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BIBM 2015: Washington, DC, USA
- Jun Huan, Satoru Miyano, Amarda Shehu, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Vijay K. Gombar, Matthieu-P. Schapranow, Illhoi Yoo, Jiayu Zhou, Brian Chen, Vinay Pai, Brian G. Pierce:
2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, DC, USA, November 9-12, 2015. IEEE Computer Society 2015, ISBN 978-1-4673-6799-8 - Philip E. Bourne:
Big data in biomedicine - An NIH perspective. 1 - Mihai Pop
:
Computational challenges in microbiome research. 2 - Srinivas Aluru:
Parallel machine learning approaches for reverse engineering genome-scale networks. 3 - Eric P. Xing:
Toward personalized pan-omic association analysis under complex structures and big data. 4 - Jose A. Arjona-Medina
, Oswaldo Trelles:
Computational Synteny Block: A framework to identify evolutionary events. 5-12 - Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu:
Evolutionary search strategies for efficient sample-based representations of multiple-basin protein energy landscapes. 13-20 - Mark Moll, Paul W. Finn, Lydia E. Kavraki
:
Structure-guided selection of Specificity Determining Positions in the human kinome. 21-28 - Kai Tian, Mingyu Shao, Shuigeng Zhou, Jihong Guan:
Boosting compound-protein interaction prediction by deep learning. 29-34 - Tatiana Maximova
, Erion Plaku, Amarda Shehu:
Computing transition paths in multiple-basin proteins with a probabilistic roadmap algorithm guided by structure data. 35-42 - Losiana Nayak
, Nitai P. Bhattacharyya, Rajat K. De:
A module tree of Wnt signal transduction pathways. 43-48 - Yetian Fan, Xingpeng Jiang, Xiaohua Hu, Bo Song, Yuan Ling, Wei Wu:
A novel dimensionality reduction algorithm based on Laplace matrix for microbiome data analysis. 49-54 - Antonio Sze-To, Sanderz Fung, En-Shiun Annie Lee, Andrew K. C. Wong:
Predicting Protein-protein interaction using co-occurring Aligned Pattern Clusters. 55-60 - Chinwe Ekenna, Shawna L. Thomas, Nancy M. Amato:
Adaptive local learning in sampling based motion planning for protein folding. 61-68 - Richard Beal, Tazin Afrin, Aliya Farheen, Don Adjeroh:
A new algorithm for "the LCS problem" with application in compressing genome resequencing data. 69-74 - Ziyi Guo, Katya Scheinberg
, Juliana Hong, Brian Yuan Chen:
Superposition of protein structures using electrostatic isopotentials. 75-82 - Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt:
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. 83-90 - Xiaoyang Jing, Qiwen Dong, Xuan Liu, Bin Liu:
Protein model quality assessment by learning-to-rank. 91-96 - Tengpeng Li, Changsheng Zhang, Bo Xu, Hongmin Cai
, Fuqiang Li:
MALBACsim: A Multiple Annealing and Looping Based Amplification Cycles simulator. 97-100 - Seth Greenstein, James Holt, Leonard McMillan:
Short read error correction using an FM-index. 101-104 - Sepideh Mazrouee, Wei Wang
:
HapColor: A graph coloring framework for polyploidy phasing. 105-108 - Xianjun Shen, Yi Li, Xingpeng Jiang, Yanli Zhao, Tingting He, Jincai Yang:
Detecting temporal protein complexes based on Neighbor Closeness and time course protein interaction networks. 109-112 - Suzanne J. Matthews
:
Accurate simulation of large collections of phylogenetic trees. 113-118 - Xingpeng Jiang, Xiaohua Hu, Tingting He:
Time series analysis of microbiome data regularized by local linear manifold. 119-122 - Dan He, Laxmi Parida:
Does encoding matter? A novel view on the quantitative genetic trait prediction problem. 123-126 - Jeremy R. Wang, Corbin D. Jones:
Fast alignment filtering of nanopore sequencing reads using locality-sensitive hashing. 127-130 - Tingyang Xu, Jiangwen Sun, Erin E. Connor, Jinbo Bi:
Quantifying feed efficiency of dairy cattle for genome-wide association analysis. 131-134 - Ahoi Jones, Hamid D. Ismail
, Jung H. Kim, Robert H. Newman, K. C. Dukka B.:
RF-Phos: Random forest-based prediction of phosphorylation sites. 135-140 - Lin Zhu, Wei-Li Guo, De-Shuang Huang, Canyi Lu:
Imputation of ChIP-seq datasets via Low Rank Convex Co-Embedding. 141-144 - Dong-Chul Kim, Mingon Kang, Ashis Kumer Biswas
, Chunyu Liu, Jean Gao:
Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to Psychiatric disorders. 145-150 - Wenwen Min
, Juan Liu, Fei Luo, Shi-Hua Zhang:
A novel two-stage method for identifying microRNA-gene regulatory modules in breast cancer. 151-156 - Qiyao Wang, Yuanfang Ren, Md Mahmudul Hasan, Ahmet Ay, Tamer Kahveci:
Construction of signaling networks with incomplete RNAi data. 157-162 - Lu Zhang
, Yen Kaow Ng
, Shuaicheng Li
:
Reconstructing directed gene regulatory network by only gene expression data. 163-170 - Yu-Chiao Chiu, Kai-Wen Liang, Tzu-Hung Hsiao, Yidong Chen, Eric Y. Chuang:
Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. 171-176 - Narmada Sambaturu
, Madhulika Mishra
, Nagasuma Chandra
:
EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks. 177-182 - Wei Lan
, Jianxin Wang, Min Li, Jin Liu, Yi Pan
:
Predicting microRNA-disease associations by integrating multiple biological information. 183-188 - Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen:
Identification of phenotypic networks based on whole transcriptome by comparative network decomposition. 189-194 - Bolin Chen, Xuequn Shang, Min Li, Jianxin Wang, Fang-Xiang Wu
:
A two-step logistic regression algorithm for identifying individual-cancer-related genes. 195-200 - Lei Huang, Li Liao, Cathy H. Wu
:
Protein-protein interaction network inference from multiple kernels with optimization based on random walk by linear programming. 201-207 - Chong He, Hui-Hui Li, Changbo Zhao, Guo-Zheng Li, Wei Zhang:
Triple imputation for microarray missing value estimation. 208-213 - Yuanhang Liu
, Desiree Wilson, Robin J. Leach
, Yidong Chen:
Model-based and context-specific background correction and differential methylation testing for MBDCap-seq. 214-219 - Joseph Crawford, Tijana Milenkovic:
GREAT: GRaphlet Edge-based network AlignmenT. 220-227 - Minkun Wang, Tsung-Heng Tsai, Guoqiang Yu, Habtom W. Ressom:
Purification of LC/GC-MS based biomolecular expression profiles using a topic model. 228-233 - Juli Petereit, Frederick C. Harris Jr., Karen Schlauch:
petal: A novel co-expression network modeling system. 234-241 - Seong Gon Kim, Nawanol Theera-Ampornpunt, Ananth Grama, Somali Chaterji:
Interpretable deep neural networks for enhancer prediction. 242-249 - Hongbo Zhang, Lin Zhu, Deshuang Huang:
DiscMLA: AUC-based discriminative motif learning. 250-255 - Neil R. Clark
, Maciej Szymkiewicz
, Zichen Wang, Caroline D. Monteiro, Matthew R. Jones, Avi Ma'ayan
:
Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. 256-262 - Yushan Qiu, Xiaoqing Cheng, Wai-Ki Ching, Hao Jiang, Tatsuya Akutsu
:
On observability of attractors in Boolean Networks. 263-266 - Nishchal K. Verma, Esha Dutta, Yan Cui
:
Hausdorff distance and global silhouette index as novel measures for estimating quality of biclusters. 267-272 - Junbai Wang, Qianqian Wu, Tianhai Tian
:
Integrated study to infer dynamic protein-gene interactions in human p53 regulatory networks. 273-276 - Xiaoqing Peng, Jianxin Wang, Jiancheng Zhong, Junwei Luo, Yi Pan
:
An efficient method to identify essential proteins for different species by integrating protein subcellular localization information. 277-280 - Emna Ben Abdallah, Maxime Folschette
, Olivier F. Roux, Morgan Magnin:
Exhaustive analysis of dynamical properties of Biological Regulatory Networks with Answer Set Programming. 281-285 - Xijun Liang, Zhonghang Xia, Ling Jian, Xinnan Niu, Andrew J. Link:
An efficient ACS algorithm for classification-based peptide identification. 286-289 - Somaye Hashemifar, Behnam Neyshabur, Jinbo Xu:
Joint inference of tissue-specific networks with a scale free topology. 290-294 - Jiang Shu
, Kevin Chiang, Dongyu Zhao, Juan Cui:
Human absorbable microRNA prediction based on an ensemble manifold ranking model. 295-300 - Jasjit K. Banwait
, Schuyler P. Dougherty, Ishwor Thapa, Dhundy Kiran Bastola:
Guilt-by association approach to identify novel human aging-related genes using protein domains. 301-304 - Ik-Soo Huh, Soojin V. Yi, Taesung Park:
A test for detecting differentially methylated regions. 305-308 - Catherine P. Jayapandian, Wei Wang, Michael G. Morrical, Dennis A. Dean, Shiqiang Tao, Daniel R. Mobley, Matthew Kim, Michael Rueschman, Kenneth A. Loparo
, Susan Redline, Guo-Qiang Zhang:
RREV: Reconfigurable Rendering Engine for visualization of clinically annotated polysomnograms. 309-316 - Fatima Boukari
, Sokratis Makrogiannis
:
Spatio-temporal diffusion-based dynamic cell segmentation. 317-324 - Guangxu Xun
, Xiaowei Jia, Aidong Zhang:
Context-learning based electroencephalogram analysis for epileptic seizure detection. 325-330 - Eric Heim, Milos Hauskrecht:
Sparse multidimensional patient modeling using auxiliary confidence labels. 331-336 - Manar D. Samad, Jonna L. Bobzien, John W. Harrington, Khan M. Iftekharuddin:
Analysis of facial muscle activation in children with autism using 3D imaging. 337-342 - Aron Henriksson, Jing Zhao, Henrik Boström, Hercules Dalianis:
Modeling electronic health records in ensembles of semantic spaces for adverse drug event detection. 343-350 - Christopher Ma, Zhendong Zhao, Tina Gui, Yixin Chen, Xin Dang, Dawn Wilkins:
A generative Bayesian model to identify cancer driver genes. 351-356 - Yizhe Zhang, Lin Yang, John D. MacKenzie, Rageshree Ramachandran, Danny Z. Chen:
A seeding-searching-ensemble method for gland segmentation and detection. 357-362 - Sadia Shakil
, Shella Dawn Keilholz, Chin-Hui Lee:
On frequency dependencies of sliding window correlation. 363-368 - JianBing Yi, Yan-Ran Li, Xuan Yang, Tiancheng He, Guoliang Chen:
Robust point matching by l1 regularization. 369-374 - Jing Zhao:
Temporal weighting of clinical events in electronic health records for pharmacovigilance. 375-381 - Dimah Dera
, Nidhal Bouaynaya, Hassan M. Fathallah-Shaykh
:
Level set segmentation using non-negative matrix factorization of brain MRI images. 382-387 - Gene Shuman, Zoran Duric, Daniel Barbará, Jessica Lin, Lynn H. Gerber:
Using myoelectric signals to recognize grips and movements of the hand. 388-394 - Jing Chen, Bin Hu, Lixin Xu, Philip Moore, Yun Su:
Feature-level fusion of multimodal physiological signals for emotion recognition. 395-399 - Fu-Hsing Wu
, Hsin-Chih Lo:
Quantitative assessment of the parallel MRI reconstruction using background noise uniformity. 400-404 - Hongxia Gao, Yinghao Luo, Kewei Chen, Ge Ma, Lixuan Wu:
An image reconstruction model and hybrid algorithm for limited-angle projection data. 405-408 - Yi Ding, Cong Zhang, Tian Lan, Zhiguang Qin, Xinjie Zhang, Wei Wang:
Classification of Alzheimer's disease based on the combination of morphometric feature and texture feature. 409-412 - Jingyao Li, Dongdong Lin, Yu-Ping 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 information. 413-416 - Shantia Yarahmadian, Vineetha Menon, Vahid Rezania:
On using Compressed Sensing and peak detection method for the Dynamic Instability parameters estimation for Microtubules modeled in three states. 417-420 - Linmin Pei
, Syed M. S. Reza, Khan M. Iftekharuddin:
Improved brain tumor growth prediction and segmentation in longitudinal brain MRI. 421-424 - Xuan Yang, Bo Wang, Yan-Ran Li, Tiancheng He:
Robust landmark-based image registration using l1 and l2 norm regularizations. 425-428 - Jian Wang, Jianhai Zhang, Yuan An, Hongfei Lin, Zhihao Yang, Yijia Zhang, Yuanyuan Sun:
Biomedical event trigger detection by dependency-based word embedding. 429-432 - Faisal M. Khan, Casimir A. Kulikowski:
Survival analysis via transduction for semi-supervised neural networks in medical prognosis. 433-437 - Paolo Rota
, Stefanie Groeneveld-Krentz, Michael Reiter
:
On automated Flow Cytometric analysis for MRD estimation of Acute Lymphoblastic Leukaemia: A comparison among different approaches. 438-441 - Hui-Hui Wang, Jia-Ming Liu, Mingyu You, Guo-Zheng Li:
Audio signals encoding for cough classification using convolutional neural networks: A comparative study. 442-445 - Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Parvin Mousavi
, Hagit Shatkay:
Using Hidden Markov Models to capture temporal aspects of ultrasound data in prostate cancer. 446-449 - Filiz Bunyak, Adel Hafiane, Zahraa Al-Milaji
, Ilker Ersoy
, Anoop Haridas, Kannappan Palaniappan:
A segmentation-based multi-scale framework for the classification of epithelial and stromal tissues in H&E images. 450-453 - Bradley Ebinger, Nidhal Bouaynaya, Petia Georgieva
, Lyudmila Mihaylova
:
EEG dynamic source localization using Marginalized Particle Filtering. 454-457 - Yongqiang Dai, Bin Hu, Yun Su, Chengsheng Mao, Jing Chen, Xiaowei Zhang, Philip Moore, Lixin Xu, Hanshu Cai:
Feature selection of high-dimensional biomedical data using improved SFLA for disease diagnosis. 458-463 - Bo Xu
, Hongfei Lin, Yuan Lin, Yunlong Ma, Liang Yang, Jian Wang, Zhihao Yang:
Learning to rank for biomedical information retrieval. 464-469 - Qiwen Dong, Shanyi Wang, Kai Wang, Xuan Liu, Bin Liu:
Identification of DNA-binding proteins by auto-cross covariance transformation. 470-475 - Ankur Agrawal, Yehoshua Perl, Christopher Ochs, Gai Elhanan:
Algorithmic detection of inconsistent modeling among SNOMED CT concepts by combining lexical and structural indicators. 476-483 - Alex S. Felmeister, Tyler J. Rivera, Aaron J. Masino, Adam C. Resnick, Jeffrey W. Pennington:
Scalable biobanking: A modular electronic Honest Broker and Biorepository for integrated clinical, specimen and genomic research. 484-490 - Hayda Almeida, Marie-Jean Meurs, Leila Kosseim, Adrian Tsang:
Supporting HIV literature screening with data sampling and supervised learning. 491-496 - Tian Bai, Leiguang Gong, Casimir A. Kulikowski, Lan Huang:
Implicit knowledge discovery in biomedical ontologies: Computing interesting relatednesses. 497-502 - Haidong Lan, Weiguo Liu, Bertil Schmidt
, Bingqiang Wang:
Accelerating large-scale biological database search on Xeon Phi-based neo-heterogeneous architectures. 503-510 - Maziyar Baran Pouyan
, Vasu Jindal, Javad Birjandtalab, Mehrdad Nourani:
A two-stage clustering technique for automatic biaxial gating of flow cytometry data. 511-516 - Qiaoli Hu, Young-Rae Cho:
An integrative measure of graph- and vector-based semantic similarity using information content distance. 517-522 - Bojian Xu:
On stabbing queries for generalized longest repeat. 523-530 - Yanqing Ji, Hao Ying, John Tran, Peter Dews, R. Michael Massanari:
Integrating association mining into relevance feedback for biomedical literature search. 531-536 - Soumitra Pal
, Sanguthevar Rajasekaran:
Improved algorithms for finding edit distance based motifs. 537-542 - Zhaohui Liang
, Gang Zhang, Jimmy Xiangji Huang
:
Discovery of the relations between genetic polymorphism and adverse drug reactions. 543-548 - Guangxu Xun
, Xiaoyi Li, Marc R. Knecht, Paras N. Prasad, Mark T. Swihart
, Tiffany R. Walsh, Aidong Zhang:
Identifying inorganic material affinity classes for peptide sequences based on context learning. 549-554 - Pei Chen
, Shuoyang Qiu, Yue Wang, Yongjun Li:
Identifying the pre-transition state during biological processes by hidden Markov model. 555-562 - Mingon Kang, Juyoung Park, Dong-Chul Kim, Ashis Kumer Biswas
, Chunyu Liu, Jean Gao:
An integrative genomic study for multimodal genomic data using multi-block bipartite graph. 563-568 - Qiang Yu, Hongwei Huo
, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter
, Jun Huan:
Reference sequence selection for motif searches. 569-574 - Akshay Balasubramanya, Ishwor Thapa, Dhundy Bastola, Dario Ghersi:
A novel approach to identify shared fragments in drugs and natural products. 575-580 - Haiying Wang
, Huiru Zheng
:
Integrating omics data for identifying disease subtypes: A multiplex network-based approach. 581-586 - Brittany R. Hoard
, Bruna Jacobson, Kasra Manavi, Lydia Tapia:
Extending rule-based methods to model molecular geometry. 587-594 - Kamal Taha
:
Semantic rules for extracting proteins functions information from biomedical abstracts. 595-598 - Fei Li, Dong-Hong Ji, Xiaomei Wei, Tao Qian:
A transition-based model for jointly extracting drugs, diseases and adverse drug events. 599-602 - Chen Qiao, Dongdong Lin, Shaolong Cao, Yu-Ping Wang:
The effective diagnosis of schizophrenia by using multi-layer RBMs deep networks. 603-606 - Patrick J. Dunn, Elizabeth Thomson, John Campbell, Thomas Smith, Vincent Desborough, Jeffrey A. Wiser, Henry Schaefer, Sanchita Bhattacharya, Atul J. Butte, Sandra Andorf
, Mazen Nasrallah:
ImmPort: Shared research data for bioinformatics and immunology. 607-610 - Oliver Bonham-Carter, Dhundy R. Bastola:
A text mining application for linking functionally stressed-proteins to their post-translational modifications. 611-614 - Michael Andel, Filip Masri, Jirí Kléma
, Zdenek Krejcík, Monika Belickova
:
Sparse omics-network regularization to increase interpretability and performance of linear classification models. 615-620 - Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg
, Barry Smith
, Michael T. Zimmermann
, Guoqian Jiang, Yu Lin, Bin Wu
, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, Zixing Liu, Ming Tan
:
A domain ontology for the Non-Coding RNA field. 621-624 - Zhenchao Jiang, Lishuang Li, Degen Huang, Liuke Jin:
Training word embeddings for deep learning in biomedical text mining tasks. 625-628