ISBRA 2019 15th International Symposium on Bioinformatics Research and Applications

June 3–6, 2019

Technical University of Catalonia Barcelona, Spain http://alan.cs.gsu.edu/isbra19/ About the Technical University of Catalonia

The Technical University of Catalonia (UPC) is a public institution of Higher Education and Research, specialized in the areas of Architecture, Engineering, Science and Technology. The UPC has a wide spread presence in Catalonia, with nine campuses located in Barcelona and nearby towns. The campuses are accessible, well connected by public transport and equipped with the necessary facilities and services to contribute to learning, research and university life.

Founded in 1968 by grouping together existing state technical schools of Architecture and Engineering in Barcelona, which date back from the mid-19th century, it gained university status in 1971. The UPC today has a student population of over 30,000, with more than 3,000 teaching and research staff and about 2,000 administrative and service staff. There are 64 bachelor’s degrees, 68 master’s degrees, and 46 doctoral programs offered by 20 schools. Further, there are 50 international double-degree agreements with 30 universities, and about 3,000 students in international mobility programs. Research teams generate e60 million in annual funding, with a total budget of about e300 million.

About the Department of Computer Science

The Department of Computer Science was created in 1987 and is one of the largest depart- ments at the UPC. It has about 90 full-time faculty and 50 Ph.D. students. The Department is responsible for teaching and research in several disciplines related to the foundations of computing and their applications.

The core of the teaching activities is concentrated in the undergraduate and master’s programs of the Barcelona School of Informatics, but the Department is also teaching at several other UPC schools. The Department is coordinating two Ph.D. programs: Computing and Artificial Intelligence.

The research activities of the Department are organized in different research groups, covering various Computer Science disciplines. It has an active presence in the main conferences of the field and an intense participation in public and industrial projects, as well as in the creation of spin-off companies. Message from the General Chairs

We are delighted to welcome you to the 15th International Symposium on Bioinformatics Research and Applications (ISBRA 2019) being held on the campus of Technical University of Catalonia in Barcelona. We are honored to serve the international community by bringing together scholars, scientists, and students from academia, laboratories, and industry to this premier meeting.

We would like to thank Program Chairs Zhipeng Cai, Pavel Skums, and Min Li for putting together a terrific technical program. We thank the program committee and reviewers for their hard work, and also thank all authors who submitted papers and abstracts for their contribu- tions. We believe that you will enjoy all contributed and keynote talks this week!

We are grateful to M´ıriam Hernandez´ and Ana Iba´nez˜ from the Technical University of Cat- alonia for help in coordinating ISBRA 2019. We also thank the Publications Chairs Olga Glebova, Mingon Kang, and Fa Zhang and Webmasters Filipp Rondel and Sergey Knyazev for their efforts in publicizing the symposium.

We would like to recognize Technical University of Catalonia for hosting ISBRA 2019. We would like to thank Carme Casas and Xavier Masso´ for their help in making these venues available for symposium presentations and on-campus housing of participants. Last but not least, we would like to thank our sponsors: the National Science Foundation, the Department of Computer Science of the Technical University of Catalonia, and the Department of Com- puter Science of Georgia State University. Thanks to their generous support we have been able to award travel fellowships to graduate students and post-doctoral scholars from USA and abroad.

We hope you will have a wonderful time at the symposium and enjoy the beautiful Barcelona.

Gabriel Valiente, Technical University of Barcelona, Spain Alexander Zelikovsky, Georgia State University, USA Message from the Program Chairs

On behalf of the Program Committee, we would like to welcome you to the proceedings of the 15th edition of the International Symposium on Bioinformatics Research and Applica- tions (ISBRA 2019), held in Barcelona, Spain, June 3–6, 2019. The symposium provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. This year we received 95 submissions in response to the call for extended abstracts. The Pro- gram Committee decided to accept 22 of them for full publication in the proceedings and oral presentation at the symposium. We also accepted 23 for oral presentation. Furthermore, we received 20 submissions in response to the call for short abstracts.

The technical program invited keynote talks were given by Prof. Niko Beerenwinkel from ETH Zurich,¨ Prof. Roderic Guigo´ from the Centre for Genomic Regulation, and Prof. Mar- tin Vingron from the Max Planck Institute for Molecular Genetics. We would like to thank the Program Committee members and the additional reviewers for volunteering their time to review and discuss symposium papers. We would like to extend special thanks to the Steer- ing and General Chairs of the symposium for their leadership, and to the Publicity and Local Chairs for their hard work in making ISBRA 2019 a successful event. Last but not least, we would like to thank all authors for presenting their work at the symposium.

Zhipeng Cai, Georgia State University Pavel Skums, Georgia State University Min Li, Central South University Keynote Speakers

Niko Beerenwinkel

Associate Professor, Computational Biology, ETH Zurich

Roderic Guigo´

Director, Bioinformatics Program, Centre for Genomic Regulation, Barcelona

Martin Vingron

Director, Max Planck Institute for Molecular Genetics, Head of Computational Molecular Biology Department Symposium Organizers

Steering Committee

Yi Pan (Georgia State University, USA), Chair 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

Gabriel Valiente (Technical University of Catalonia, Spain) Alexander Zelikovsky (Georgia State University, USA)

Local Chair

Gabriel Valiente (Technical University of Catalonia, Spain)

Program Chairs

Zhipeng Cai (Georgia State University, USA) Pavel Skums (Georgia State University, USA) Min Li (Central South University, China)

Publicity Chairs

Olga Glebova (Georgia State University, USA) Mingon Kang (Kennesaw State University, USA) Fa Zhang (Chinese Academy of Science, China)

Webmasters

Filipp Rondel (Georgia State University, USA) Sergey Knyazev (Georgia State University, USA) Program Committee Members

Kamal Al Nasr (Tennessee State University) Fenglou Mao (National Institute of Health) Max Alekseyev (George Washington Univer- Yuri Orlovich (Belarusian State Univ.) sity) Andrei Paun (University of Bucharest) Nikita Alexeev (ITMO University) Nadia Pisanti (Universita di Pisa) Mukul S. Bansal (University of Connecticut) Yuri Porozov (ITMO University) Paola Bonizzoni (Universita di Milano- Russell Schwartz (Carnegie Mellon Univer- Bicocca) sity) Zhipeng Cai (Georgia State University) Joao Setubal (University of Sao Paulo) Hongmin Cai (South China University of Yi Shi (Shanghai Jiaotong University) Technology) Xinghua Shi (University of North Carolina at Xing Chen (Chinese Academy of Sciences) Charlotte) Xuefeng Cui (Tsinghua University) Dong Si (University of Washington) Ovidiu Daescu (Univ. of Texas at Dallas) Pavel Skums (Georgia State University) Lei Deng (Central South University) Ileana Streinu (University of Massachusetts Pufeng Du (Tianjin University) Amherst) Oliver Eulenstein (Iowa State University) Emily Su (Taipei Medical University) Xin Gao (King Abdullah University of Sci- Shiwei Sun (Chinese Academy of Sciences) ence and Technology) Sing-Hoi Sze (Texas A&M University) Xuan Guo (University of North Texas) Weitian Tong (Georgia Southern University) Olga Glebova (Georgia State University) Gabriel Valiente (Technical University of Cat- Zengyou He (Dalian University of Technol- alonia) ogy) Jianxin Wang (Central South University) Steffen Heber (North Carolina State Univ.) Li-San Wang (University of Pennsylvania) Jinling Huang (East Carolina University) Guohua Wang (Harbin Institute of Technol- Mingon Kang (Kennesaw State University) ogy) Wooyoung Kim (University of Washington) Seth Weinberg (Virginia Commonwealth Uni- Danny Krizanc (Wesleyan University) versity) Xiujuan Lei (Shaanxi Normal University) Yubao Wu (Georgia State University) Shuai-Cheng Li (City University of Hong Fangxiang Wu (University of Saskatchewan) Kong) Yufeng Wu (University of Connecticut) Yaohang Li (Old Dominion University) Zeng Xiangxiang (Xiamen University) Jing Li (Case Western Reserve University) Guoxian Yu (Southwest University) Min Li (Central South University) Ning Yu (Georgia State University) Xiaowen Liu (Indiana University) Alex Zelikovsky (Georgia State University) Bingqiang Liu (Shandong University) Le Zhang (Southwest University) Ion Mandoiu (University of Connecticut) Xuegong Zhang (Tsinghua University) Igor Mandric (University of California, Los Xing-Ming Zhao (Tongji University) Angeles) Leming Zhou (University of Pittsburgh) Serghei Mangul (University of California, Los Shuigeng Zhou (Fudan University) Angeles) Quan Zou (Tianjin University) Sponsors

Technical University of Catalonia Georgia State University National Science Foundation Department of Department of Computer Science Computer Science ISBRA 2019 Program

Monday, June 3rd, 2019

7:00pm- Reception Jordi Girona, 31 9:00pm Gardens of the Torre Girona estate 08034 Barcelona

Tuesday, June 4th, 2019

9:00am- Plenary Session 10:00am Room: Aula Master` Chair: Pavel Skums Session 1: Keynote Talk Predicting enhancers from chromatin marks Martin Vingron, Max Planck Institute for Molecular Genetics 10:00am- Coffee Break 10:20am Room: Sala Polivalent

10:20am- Parallel Sessions 12:20pm Room: Aula Master` Room: Sala Agora` Session 2A: Session 2B: Machine Learning 1 Protein-Protein Interactions Chair: Ion Mandoiu Chair: Gabriel Valiente 10:20am- DeepFrag-k: A fragment-based Improving identification of 10:45am deep learning approach for essential proteins by a novel protein fold recognition, Wessam ensemble method, Wei Dai, Xia Li, Elhefnawy, Yaohang Li Wei Peng, Junrong Song, Jiancheng Zhong, Jianxin Wang 10:45am- A machine learning algorithm for Automated hub-protein detection 11:10am genotyping the mixture dataset via a new fused similarity measure- considering copy number variant, based multi-objective clustering Tian Zheng, Xuanping Zhang, framework, Sudipta Acharya, Cui Zhongmeng Zhao, Xiao Xiao, Laizhong, Pan Yi Jiayin Wang 11:10am- Machine and deep learning-based AligNet: Alignment of protein- 11:35am augmentation of small RNA data protein interaction networks, expression data profiles, Jelena Ricardo Alberich, Adria` Alcala,´ Fiosina, Maksims Fiosins Merce` Llabres,´ Francesc Rossello,´ Gabriel Valiente 11:35am- DeepiRNA: Predicting transposon- Identifying human essential genes 12:00pm derived piRNAs with deep learning, by network embedding protein- Wen Zhang, Jiangtao Song, Feng protein interaction network, Wei Liu Dai, Qi Chang, Wei Peng, Jiancheng Zhong 12:00pm- PU-Caller: Sensitive somatic variant Alignment of biological networks by 12:20pm calling using positive-unlabeled integer linear programming: Virus- learning, Elham Sherafat, Ion host protein-protein interaction Mandoiu networks, Merce` Llabres,´ Gabriel Riera, Francesc Rossello,´ Gabriel Valiente 12:20pm- Lunch Break 2:00pm Restaurant: Unity Sodexo

2:00pm- Parallel Sessions 3:35pm Room: Aula Master` Room: Sala Agora` Session 3A: Session 3B: Machine Learning 2 Phylogeny 1 Chair: Heta Desai Chair: Sagi Snir 2:00pm- Iterative sure independent ranking Simultaneous multi-domain-multi- 2:25pm and screening for drug response gene reconciliation under the prediction, Yufang Qin, Biao An, domain-gene-species reconciliation Qianwen Zhang, Yun Fang, Ming model, Lei Li, Mukul S. Bansal Chen 2:25pm- Gene and pathway-based deep Greedy partition distance under 2:50pm neural network for multi-omics stochastic models: Analytic results, data integration to predict cancer Sagi Snir survival outcomes, Jie Hao, Mohammad Masum, Jung Hun Oh, Mingon Kang 2:50pm- On tower and checkerboard neural Computing a consensus phylogeny 3:15pm network architectures for gene via leaf removal, Zhi-Zhong Chen, expression inference, Vladim´ır Kunc, Shohei Ueta, Jingyu Li, Lusheng Jiri Klema Wang 3:15pm- 16S ribosomal gene classification Spanning trees with extremal 3:35pm using recurrent neural network s-metric and their applications in models, Heta Desai, Anuja molecular epidemiology, Yury Parameshwaran, Michael Weeks, Orlovich, Volker Kaibel, Kirill Rajshekhar Sunderraman Kukharenko, Pavel Skums 3:35pm- Coffee Break 3:55pm Room: Sala Polivalent 3:55pm- Parallel Sessions 5:05pm Room: Aula Master` Room: Sala Agora` Session 4A: Session 4B: Sequence Analysis Privacy Chair: Fa Zhang Chair: Pavel Skums 3:55pm- Paired-end small RNA sequencing Detecting illicit drug ads in Google 4:20pm reveals a possible overestimation in Plus, Fengpan Zhao, Pavel Skums, isomiR sequence repertoire Alex Zelikovsky, Eric L. Sevigny, previously reported from Monica Haavisto Swahn, Sheryl M. conventional single read data Strasser, Yubao Wu analysis, Antonio Luna de Haro, Raquel Pluvinet, Jose Francisco Sanchez Herrero, Lauro Sumoy 4:20pm- Analysis of codon usage patterns in Differentially private genomic data 4:45pm citrus based on coding sequence publishing, Zaobo He, Jianqiang Li data, Zenan Shen, Zhimeng Gan, Fa Zhang, Xinyao Yi, Xiaohua Wan, Jinzhi Zhang 4:45pm- CleanBreak: Complex genomic Identifying relatives (almost) 5:05pm structural variant discovery in high- privately, Benny Chor, Orit throughput sequencing data, Moskovich, Benny Pinkas Matthew Hayes, Derrick Mullins

Wednesday, June 5th, 2019

9:00am- Parallel Sessions 10:10am Room: Aula Master` Room: Sala Agora` Session 5A: Session 5B: Protein Structure Comparative Genomics Chair: Tun-Wen Pai Chair: Alex Zelikovsky 9:00am- PSLDoc3: A high-throughput Using earth mover’s distance 9:25am protein function prediction by the between k-mers for viral outbreak novel k-nearest neighbor and voting investigations, Andrii Melnyk, algorithms, Yi-Wei Liu, Tz-Wei Hsu, Sergey Knyazev, Yury Khudyakov, Che-Yu Chang, Wen-Hung Liao, Leonid Bunimovich, Fredrik Jia-Ming Chang Vannberg, Pavel Skums, Alex Zelikovsky 9:25am- Conformational epitope matching Iterative spaced seed hashing: 9:50am and prediction based on protein Closing the gap between spaced surface spiral features, Tun-Wen Pai seed hashing and k-mer hashing, Enrico Petrucci, Laurent Noe, Cinzia Pizzi, Matteo Comin 9:50am- TLC SDSB: A two-layer structured Toward a dynamic threshold for 10:10am classifier for identifying single-stranded quality-score distortion in reference- and double-stranded DNA-binding based alignment, Ana Hernandez, proteins from protein sequence, Jing Marco Mattavelli, Claudio Alberti Hu, Filip Keri

10:10am- Coffee Break 10:30am Room: Sala Polivalent

10:30am- Parallel Sessions 12:30pm Room: Aula Master` Room: Sala Agora` Session 6A: Session 6B: Networks Structural Analysis Chair: Merce` Llabres´ Chair: Nikita Alexeev 10:30am- Model revision of boolean The review of bioinformatics tool 10:55am regulatory networks at stable state, for 3D plant genomics research, Filipe Gouveia, Ines Lynce, Pedro Xiangyu Yang, Jingtian Zhao, T. Monteiro Zhenghao Li, Pengcao Li, Le Zhang 10:55am- Constructing cancer patient-specific Maximum stacking base pairs: 11:20am and group-specific gene networks Hardness and approximation by with multi-omics data, Wook Lee, nonlinear LP-rounding, Lixin Liu, Kyungsook Han Haitao Jiang, Peiqing Liu, Binhai Zhu, Daming Zhu 11:20am- Flexible comparative genomics of Graph transformations, semigroups, 11:45am prokaryotic transcriptional and isotopic labeling, Jakob Lykke regulatory networks, Sefa Kilic, Andersen, Daniel Merkle, Peter Miquel Sanchez-Osuna,´ Antonio Severin Rasmussen Collado-Padilla, Jordi Barbe,´ Ivan Erill 11:45am- IDNDDI: An integrated drug A robustness analysis of dynamic 12:10am similarity network method for boolean models of cellular circuits, predicting drug-drug interactions, Roded Sharan, Ariel Bruner Cheng Yan, Guihua Duan, Yayan Zhang, Fangxiang Wu, Yi Pan, Jianxin Wang 12:10am- Comparison of parameter Evolutionary switches structural 12:30am estimation methods in the presence transition states explored with of overdispersion: An infectious minimalist coarse grained models, disease based simulation study, Francesco Delfino, Yuri Porozov, Kimberlyn Roosa, Ruiyan Luo, Eugene Stepanov, Gaik Tamazian, Gerardo Chowell Valentina Tozzini 12:30pm- Lunch Break 2:00pm Restaurant: Unity Sodexo 2:00pm- Plenary Session 3:00pm Room: Aula Master` Chair: Alex Zelikovsky Session 7: Keynote Talk Learning tumor phylogenies from single-cell data Niko Beerenwinkel, ETH Zurich¨ 3:00pm- Coffee Break 3:20pm Room: Sala Polivalent

3:20pm- Parallel Sessions 4:55pm Room: Aula Master` Room: Sala Agora` Session 8A: Session 8B: Phylogeny 2 Epigenomics Chair: Oliver Eulenstein Chair: Ion Mandoiu 3:20pm- The cluster affinity distance for PeakPass: Automating ChIP-Seq 3:45pm phylogenies, Jucheol Moon, Oliver blacklist creation, Charles Eulenstein Wimberley, Steffen Heber 3:45pm- An alignment-free heuristic for fast A novel neoantigen discovery 4:10pm sequence comparisons with approach based on chromatin high applications to phylogeny order conformation, Yi Shi, reconstruction, Jodh Pannu, Sahar Mingxuan Zhang, Luming Meng, Hooshmand, Sriram P. Xianbin Su, Xueying Shang, Chockalingam, Sharma V. Qingjiao Li, Mengna Lin, Xin Zou, Thankachan, Srinivas Aluru Qing Luo, Yangyang Zhai, Kunyan He, Lan Wang, Cong Chen, Xiaofang Cui, Na Wang, Jian He, Yaoliang Yu, Yanting Wu, Lintai Da, Weidong Cai, Ze-Guang Han 4:10pm- Unifying gene duplication, loss, and MADA: A web service for analysing 4:35pm coalescence on phylogenetic DNA methylation array data, Xinyu networks, Peng Du, Huw Ogilvie, Hu, Li Tang, Linconghua Wang, Luay Nakhleh Fangxiang Wu, Min Li 4:35pm- Reconstruction of fitness landscapes ZCMM: A novel algorithm of 4:55pm of intra-host viral populations using Z-curve based and position weight NGS data, Viachaslau Tsyvina, matrix for nucleosome positioning, Yury Khudyakov, Pavel Skums Ying Cui, Jianzhong Li

7:00pm- Banquet Provenc¸a, 286–288 9:00pm El Principal del Eixample 08008 Barcelona Thursday, June 6th, 2019

9:00am- Plenary Session 10:00am Room: Aula Master` Chair: Gabriel Valiente Session 9: Keynote Talk The molecular anatomy of the human body Roderic Guigo,´ Centre for Genomic Regulation, Barcelona 10:00am- Coffee Break 10:20am Room: Sala Polivalent

10:20am- Parallel Sessions 12:45pm Room: Aula Master` Room: Sala Agora` Session 10A: Session 10B: Image Analysis Clustering Chair: Fa Zhang Chair: Yuri Porozov 10:20am- Identification of early mild cognitive Markov chain Monte Carlo for 10:45am impairment using multi-modal data active module identification and graph convolutional networks, problem, Nikita Alexeev, Javlon Guanxin Tan, Jin Liu, Wei Lan, Isomurodov, Gennady Korotkevich, Jianxin Wang Alexey Sergushichev 10:45am- Anomaly detection of pedestrian Sorting by reversals, transpositions, 11:10am trajectory based on adaptive and indels on both gene order and density clustering, Aiguo Chen, intergenic sizes, Klairton Lima Jiacheng Luo, Ling Tian, Haotian Brito, Geraldine´ Jean, Guillaume Rao Fertin, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias 11:10am- Compressed sensing improved Using DenseFly algorithm for cell 11:35am reconstruction-reprojection searching on massive scRNA-seq algorithm for electron tomography, datasets, Yixin Chen, Sijie Chen, Lun Li, Renmin Han, Zhiyong Liu, Xuegong Zhang Fa Zhang 11:35am- DM-SIRT: A distribute method A multi-view clustering method for 12:00pm for multi-tilt reconstruction in microbiome analysis by symmetric electron tomography, Zihao Wang, nonnegative matrix factorization Jingrong Zhang, Xintong Liu, with Hessian regularization, Zhiyong Liu, Xiaohua Wan, Fa Yuanyuan Ma Zhang 12:00pm- A multi-label classification model MDAPlatform: A component-based 12:25pm for full slice brain computerised platform for constructing and tomography image, Guanghui Fu, assessing miRNA-disease Jianqiang Li, Yan Pei associations prediction method, Yayan Zhang, Cheng Yan, Haolun Yi, Jianxin Wang 12:25pm- An attention-based framework for Unveiling deeper relationships 12:45pm microaneurysms detection on among circulating virus sequences: Fundus images, Lizong Zhang, Ying Using a shared change search Li, Guiduo Duan, Guangchun Luo, method, Kun Zhao Ling Tian 12:45pm- Lunch Break 2:00pm Restaurant: Unity Sodexo ISBRA 2019 Map

Reception

Symposium