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2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Nov. 9 2015 to Nov. 12 2015

Washington, DC, USA

Table of Contents

Big data in biomedicine — An NIH perspectiveFreely available from IEEE.pp. 1-1
by Philip E. Bourne
Computational challenges in microbiome researchFreely available from IEEE.pp. 2-2
by Mihai Pop
Parallel machine learning approaches for reverse engineering genome-scale networksFreely available from IEEE.pp. 3-3
by Srinivas Aluru
Toward personalized pan-omic association analysis under complex structures and big dataFreely available from IEEE.pp. 4-4
by Eric Xing
Computational Synteny Block: A framework to identify evolutionary eventsFull-text access may be available. Sign in or learn about subscription options.pp. 5-12
by Jose A. Arjona-Medina, Oswaldo Trelles
Evolutionary search strategies for efficient sample-based representations of multiple-basin protein energy landscapesFull-text access may be available. Sign in or learn about subscription options.pp. 13-20
by Emmanuel Sapin, Kenneth A De Jong, Amarda Shehu
Structure-guided selection of Specificity Determining Positions in the human kinomeFull-text access may be available. Sign in or learn about subscription options.pp. 21-28
by Mark Moll, Paul W. Finn, Lydia E. Kavraki
Boosting compound-protein interaction prediction by deep learningFull-text access may be available. Sign in or learn about subscription options.pp. 29-34
by Kai Tian, Mingyu Shao, Shuigeng Zhou, Jihong Guan
Computing transition paths in multiple-basin proteins with a probabilistic roadmap algorithm guided by structure dataFull-text access may be available. Sign in or learn about subscription options.pp. 35-42
by Tatiana Maximova, Erion Plaku, Amarda Shehu
A module tree of Wnt signal transduction pathwaysFull-text access may be available. Sign in or learn about subscription options.pp. 43-48
by Losiana Nayak, Nitai P. Bhattacharyya, Rajat K. De
A novel dimensionality reduction algorithm based on Laplace matrix for microbiome data analysisFull-text access may be available. Sign in or learn about subscription options.pp. 49-54
by Yetian Fan, Xingpeng Jiang, Xiaohua Hu, Bo Song, Yuan Ling, Wei Wu
Predicting Protein-protein interaction using co-occurring Aligned Pattern ClustersFull-text access may be available. Sign in or learn about subscription options.pp. 55-60
by Antonio Sze-To, Sanderz Fung, En-Shiun Annie Lee, Andrew K. C. Wong
Adaptive local learning in sampling based motion planning for protein foldingFull-text access may be available. Sign in or learn about subscription options.pp. 61-68
by Chinwe Ekenna, Shawna Thomas, Nancy M. Amato
A new algorithm for “the LCS problem” with application in compressing genome resequencing dataFull-text access may be available. Sign in or learn about subscription options.pp. 69-74
by Richard Beal, Tazin Afrin, Aliya Farheen, Don Adjeroh
Superposition of protein structures using electrostatic isopotentialsFull-text access may be available. Sign in or learn about subscription options.pp. 75-82
by Ziyi Guo, Katya Scheinberg, Juliana Hong, Brian Y. Chen
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian modelsFull-text access may be available. Sign in or learn about subscription options.pp. 83-90
by Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
Protein model quality assessment by learning-to-rankFull-text access may be available. Sign in or learn about subscription options.pp. 91-96
by Xiaoyang Jing, Qiwen Dong, Xuan Liu, Bin Liu
MALBACsim: A Multiple Annealing and Looping Based Amplification Cycles simulatorFull-text access may be available. Sign in or learn about subscription options.pp. 97-100
by Tengpeng Li, Changsheng Zhang, Bo Xu, Hongmin Cai, Fuqiang Li
Short read error correction using an FM-indexFull-text access may be available. Sign in or learn about subscription options.pp. 101-104
by Seth Greenstein, James Holt, Leonard McMillan
HapColor: A graph coloring framework for polyploidy phasingFull-text access may be available. Sign in or learn about subscription options.pp. 105-108
by Sepideh Mazrouee, Wei Wang
Detecting temporal protein complexes based on Neighbor Closeness and time course protein interaction networksFull-text access may be available. Sign in or learn about subscription options.pp. 109-112
by Xianjun Shen, Yi Li, Xingpeng Jiang, Yanli Zhao, Tingting He, Jincai Yang
Accurate simulation of large collections of phylogenetic treesFull-text access may be available. Sign in or learn about subscription options.pp. 113-118
by Suzanne J. Matthews
Time series analysis of microbiome data regularized by local linear manifoldFull-text access may be available. Sign in or learn about subscription options.pp. 119-122
by Xingpeng Jiang, Xiaohua Hu, Tingting He
Does encoding matter? A novel view on the quantitative genetic trait prediction problemFull-text access may be available. Sign in or learn about subscription options.pp. 123-126
by Dan He, Laxmi Parida
Fast alignment filtering of nanopore sequencing reads using locality-sensitive hashingFull-text access may be available. Sign in or learn about subscription options.pp. 127-130
by Jeremy R. Wang, Corbin D. Jones
Quantifying feed efficiency of dairy cattle for genome-wide association analysisFull-text access may be available. Sign in or learn about subscription options.pp. 131-134
by Tingyang Xu, Jiangwen Sun, Erin E Connor, Jinbo Bi
RF-Phos: Random forest-based prediction of phosphorylation sitesFull-text access may be available. Sign in or learn about subscription options.pp. 135-140
by Ahoi Jones, Hamid Ismail, Jung H. Kim, Robert Newman, B KC Dukka
Imputation of ChIP-seq datasets via Low Rank Convex Co-EmbeddingFull-text access may be available. Sign in or learn about subscription options.pp. 141-144
by Lin Zhu, Wei-Li Guo, De-Shuang Huang, Can-Yi Lu
Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to Psychiatric disordersFull-text access may be available. Sign in or learn about subscription options.pp. 145-150
by Dong-Chul Kim, Mingon Kang, Ashis Biswas, Chunyu Liu, Jean Gao
A novel two-stage method for identifying microRNA-gene regulatory modules in breast cancerFull-text access may be available. Sign in or learn about subscription options.pp. 151-156
by Wenwen Min, Juan Liu, Fei Luo, Shihua Zhang
Construction of signaling networks with incomplete RNAi dataFull-text access may be available. Sign in or learn about subscription options.pp. 157-162
by Qiyao Wang, Yuanfang Ren, Md Mahmudul Hasan, Ahmet Ay, Tamer Kahveci
Reconstructing directed gene regulatory network by only gene expression dataFull-text access may be available. Sign in or learn about subscription options.pp. 163-170
by Lu Zhang, Yen Kaow Ng, ShuaiCheng Li
Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiformeFull-text access may be available. Sign in or learn about subscription options.pp. 171-176
by Yu-Chiao Chiu, Kai-Wen Liang, Tzu-Hung Hsiao, Yidong Chen, Eric Y. Chuang
EpiTracer - an algorithm for identifying epicenters in condition-specific biological networksFull-text access may be available. Sign in or learn about subscription options.pp. 177-182
by Narmada Sambaturu, Madhulika Mishra, Nagasuma Chandra
Predicting microRNA-disease associations by integrating multiple biological informationFull-text access may be available. Sign in or learn about subscription options.pp. 183-188
by Wei Lan, Jianxin Wang, Min Li, Jin Liu, Yi Pan
Identification of phenotypic networks based on whole transcriptome by comparative network decompositionFull-text access may be available. Sign in or learn about subscription options.pp. 189-194
by Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
A two-step logistic regression algorithm for identifying individual-cancer-related genesFull-text access may be available. Sign in or learn about subscription options.pp. 195-200
by Bolin Chen, Xuequn Shang, Min Li, Jianxin Wang, Fang-Xiang Wu
Protein-protein interaction network inference from multiple kernels with optimization based on random walk by linear programmingFull-text access may be available. Sign in or learn about subscription options.pp. 201-207
by Lei Huang, Li Liao, Cathy H. Wu
Triple imputation for microarray missing value estimationFull-text access may be available. Sign in or learn about subscription options.pp. 208-213
by Chong He, Hui-Hui Li, Changbo Zhao, Guo-Zheng Li, Wei Zhang
Model-based and context-specific background correction and differential methylation testing for MBDCap-seqFull-text access may be available. Sign in or learn about subscription options.pp. 214-219
by Yuanhang Liu, Desiree Wilson, Robin J. Leach, Yidong Chen
GREAT: GRaphlet Edge-based network AlignmenTFull-text access may be available. Sign in or learn about subscription options.pp. 220-227
by Joseph Crawford, Tijana Milenkovic
Purification of LC/GC-MS based biomolecular expression profiles using a topic modelFull-text access may be available. Sign in or learn about subscription options.pp. 228-233
by Minkun Wang, Tsung-Heng Tsai, Guoqiang Yu, Habtom W. Ressom
petal: A novel co-expression network modeling systemFull-text access may be available. Sign in or learn about subscription options.pp. 234-241
by Juli Petereit, Frederick C. Harris, Karen Schlauch
Interpretable deep neural networks for enhancer predictionFull-text access may be available. Sign in or learn about subscription options.pp. 242-249
by Seong Gon Kim, Nawanol Theera-Ampornpunt, Ananth Grama, Somali Chaterji
DiscMLA: AUC-based discriminative motif learningFull-text access may be available. Sign in or learn about subscription options.pp. 250-255
by Hongbo Zhang, Lin Zhu, Deshuang Huang
Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis toolFull-text access may be available. Sign in or learn about subscription options.pp. 256-262
by Neil R. Clark, Maciej Szymkiewicz, Zichen Wang, Caroline D. Monteiro, Matthew R. Jones, Avi Ma'ayan
On observability of attractors in Boolean NetworksFull-text access may be available. Sign in or learn about subscription options.pp. 263-266
by Yushan Qiu, Xiaoqing Cheng, Wai-Ki Ching, Hao Jiang, Tatsuya Akutsu
Hausdorff distance and global silhouette index as novel measures for estimating quality of biclustersFull-text access may be available. Sign in or learn about subscription options.pp. 267-272
by Nishchal K. Verma, Esha Dutta, Yan Cui
Integrated study to infer dynamic protein-gene interactions in human p53 regulatory networksFull-text access may be available. Sign in or learn about subscription options.pp. 273-276
by Junbai Wang, Qianqian Wu, Tianhai Tian
An efficient method to identify essential proteins for different species by integrating protein subcellular localization informationFull-text access may be available. Sign in or learn about subscription options.pp. 277-280
by Xiaoqing Peng, Jianxin Wang, Jiancheng Zhong, Junwei Luo, Yi Pan
Exhaustive analysis of dynamical properties of Biological Regulatory Networks with Answer Set ProgrammingFull-text access may be available. Sign in or learn about subscription options.pp. 281-285
by Emna Ben Abdallah, Maxime Folschette, Olivier Roux, Morgan Magnin
An efficient ACS algorithm for classification-based peptide identificationFull-text access may be available. Sign in or learn about subscription options.pp. 286-289
by Xijun Liang, Zhonghang Xia, Ling Jian, Xinnan Niu, Andrew Link
Joint inference of tissue-specific networks with a scale free topologyFull-text access may be available. Sign in or learn about subscription options.pp. 290-294
by Somaye Hashemifar, Behnam Neyshabur, Jinbo Xu
Human absorbable microRNA prediction based on an ensemble manifold ranking modelFull-text access may be available. Sign in or learn about subscription options.pp. 295-300
by Jiang Shu, Kevin Chiang, Dongyu Zhao, Juan Cui
Guilt-by association approach to identify novel human aging-related genes using protein domainsFull-text access may be available. Sign in or learn about subscription options.pp. 301-304
by Jasjit K Banwait, Schuyler P Dougherty, Ishwor Thapa, Dhundy K Bastola
A test for detecting differentially methylated regionsFull-text access may be available. Sign in or learn about subscription options.pp. 305-308
by Iksoo Huh, Soojin V. Yi, Taesung Park
RREV: Reconfigurable Rendering Engine for visualization of clinically annotated polysomnogramsFull-text access may be available. Sign in or learn about subscription options.pp. 309-316
by Catherine P. Jayapandian, Wei Wang, Michael G. Morrical, Dennis A. Dean, Shiqiang Tao, Daniel R. Mobley, Mathew Kim, Michael Rueschman, Kenneth A. Loparo, Susan Redline, Guo-Qiang Zhang
Spatio-temporal diffusion-based dynamic cell segmentationFull-text access may be available. Sign in or learn about subscription options.pp. 317-324
by Fatima Boukari, Sokratis Makrogiannis
Context-learning based electroencephalogram analysis for epileptic seizure detectionFull-text access may be available. Sign in or learn about subscription options.pp. 325-330
by Guangxu Xun, Xiaowei Jia, Aidong Zhang
Sparse multidimensional patient modeling using auxiliary confidence labelsFull-text access may be available. Sign in or learn about subscription options.pp. 331-336
by Eric Heim, Milos Hauskrecht
Analysis of facial muscle activation in children with autism using 3D imagingFull-text access may be available. Sign in or learn about subscription options.pp. 337-342
by Manar D. Samad, Jonna L. Bobzien, John W. Harrington, Khan M. Iftekharuddin
Modeling electronic health records in ensembles of semantic spaces for adverse drug event detectionFull-text access may be available. Sign in or learn about subscription options.pp. 343-350
by Aron Henriksson, Jing Zhao, Henrik Bostrom, Hercules Dalianis
A generative Bayesian model to identify cancer driver genesFull-text access may be available. Sign in or learn about subscription options.pp. 351-356
by Christopher Ma, Zhendong Zhao, Tina Gui, Yixin Chen, Xin Dang, Dawn Wilkins
A seeding-searching-ensemble method for gland segmentation and detectionFull-text access may be available. Sign in or learn about subscription options.pp. 357-362
by Yizhe Zhang, Lin Yang, John D. MacKenzie, Rageshree Ramachandran, Danny Z. Chen
On frequency dependencies of sliding window correlationFull-text access may be available. Sign in or learn about subscription options.pp. 363-368
by Sadia Shakil, Shella Dawn Keilholz, Chin-Hui Lee
Robust point matching by l1 regularizationFull-text access may be available. Sign in or learn about subscription options.pp. 369-374
by Jianbing Yi, Yan-Ran Li, Xuan Yang, Tiancheng He, Guoliang Chen
Temporal weighting of clinical events in electronic health records for pharmacovigilanceFull-text access may be available. Sign in or learn about subscription options.pp. 375-381
by Jing Zhao
Level set segmentation using non-negative matrix factorization of brain MRI imagesFull-text access may be available. Sign in or learn about subscription options.pp. 382-387
by Dimah Dera, Nidhal Bouaynaya, Hassan M Fathallah-Shaykh
Using myoelectric signals to recognize grips and movements of the handFull-text access may be available. Sign in or learn about subscription options.pp. 388-394
by Gene Shuman, Zoran Duric, Daniel Barbara, Jessica Lin, Lynn H. Gerber
Feature-level fusion of multimodal physiological signals for emotion recognitionFull-text access may be available. Sign in or learn about subscription options.pp. 395-399
by Jing Chen, Bin Hu, Lixin Xu, Philip Moore, Yun Su
Quantitative assessment of the parallel MRI reconstruction using background noise uniformityFull-text access may be available. Sign in or learn about subscription options.pp. 400-404
by Fu-Hsing Wu, Hsin-Chih Lo
An image reconstruction model and hybrid algorithm for limited-angle projection dataFull-text access may be available. Sign in or learn about subscription options.pp. 405-408
by Gao Hongxia, Luo Yinghao, Chen Kewei, Ma Ge, Wu Lixuan
Classification of Alzheimer's disease based on the combination of morphometric feature and texture featureFull-text access may be available. Sign in or learn about subscription options.pp. 409-412
by Yi Ding, Cong Zhang, Tian Lan, Zhiguang Qin, Xinjie Zhang, Wei Wang
Segmentation of Multicolor Fluorescence In-Situ Hybridization (M-FISH) image using an improved Fuzzy C-means clustering algorithm while incorporating both spatial and spectral informationFull-text access may be available. Sign in or learn about subscription options.pp. 413-416
by Jingyao Li, Dongdong Lin, Yu-Ping Wang
On using Compressed Sensing and peak detection method for the Dynamic Instability parameters estimation for Microtubules modeled in three statesFull-text access may be available. Sign in or learn about subscription options.pp. 417-420
by Shantia Yarahmadian, Vineetha Menon, Vahid Rezania
Improved brain tumor growth prediction and segmentation in longitudinal brain MRIFull-text access may be available. Sign in or learn about subscription options.pp. 421-424
by Linmin Pei, Syed M. S. Reza, Khan M. Iftekharuddin
Robust landmark-based image registration using l1 and l2 norm regularizationsFull-text access may be available. Sign in or learn about subscription options.pp. 425-428
by Xuan Yang, Bo Wang, Yan-Ran Li, Tiancheng He
Biomedical event trigger detection by dependency-based word embeddingFull-text access may be available. Sign in or learn about subscription options.pp. 429-432
by Jian Wang, Jianhai Zhang, Yuan An, Hongfei Lin, Zhihao Yang, Yijia Zhang, Yuanyuan Sun
Survival analysis via transduction for semi-supervised neural networks in medical prognosisFull-text access may be available. Sign in or learn about subscription options.pp. 433-437
by Faisal M. Khan, Casimir A. Kulikowski
On automated Flow Cytometric analysis for MRD estimation of Acute Lymphoblastic Leukaemia: A comparison among different approachesFull-text access may be available. Sign in or learn about subscription options.pp. 438-441
by Paolo Rota, Stefanie Groeneveld-Krentz, Michael Reiter
Audio signals encoding for cough classification using convolutional neural networks: A comparative studyFull-text access may be available. Sign in or learn about subscription options.pp. 442-445
by Hui-Hui Wang, Jia-Ming Liu, Mingyu You, Guo-Zheng Li
Using Hidden Markov Models to capture temporal aspects of ultrasound data in prostate cancerFull-text access may be available. Sign in or learn about subscription options.pp. 446-449
by Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Parvin Mousavi, Hagit Shatkay
A segmentation-based multi-scale framework for the classification of epithelial and stromal tissues in H&E imagesFull-text access may be available. Sign in or learn about subscription options.pp. 450-453
by Filiz Bunyak, Adel Hafiane, Zahraa Al-Milaji, Ilker Ersoy, Anoop Haridas, Kannappan Palaniappan
EEG dynamic source localization using Marginalized Particle FilteringFull-text access may be available. Sign in or learn about subscription options.pp. 454-457
by Bradley Ebinger, Nidhal Bouaynaya, Petia Georgieva, Lyudmila Mihaylova
Feature selection of high-dimensional biomedical data using improved SFLA for disease diagnosisFull-text access may be available. Sign in or learn about subscription options.pp. 458-463
by Yongqiang Dai, Bin Hu, Yun Su, Chengsheng Mao, Jing Chen, Xiaowei Zhang, Philip Moore, Lixin Xu, Hanshu Cai
Learning to rank for biomedical information retrievalFull-text access may be available. Sign in or learn about subscription options.pp. 464-469
by Bo Xu, Hongfei Lin, Yuan Lin, Yunlong Ma, Liang Yang, Jian Wang, Zhihao Yang
Identification of DNA-binding proteins by auto-cross covariance transformationFull-text access may be available. Sign in or learn about subscription options.pp. 470-475
by Qiwen Dong, Shanyi Wang, Kai Wang, Xuan Liu, Bin Liu
Algorithmic detection of inconsistent modeling among SNOMED CT concepts by combining lexical and structural indicatorsFull-text access may be available. Sign in or learn about subscription options.pp. 476-483
by Ankur Agrawal, Yehoshua Perl, Chris Ochs, Gai Elhanan
Scalable biobanking: A modular electronic Honest Broker and Biorepository for integrated clinical, specimen and genomic researchFull-text access may be available. Sign in or learn about subscription options.pp. 484-490
by Alex S. Felmeister, Tyler J. Rivera, Aaron J. Masino, Adam C. Resnick, Jeffrey W. Pennington
Supporting HIV literature screening with data sampling and supervised learningFull-text access may be available. Sign in or learn about subscription options.pp. 491-496
by Hayda Almeida, Marie-Jean Meurs, Leila Kosseim, Adrian Tsang
Implicit knowledge discovery in biomedical ontologies: Computing interesting relatednessesFull-text access may be available. Sign in or learn about subscription options.pp. 497-502
by Tian Bai, Leiguang Gong, Casimir A. Kulikowski, Lan Huang
Accelerating large-scale biological database search on Xeon Phi-based neo-heterogeneous architecturesFull-text access may be available. Sign in or learn about subscription options.pp. 503-510
by Haidong Lan, Weiguo Liu, Bertil Schmidt, Bingqiang Wang
A two-stage clustering technique for automatic biaxial gating of flow cytometry dataFull-text access may be available. Sign in or learn about subscription options.pp. 511-516
by M. Baran Pouyan, V. Jindal, J. Birjandtalab, M. Nourani
An integrative measure of graph- and vector-based semantic similarity using information content distanceFull-text access may be available. Sign in or learn about subscription options.pp. 517-522
by Qiaoli Hu, Young-Rae Cho
On stabbing queries for generalized longest repeatFull-text access may be available. Sign in or learn about subscription options.pp. 523-530
by Bojian Xu
Integrating association mining into relevance feedback for biomedical literature searchFull-text access may be available. Sign in or learn about subscription options.pp. 531-536
by Yanqing Ji, Hao Ying, John Tran, Peter Dews, R. Michael Massanari
Improved algorithms for finding edit distance based motifsFull-text access may be available. Sign in or learn about subscription options.pp. 537-542
by Soumitra Pal, Sanguthevar Rajasekaran
Discovery of the relations between genetic polymorphism and adverse drug reactionsFull-text access may be available. Sign in or learn about subscription options.pp. 543-548
by Zhaohui Liang, Gang Zhang, Jimmy Xiangji Huang
Identifying inorganic material affinity classes for peptide sequences based on context learningFull-text access may be available. Sign in or learn about subscription options.pp. 549-554
by Guangxu Xun, Xiaoyi Li, Marc R. Knecht, Paras N. Prasad, Mark T. Swihart, Tiffany R. Walsh, Aidong Zhang
Identifying the pre-transition state during biological processes by hidden Markov modelFull-text access may be available. Sign in or learn about subscription options.pp. 555-562
by Pei Chen, Shuoyang Qiu, Yue Wang, Yongjun Li
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