskaya Institute of Protein Research, Russia
Xin Gao King Abdullah University of Science and Technology,
Saudi Arabia
Xuan Guo University of North Texas, USA
Matthew Hayes Xavier University of Louisiana, USA
Zengyou He Dalian University of Technology, China
Steffen Heber North Carolina State University, USA
Wooyoung Kim University of Washington, USA
Danny Krizanc Wesleyan University, USA
Xiujuan Lei Shaanxi Normal University, China
Yuk Yee Leung University of Pennsylvania, USA
Shuai Cheng Li City University of Hong Kong, China
Yaohang Li Old Dominion University, USA
Min Li Central South University, China
Jing Li Case Western Reserve University, USA
Xiaowen Liu Indiana University – Purdue University Indianapolis,
USA
Bingqiang Liu Shandong University, China
Ion Mandoiu University of Connecticut, USA
Serghei Mangul University of Southern California, USA
Fenglou Mao National Institute of Health, USA
Yury Orlovich Belarus State University, Belarus
Andrei Paun University of Bucharest, Romania
Nadia Pisanti Università di Pisa, Italy
Yuri Porozov Sechenov University, Russia
Russell Schwartz Carnegie Mellon University, USA
Joao Setubal University of São Paulo, Brazil
Xinghua Shi The University of North Carolina at Charlotte, USA
Yi Shi Shanghai Jiao Tong University, China
Pavel Skums Georgia State University, USA
Ileana Streinu Smith College, USA
Emily Chia-Yu Su Taipei Medical University, China
Shiwei Sun Chinese Academy of Sciences, China
Sing-Hoi Sze Texas A&M University, USA
Weitian Tong Eastern Michigan University, USA
Organization ix
Valentina Tozzini CNR, Institute of Nanoscience, Italy
Gabriel Valiente Universitat Politècnica de Catalunya, Spain
Alexandre Varnek Université de Strasbourg, France
Jianxin Wang Central South University, China
Seth Weinberg Virginia Commonwealth University, USA
Fangxiang Wu University of Saskatchewan, Canada
Yubao Wu Georgia State University, USA
Yufeng Wu University of Connecticut, USA
Zeng Xiangxiang Xiamen University, USA
Alex Zelikovsky Georgia State University, USA
Le Zhang Sichuan University, China
Fa Zhang Chinese Academy of Sciences, China
Xuegong Zhang Tsinghua University, China
Shuigeng Zhou Fudan University, China
Quan Zou Tianjin University, China
Poroikov Vladimir Institute of Biomedical Chemistry, Russia
Dmitry Osolodkin Russian Academy of Sciences, Russia
Orlov Yuri Russian Academy of Sciences, Russia
Additional Reviewers
Alexey Markin Luca Denti
Alexey Sergushichev Madalina Caea
Ana Rogoz Manal Almaeen
Andrei Zugravu Marian Lupascu
Arnav Jhala Mengyao Wang
Arseny Shur Mikhail Kolmogorov
Avin Chon Ming Shi
Chong Chu Ming Xiao
Cristian Stanescu Mohammed Alser
Emanuel Nazare Natalia Petukhova
Fanny Leung Pavel Avdeyev
Fatima Zohra Smaili Pijus Simonaitis
Gianluca Della Vedova Renmin Han
Haoyang Li Rocco Zaccagnino
Harry Taegyun Yang Sergey Aganezov
Hind Aldabagh Sergey Knyazev
Hossein Saghaian Steluta Talpau
Igor Mandric Tareq Alghamdi
Ilia Minkin Viachaslau Tsyvina
Jaqueline Joice Brito Yanting Luo
Kunihiko Sadakane Yasir Alanazi
Lintai Da Zehua Guo
Contents
Mitochondrial Haplogroup Assignment for High-Throughput Sequencing
Data from Single Individual and Mixed DNA Samples . . . . . . . . . . . . . . . . 1
Fahad Alqahtani and Ion I. Măndoiu
Signet Ring Cell Detection with Classification Reinforcement
Detection Network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Sai Wang, Caiyan Jia, Zhineng Chen, and Xieping Gao
SPOC: Identification of Drug Targets in Biological Networks via Set
Preference Output Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Hao Gao, Min Li, and Fang-Xiang Wu
Identification of a Novel Compound Heterozygous Variant in NBAS
Causing Bone Fragility by the Type of Osteogenesis Imperfecta. . . . . . . . . . 38
D. A. Petukhova, E. E. Gurinova, A. L. Sukhomyasova,
and N. R. Maksimova
Isoform-Disease Association Prediction by Data Fusion. . . . . . . . . . . . . . . . 44
Qiuyue Huang, Jun Wang, Xiangliang Zhang, and Guoxian Yu
EpIntMC: Detecting Epistatic Interactions Using Multiple Clusterings. . . . . . 56
Huiling Zhang, Guoxian Yu, Wei Ren, Maozu Guo, and Jun Wang
Improving Metagenomic Classification Using Discriminative k-mers
from Sequencing Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Davide Storato and Matteo Comin
Dilated-DenseNet for Macromolecule Classification
in Cryo-electron Tomography. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Shan Gao, Renmin Han, Xiangrui Zeng, Xuefeng Cui, Zhiyong Liu,
Min Xu, and Fa Zhang
Ess-NEXG: Predict Essential Proteins by Constructing a Weighted Protein
Interaction Network Based on Node Embedding and XGBoost. . . . . . . . . . . 95
Nian Wang, Min Zeng, Jiashuai Zhang, Yiming Li, and Min Li
mapAlign: An Efficient Approach for Mapping and Aligning Long Reads
to Reference Genomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Wen Yang and Lusheng Wang
Functional Evolutionary Modeling Exposes Overlooked Protein-Coding
Genes Involved in Cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Nadav Brandes, Nathan Linial, and Michal Linial