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ISBRA 201915th International Symposiumon Bioinformatics Researchand Applications
June 3–6, 2019
Technical University of CataloniaBarcelona, Spain
http://alan.cs.gsu.edu/isbra19/
About the Technical University ofCatalonia
The Technical University of Catalonia (UPC) is a public institution of Higher Education andResearch, specialized in the areas of Architecture, Engineering, Science and Technology. TheUPC has a wide spread presence in Catalonia, with nine campuses located in Barcelona andnearby towns. The campuses are accessible, well connected by public transport and equippedwith the necessary facilities and services to contribute to learning, research and universitylife.
Founded in 1968 by grouping together existing state technical schools of Architecture andEngineering in Barcelona, which date back from the mid-19th century, it gained universitystatus in 1971. The UPC today has a student population of over 30,000, with more than3,000 teaching and research staff and about 2,000 administrative and service staff. There are64 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 about3,000 students in international mobility programs. Research teams generate e60 million inannual funding, with a total budget of about e300 million.
About the Department of ComputerScience
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 Departmentis responsible for teaching and research in several disciplines related to the foundations ofcomputing and their applications.
The core of the teaching activities is concentrated in the undergraduate and master’s programsof the Barcelona School of Informatics, but the Department is also teaching at several otherUPC schools. The Department is coordinating two Ph.D. programs: Computing and ArtificialIntelligence.
The research activities of the Department are organized in different research groups, coveringvarious Computer Science disciplines. It has an active presence in the main conferences of thefield and an intense participation in public and industrial projects, as well as in the creation ofspin-off companies.
Message from the General Chairs
We are delighted to welcome you to the 15th International Symposium on BioinformaticsResearch and Applications (ISBRA 2019) being held on the campus of Technical Universityof Catalonia in Barcelona. We are honored to serve the international community by bringingtogether scholars, scientists, and students from academia, laboratories, and industry to thispremier meeting.
We would like to thank Program Chairs Zhipeng Cai, Pavel Skums, and Min Li for puttingtogether a terrific technical program. We thank the program committee and reviewers for theirhard 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 Mıriam Hernandez and Ana Ibanez from the Technical University of Cat-alonia for help in coordinating ISBRA 2019. We also thank the Publications Chairs OlgaGlebova, Mingon Kang, and Fa Zhang and Webmasters Filipp Rondel and Sergey Knyazevfor their efforts in publicizing the symposium.
We would like to recognize Technical University of Catalonia for hosting ISBRA 2019. Wewould like to thank Carme Casas and Xavier Masso for their help in making these venuesavailable for symposium presentations and on-campus housing of participants. Last but notleast, we would like to thank our sponsors: the National Science Foundation, the Departmentof 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 beenable to award travel fellowships to graduate students and post-doctoral scholars from USAand abroad.
We hope you will have a wonderful time at the symposium and enjoy the beautiful Barcelona.
Gabriel Valiente, Technical University of Barcelona, SpainAlexander 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 ofthe 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 aforum for the exchange of ideas and results among researchers, developers, and practitionersworking 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 oralpresentation at the symposium. We also accepted 23 for oral presentation. Furthermore, wereceived 20 submissions in response to the call for short abstracts.
The technical program invited keynote talks were given by Prof. Niko Beerenwinkel fromETH 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 thankthe Program Committee members and the additional reviewers for volunteering their time toreview 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 LocalChairs for their hard work in making ISBRA 2019 a successful event. Last but not least, wewould like to thank all authors for presenting their work at the symposium.
Zhipeng Cai, Georgia State UniversityPavel Skums, Georgia State UniversityMin Li, Central South University
Keynote Speakers
Niko Beerenwinkel
Associate Professor, Computational Biology,ETH Zurich
Roderic Guigo
Director, Bioinformatics Program, Centre forGenomic Regulation, Barcelona
Martin Vingron
Director, Max Planck Institute for MolecularGenetics, Head of Computational MolecularBiology Department
Symposium Organizers
Steering Committee
Yi Pan (Georgia State University, USA), ChairDan 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)Max Alekseyev (George Washington Univer-sity)Nikita Alexeev (ITMO University)Mukul S. Bansal (University of Connecticut)Paola Bonizzoni (Universita di Milano-Bicocca)Zhipeng Cai (Georgia State University)Hongmin Cai (South China University ofTechnology)Xing Chen (Chinese Academy of Sciences)Xuefeng Cui (Tsinghua University)Ovidiu Daescu (Univ. of Texas at Dallas)Lei Deng (Central South University)Pufeng Du (Tianjin University)Oliver Eulenstein (Iowa State University)Xin Gao (King Abdullah University of Sci-ence and Technology)Xuan Guo (University of North Texas)Olga Glebova (Georgia State University)Zengyou He (Dalian University of Technol-ogy)Steffen Heber (North Carolina State Univ.)Jinling Huang (East Carolina University)Mingon Kang (Kennesaw State University)Wooyoung Kim (University of Washington)Danny Krizanc (Wesleyan University)Xiujuan Lei (Shaanxi Normal University)Shuai-Cheng Li (City University of HongKong)Yaohang Li (Old Dominion University)Jing Li (Case Western Reserve University)Min Li (Central South University)Xiaowen Liu (Indiana University)Bingqiang Liu (Shandong University)Ion Mandoiu (University of Connecticut)Igor Mandric (University of California, LosAngeles)Serghei Mangul (University of California, LosAngeles)
Fenglou Mao (National Institute of Health)Yuri Orlovich (Belarusian State Univ.)Andrei Paun (University of Bucharest)Nadia Pisanti (Universita di Pisa)Yuri Porozov (ITMO University)Russell Schwartz (Carnegie Mellon Univer-sity)Joao Setubal (University of Sao Paulo)Yi Shi (Shanghai Jiaotong University)Xinghua Shi (University of North Carolina atCharlotte)Dong Si (University of Washington)Pavel Skums (Georgia State University)Ileana Streinu (University of MassachusettsAmherst)Emily Su (Taipei Medical University)Shiwei Sun (Chinese Academy of Sciences)Sing-Hoi Sze (Texas A&M University)Weitian Tong (Georgia Southern University)Gabriel Valiente (Technical University of Cat-alonia)Jianxin Wang (Central South University)Li-San Wang (University of Pennsylvania)Guohua Wang (Harbin Institute of Technol-ogy)Seth Weinberg (Virginia Commonwealth Uni-versity)Yubao Wu (Georgia State University)Fangxiang Wu (University of Saskatchewan)Yufeng Wu (University of Connecticut)Zeng Xiangxiang (Xiamen University)Guoxian Yu (Southwest University)Ning Yu (Georgia State University)Alex Zelikovsky (Georgia State University)Le Zhang (Southwest University)Xuegong Zhang (Tsinghua University)Xing-Ming Zhao (Tongji University)Leming Zhou (University of Pittsburgh)Shuigeng Zhou (Fudan University)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-9:00pm
ReceptionGardens of the Torre Girona estate
Jordi Girona, 3108034 Barcelona
Tuesday, June 4th, 2019
9:00am-10:00am
Plenary SessionRoom: Aula MasterChair: Pavel Skums
Session 1: Keynote TalkPredicting enhancers from chromatin marksMartin Vingron, Max Planck Institute for Molecular Genetics
10:00am-10:20am
Coffee BreakRoom: Sala Polivalent
10:20am-12:20pm
Parallel SessionsRoom: Aula Master Room: Sala Agora
Session 2A:Machine Learning 1Chair: Ion Mandoiu
Session 2B:Protein-Protein InteractionsChair: Gabriel Valiente
10:20am-10:45am
DeepFrag-k: A fragment-baseddeep learning approach forprotein fold recognition, WessamElhefnawy, Yaohang Li
Improving identification ofessential proteins by a novelensemble method, Wei Dai, Xia Li,Wei Peng, Junrong Song,Jiancheng Zhong, Jianxin Wang
10:45am-11:10am
A machine learning algorithm forgenotyping the mixture datasetconsidering copy number variant,Tian Zheng, Xuanping Zhang,Zhongmeng Zhao, Xiao Xiao,Jiayin Wang
Automated hub-protein detectionvia a new fused similarity measure-based multi-objective clusteringframework, Sudipta Acharya, CuiLaizhong, Pan Yi
11:10am-11:35am
Machine and deep learning-basedaugmentation of small RNA dataexpression data profiles, JelenaFiosina, Maksims Fiosins
AligNet: Alignment of protein-protein interaction networks,Ricardo Alberich, Adria Alcala,Merce Llabres, Francesc Rossello,Gabriel Valiente
11:35am-12:00pm
DeepiRNA: Predicting transposon-derived piRNAs with deep learning,Wen Zhang, Jiangtao Song, FengLiu
Identifying human essential genesby network embedding protein-protein interaction network, WeiDai, Qi Chang, Wei Peng,Jiancheng Zhong
12:00pm-12:20pm
PU-Caller: Sensitive somatic variantcalling using positive-unlabeledlearning, Elham Sherafat, IonMandoiu
Alignment of biological networks byinteger linear programming: Virus-host protein-protein interactionnetworks, Merce Llabres, GabrielRiera, Francesc Rossello, GabrielValiente
12:20pm-2:00pm
Lunch BreakRestaurant: Unity Sodexo
2:00pm-3:35pm
Parallel SessionsRoom: Aula Master Room: Sala Agora
Session 3A:Machine Learning 2Chair: Heta Desai
Session 3B:Phylogeny 1Chair: Sagi Snir
2:00pm-2:25pm
Iterative sure independent rankingand screening for drug responseprediction, Yufang Qin, Biao An,Qianwen Zhang, Yun Fang, MingChen
Simultaneous multi-domain-multi-gene reconciliation under thedomain-gene-species reconciliationmodel, Lei Li, Mukul S. Bansal
2:25pm-2:50pm
Gene and pathway-based deepneural network for multi-omicsdata integration to predict cancersurvival outcomes, Jie Hao,Mohammad Masum, Jung Hun Oh,Mingon Kang
Greedy partition distance understochastic models: Analytic results,Sagi Snir
2:50pm-3:15pm
On tower and checkerboard neuralnetwork architectures for geneexpression inference, Vladimır Kunc,Jiri Klema
Computing a consensus phylogenyvia leaf removal, Zhi-Zhong Chen,Shohei Ueta, Jingyu Li, LushengWang
3:15pm-3:35pm
16S ribosomal gene classificationusing recurrent neural networkmodels, Heta Desai, AnujaParameshwaran, Michael Weeks,Rajshekhar Sunderraman
Spanning trees with extremals-metric and their applications inmolecular epidemiology, YuryOrlovich, Volker Kaibel, KirillKukharenko, Pavel Skums
3:35pm-3:55pm
Coffee BreakRoom: Sala Polivalent
3:55pm-5:05pm
Parallel SessionsRoom: Aula Master Room: Sala Agora
Session 4A:Sequence AnalysisChair: Fa Zhang
Session 4B:PrivacyChair: Pavel Skums
3:55pm-4:20pm
Paired-end small RNA sequencingreveals a possible overestimation inisomiR sequence repertoirepreviously reported fromconventional single read dataanalysis, Antonio Luna de Haro,Raquel Pluvinet, Jose FranciscoSanchez Herrero, Lauro Sumoy
Detecting illicit drug ads in GooglePlus, Fengpan Zhao, Pavel Skums,Alex Zelikovsky, Eric L. Sevigny,Monica Haavisto Swahn, Sheryl M.Strasser, Yubao Wu
4:20pm-4:45pm
Analysis of codon usage patterns incitrus based on coding sequencedata, Zenan Shen, Zhimeng Gan, FaZhang, Xinyao Yi, Xiaohua Wan,Jinzhi Zhang
Differentially private genomic datapublishing, Zaobo He, Jianqiang Li
4:45pm-5:05pm
CleanBreak: Complex genomicstructural variant discovery in high-throughput sequencing data,Matthew Hayes, Derrick Mullins
Identifying relatives (almost)privately, Benny Chor, OritMoskovich, Benny Pinkas
Wednesday, June 5th, 2019
9:00am-10:10am
Parallel SessionsRoom: Aula Master Room: Sala Agora
Session 5A:Protein StructureChair: Tun-Wen Pai
Session 5B:Comparative GenomicsChair: Alex Zelikovsky
9:00am-9:25am
PSLDoc3: A high-throughputprotein function prediction by thenovel k-nearest neighbor and votingalgorithms, Yi-Wei Liu, Tz-Wei Hsu,Che-Yu Chang, Wen-Hung Liao,Jia-Ming Chang
Using earth mover’s distancebetween k-mers for viral outbreakinvestigations, Andrii Melnyk,Sergey Knyazev, Yury Khudyakov,Leonid Bunimovich, FredrikVannberg, Pavel Skums, AlexZelikovsky
9:25am-9:50am
Conformational epitope matchingand prediction based on proteinsurface spiral features, Tun-Wen Pai
Iterative spaced seed hashing:Closing the gap between spacedseed hashing and k-mer hashing,Enrico Petrucci, Laurent Noe,Cinzia Pizzi, Matteo Comin
9:50am-10:10am
TLC SDSB: A two-layer structuredclassifier for identifying single-strandedand double-stranded DNA-bindingproteins from protein sequence, JingHu, Filip Keri
Toward a dynamic threshold forquality-score distortion in reference-based alignment, Ana Hernandez,Marco Mattavelli, Claudio Alberti
10:10am-10:30am
Coffee BreakRoom: Sala Polivalent
10:30am-12:30pm
Parallel SessionsRoom: Aula Master Room: Sala Agora
Session 6A:NetworksChair: Merce Llabres
Session 6B:Structural AnalysisChair: Nikita Alexeev
10:30am-10:55am
Model revision of booleanregulatory networks at stable state,Filipe Gouveia, Ines Lynce, PedroT. Monteiro
The review of bioinformatics toolfor 3D plant genomics research,Xiangyu Yang, Jingtian Zhao,Zhenghao Li, Pengcao Li, Le Zhang
10:55am-11:20am
Constructing cancer patient-specificand group-specific gene networkswith multi-omics data, Wook Lee,Kyungsook Han
Maximum stacking base pairs:Hardness and approximation bynonlinear LP-rounding, Lixin Liu,Haitao Jiang, Peiqing Liu, BinhaiZhu, Daming Zhu
11:20am-11:45am
Flexible comparative genomics ofprokaryotic transcriptionalregulatory networks, Sefa Kilic,Miquel Sanchez-Osuna, AntonioCollado-Padilla, Jordi Barbe, IvanErill
Graph transformations, semigroups,and isotopic labeling, Jakob LykkeAndersen, Daniel Merkle, PeterSeverin Rasmussen
11:45am-12:10am
IDNDDI: An integrated drugsimilarity network method forpredicting drug-drug interactions,Cheng Yan, Guihua Duan, YayanZhang, Fangxiang Wu, Yi Pan,Jianxin Wang
A robustness analysis of dynamicboolean models of cellular circuits,Roded Sharan, Ariel Bruner
12:10am-12:30am
Comparison of parameterestimation methods in the presenceof overdispersion: An infectiousdisease based simulation study,Kimberlyn Roosa, Ruiyan Luo,Gerardo Chowell
Evolutionary switches structuraltransition states explored withminimalist coarse grained models,Francesco Delfino, Yuri Porozov,Eugene Stepanov, Gaik Tamazian,Valentina Tozzini
12:30pm-2:00pm
Lunch BreakRestaurant: Unity Sodexo
2:00pm-3:00pm
Plenary SessionRoom: Aula MasterChair: Alex Zelikovsky
Session 7: Keynote TalkLearning tumor phylogenies from single-cell dataNiko Beerenwinkel, ETH Zurich
3:00pm-3:20pm
Coffee BreakRoom: Sala Polivalent
3:20pm-4:55pm
Parallel SessionsRoom: Aula Master Room: Sala Agora
Session 8A:Phylogeny 2Chair: Oliver Eulenstein
Session 8B:EpigenomicsChair: Ion Mandoiu
3:20pm-3:45pm
The cluster affinity distance forphylogenies, Jucheol Moon, OliverEulenstein
PeakPass: Automating ChIP-Seqblacklist creation, CharlesWimberley, Steffen Heber
3:45pm-4:10pm
An alignment-free heuristic for fastsequence comparisons withapplications to phylogenyreconstruction, Jodh Pannu, SaharHooshmand, Sriram P.Chockalingam, Sharma V.Thankachan, Srinivas Aluru
A novel neoantigen discoveryapproach based on chromatin highorder conformation, Yi Shi,Mingxuan Zhang, Luming Meng,Xianbin Su, Xueying Shang,Qingjiao Li, Mengna Lin, Xin Zou,Qing Luo, Yangyang Zhai, KunyanHe, Lan Wang, Cong Chen,Xiaofang Cui, Na Wang, Jian He,Yaoliang Yu, Yanting Wu, LintaiDa, Weidong Cai, Ze-Guang Han
4:10pm-4:35pm
Unifying gene duplication, loss, andcoalescence on phylogeneticnetworks, Peng Du, Huw Ogilvie,Luay Nakhleh
MADA: A web service for analysingDNA methylation array data, XinyuHu, Li Tang, Linconghua Wang,Fangxiang Wu, Min Li
4:35pm-4:55pm
Reconstruction of fitness landscapesof intra-host viral populations usingNGS data, Viachaslau Tsyvina,Yury Khudyakov, Pavel Skums
ZCMM: A novel algorithm ofZ-curve based and position weightmatrix for nucleosome positioning,Ying Cui, Jianzhong Li
7:00pm-9:00pm
BanquetEl Principal del Eixample
Provenca, 286–28808008 Barcelona
Thursday, June 6th, 2019
9:00am-10:00am
Plenary SessionRoom: Aula MasterChair: Gabriel Valiente
Session 9: Keynote TalkThe molecular anatomy of the human bodyRoderic Guigo, Centre for Genomic Regulation, Barcelona
10:00am-10:20am
Coffee BreakRoom: Sala Polivalent
10:20am-12:45pm
Parallel SessionsRoom: Aula Master Room: Sala Agora
Session 10A:Image AnalysisChair: Fa Zhang
Session 10B:ClusteringChair: Yuri Porozov
10:20am-10:45am
Identification of early mild cognitiveimpairment using multi-modal dataand graph convolutional networks,Guanxin Tan, Jin Liu, Wei Lan,Jianxin Wang
Markov chain Monte Carlo foractive module identificationproblem, Nikita Alexeev, JavlonIsomurodov, Gennady Korotkevich,Alexey Sergushichev
10:45am-11:10am
Anomaly detection of pedestriantrajectory based on adaptivedensity clustering, Aiguo Chen,Jiacheng Luo, Ling Tian, HaotianRao
Sorting by reversals, transpositions,and indels on both gene order andintergenic sizes, Klairton LimaBrito, Geraldine Jean, GuillaumeFertin, Andre Rodrigues Oliveira,Ulisses Dias, Zanoni Dias
11:10am-11:35am
Compressed sensing improvedreconstruction-reprojectionalgorithm for electron tomography,Lun Li, Renmin Han, Zhiyong Liu,Fa Zhang
Using DenseFly algorithm for cellsearching on massive scRNA-seqdatasets, Yixin Chen, Sijie Chen,Xuegong Zhang
11:35am-12:00pm
DM-SIRT: A distribute methodfor multi-tilt reconstruction inelectron tomography, Zihao Wang,Jingrong Zhang, Xintong Liu,Zhiyong Liu, Xiaohua Wan, FaZhang
A multi-view clustering method formicrobiome analysis by symmetricnonnegative matrix factorizationwith Hessian regularization,Yuanyuan Ma
12:00pm-12:25pm
A multi-label classification modelfor full slice brain computerisedtomography image, Guanghui Fu,Jianqiang Li, Yan Pei
MDAPlatform: A component-basedplatform for constructing andassessing miRNA-diseaseassociations prediction method,Yayan Zhang, Cheng Yan, HaolunYi, Jianxin Wang
12:25pm-12:45pm
An attention-based framework formicroaneurysms detection onFundus images, Lizong Zhang, YingLi, Guiduo Duan, Guangchun Luo,Ling Tian
Unveiling deeper relationshipsamong circulating virus sequences:Using a shared change searchmethod, Kun Zhao
12:45pm-2:00pm
Lunch BreakRestaurant: Unity Sodexo
ISBRA 2019 Map
Reception
Symposium