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Biocomputing 2018 - Proceedings Of The Pacific Symposium [Kietas viršelis]

Edited by (Stanford Univ, Usa), Edited by (Univ Of Pennsylvania, Usa), Edited by (Univ Of Colorado Health Sciences Center, Usa), Edited by (Indiana Univ, Usa), Edited by (Stanford Univ, Usa), Edited by (Stanford Univ, Usa)
  • Formatas: Hardback, 648 pages
  • Išleidimo metai: 17-Jan-2018
  • Leidėjas: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 9813235527
  • ISBN-13: 9789813235526
Kitos knygos pagal šią temą:
  • Formatas: Hardback, 648 pages
  • Išleidimo metai: 17-Jan-2018
  • Leidėjas: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 9813235527
  • ISBN-13: 9789813235526
Kitos knygos pagal šią temą:
The Pacific Symposium on Biocomputing (PSB) 2018 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2018 will be held on January 3 - 7, 2018 in Kohala Coast, Hawaii.PSB 2018 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.
Preface vii
Applications Of Genetics, Genomics And Bioinformatics In Drug Discovery
Session introduction
1(7)
Richard Bourgon
Frederick E. Dewey
Zhengyan Kan
Shuyu D. Li
Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology
8(12)
Xintong Chen
Sander Houten
Kimaada Allette
Robert P. Sebra
Gustavo Stolovitzky
Bojan Losic
Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures
20(12)
Peyton Greenside
Maureen Hillenmeyer
Anshul Kundaje
Cell-specific prediction and application of drug-induced gene expression profiles
32(12)
Rachel Hodos
Ping Zhang
Hao-Chih Lee
Qiaonan Duan
Zichen Wang
Neil R. Clark
Avi Ma'ayan
Fei Wang
Brian Kidd
Jianying Hu
David Sontag
Joel Dudley
Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action
44(12)
Yunan Luo
Sheng Wang
Jinfeng Xiao
Jian Peng
Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome
56(12)
Emily K. Mallory
Ambika Acharya
Stefano E. Rensi
Peter J. Turnbaugh
Roselie A. Bright
Russ B. Altman
Loss-of-function of neuroplasticity-related genes confers risk for human neurodevelopmental disorders
68(12)
Milo R. Smith
Benjamin S. Glicksberg
Li Li
Rong Chen
Hirofumi Morishita
Joel T. Dudley
Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders
80(12)
Gregory P. Way
Casey S. Greene
Diffusion mapping of drug targets on disease signaling network elements reveals drug combination strategies
92(12)
Jielin Xu
Kelly Regan-Fendt
Siyuan Deng
William E. Carson III
Philip R.O. Payne
Fuhai Li
Challenges Of Pattern Recognition In Biomedical Data
Session introduction
104(7)
Shefali Setia Verma
Anurag Verma
Anna Okula Basile
Marta-Byrska Bishop
Christian Darabos
Large-scale analysis of disease pathways in the human interactome
111(12)
Monica Agrawal
Marinka Zitnik
Jure Leskovec
Mapping patient trajectories using longitudinal extraction and deep learning in the MIMIC-HI Critical Care Database
123(10)
Brett K. Beaulieu-Jones
Patryk Orzechowski
Jason H. Moore
OWL-NETS: Transforming OWL representations for improved network inference
133(12)
Tiffany J. Callahan
William A. Baumgartner Jr
Michael Bada
Adrianne L. Stefanski
Ignacio Tripodi
Elizabeth K. White
Lawrence E. Hunter
Automated disease cohort selection using word embeddings from Electronic Health Records
145(12)
Benjamin S. Glicksberg
Riccardo Miotto
Kipp W. Johnson
Khader Shameer
Li Li
Rong Chen
Joel T. Dudley
Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses
157(11)
Lia X. Harrington
Gregory P. Way
Jennifer A. Doherty
Casey S. Greene
An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data
168(12)
Hyun-Hwan Jeong
Hari Krishna Yalamanchili
Caiwei Guo
Joshua M. Shulman
Zhandong Liu
Causal inference on electronic health records to assess blood pressure treatment targets: An application of the parametric g formula
180(12)
Kipp W. Johnson
Benjamin S. Glicksberg
Rachel Hodos
Khader Shameer
Joel T. Dudley
Data-driven advice for applying machine learning to bioinformatics problems
192(12)
Randal S. Olson
William La Cava
Zairah Mustahsan
Akshay Varik
Jason H. Moore
Improving the explainability of Random Forest classifier - user centered approach
204(12)
Dragutin Petkovic
Russ B. Altman
Mike Wong
Arthur Vigil
Tree-based methods for characterizing tumor density heterogeneity
216(12)
Katherine Shoemaker
Brian P. Hobbs
Karthik Bharath
Chaan S. Ng
Veerabhadran Baladandayuthapani
How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures?
228(12)
Yogasudha Veturi
Marylyn D. Ritchie
Democratizing Health Data For Translational Research
Session introduction
240(7)
Philip R.O Payne
Nigam H. Shah
Jessica D. Tenenbaum
Lara Mangravite
ClinGen Cancer Somatic Working Group - Standardizing and democratizing access to cancer molecular diagnostic data to drive translational research
247(12)
Subha Madhavan
Deborah Ritter
Christine Micheel
Shruti Rao
Angshumoy Roy
Dmitriy Sonkin
Matthew McCoy
Malachi Griffith
Obi L Griffith
Peter Mcgarvey
Shashikant Kulkarni
A heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methods
259(9)
Jason H. Moore
Maksim Shestov
Peter Schmitt
Randal S. Olson
Identifying natural health product and dietary supplement information within adverse event reporting systems
268(12)
Vivekanand Sharma
Indra Neil Sarkar
Best practices and lessons learned from reuse of 4 patient-derived metabolomics datasets in Alzheimer's disease
280(12)
Jessica D. Tenenbaum
Colette Blach
Democratizing data science through data science training
292(12)
John Darrell Van Horn
Lily Fierro
Jeana Kamdar
Jonathan Gordon
Crystal Stewart
Avnish Bhattrai
Sumiko Abe
Xiaoxiao Lei
Caroline O'Driscoll
Aakanchha Sinha
Priyambada Jain
Gully Burns
Kristina Lerman
Jose Luis Ambite
Imaging Genomics
Session introduction
304(3)
Heng Huang
Li Shen
Paul M. Thompson
Kim Huang
Junzhou Huang
Lin Yang
Heritability estimates on resting state fMRI data using the ENIGMA analysis pipeline
307(12)
Bhim M. Adhikari
Neda Jahanshad
Dinesh Shukla
David C. Glahn
John Blangero
Richard C. Reynolds
Robert W. Cox
Els Fieremans
Jelle Veraart
Dmitry S. Novikov
Thomas E. Nichols
L. Elliot Hong
Paul M. Thompson
Peter Kochunov
Discriminative bag-of-cells for imaging-genomics
319(12)
Benjamin Chidester
Minh N. Do
Jian Ma
MRI to MGMT: Predicting methylation status in glioblastoma patients using convolutional recurrent neural networks
331(12)
Lichy Han
Maulik R. Kamdar
Deep integrative analysis for survival prediction
343(10)
Chenglong Huang
Albert Zhang
Guanghua Xiao
Genotype-Phenotype association study via new multi-task learning model
353(12)
Zhouyuan Huo
Dinggang Shen
Heng Huang
Codon bias among synonymous rare variants is associated with Alzheimer's disease imaging biomarker
365(12)
Jason E. Miller
Manu K. Shivakumar
Shannon L. Risacher
Andrew J. Saykin
Seunggeun Lee
Kwangsik Nho
Dokyoon Kim
Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles
377(12)
Anima Srivastava
Chaitanya Kulkarni
Parag Mallick
Kun Huang
Raghu Machiraju
Precision Medicine: From Diplotypes to Disparties Towards Improved Health And Therapies
Session Introduction
389(11)
Dana C. Crawford
Alexander A. Morgan
Joshua C. Denny
Bruce J. Aronow
Steven E. Brenner
Single subject transcriptome analysis to identify functionally signed gene set or pathway activity
400(12)
Joanne Berghout
Qike Li
Nima Pouladi
Jianrong Li
Yves A. Lussier
Using simulation and optimization approach to improve outcome through warfarin precision treatment
412(12)
Chih-Lin Chi
Lu He
Kourosh Ravvaz
John Weissert
Peter J. Tonellato
Local ancestry transitions modify snp-trait associations
424(12)
Alexandra E. Fish
Dana C. Crawford
John A. Capra
William S. Bush
Coalitional game theory as a promising approach to identify candidate autism genes
436(12)
Anika Gupta
Min Woo Sun
Kelley M. Paskov
Nate T. Stockham
Jae-Yoon Jung
Dennis P. Wall
Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expression
448(12)
Binglan Li
Shefali S. Verma
Yogasudha C. Veturi
Anurag Verma
Yuki Bradford
David W. Haas
Marylyn D. Ritchie
Considerations for automated machine learning in clinical metabolic profiling: Altered homocysteine plasma concentration associated with metformin exposure
460(12)
Alena Orlenko
Jason H. Moore
Patryk Orzechowski
Randal S. Olson
Junmei Cairns
Pedro J. Caraballo
Richard M. Weinshilboum
Liewei Wang
Matthew K. Breitenstein
Addressing vital sign alarm fatigue using personalized alarm thresholds
472(12)
Sarah Poole
Nigam Shah
Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses
484(12)
Samir Rachid Zaim
Qike Li
A. Grant Schissler
Yves A. Lussier
Analyzing metabolomics data for association with genotypes using two-component Gaussian mixture distributions
496(11)
Jason Westra
Nicholas Hartman
Bethany Lake
Gregory Shearer
Nathan Tintle
Reading Between The Genes: Computational Models To Discover Function From Noncoding DNA
Session Introduction
507(5)
Yves A. Lussiert
Joanne Berghout
Francesca Vitali
Kenneth S. Ramos
Maricel Kann
Jason H. Moore
Pan-cancer analysis of expressed somatic nucleotide variants in long intergenic non-coding RNA
512(12)
Travers Ching
Lana X. Garmire
Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements
524(12)
Jiali Han
Jianrong Li
Ikbel Achour
Lorenzo Pesce
Ian Foster
Haiquan Li
Yves A. Lussier
Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials
536(12)
Travis S. Johnson
Sihong Li
Jonathan R. Kho
Kum Huang
Yan Zhang
Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS
548(11)
Elisabetta Manduchi
Alessandra Chesi
Molly A. Hall
Struan F.A. Grant
Jason H. Moore
Advances In Text Mining And Visualization For Precision Medicine
Session Introduction
559(7)
Graciela Gonzalez-Hernandez
Abeed Sarker
Karen O'Connor
Casey Greene
Hongfang Liu
Improving precision in concept normalization
566(12)
Mayla Boguslav
K. Bretonnel Cohen
William A. Baumgartner Jr
Lawrence E. Hunter
VisAGE: Integrating external knowledge into electronic medical record visualization
578(12)
Edward W. Huang
Sheng Wang
Cheng Xiang Zhai
GeneDive: A gene interaction search and visualization tool to facilitate precision medicine
590(12)
Paul Previde
Brook Thomas
Mike Wong
Emily K. Mallory
Dragutin Petkovic
Russ B. Altman
Anagha Kulkarni
Annotating gene sets by mining large literature collections with protein networks
602(12)
Sheng Wang
Jianzhu Ma
Michael Ku Yu
Fan Zheng
Edward W. Huang
Jiawei Han
Jian Peng
Trey Ideker
Workshops
The diversity and disparity in biomedical informatics (DDBI) workshop
614(4)
William Southerland
S. Joshua Swamidass
Philip R.O. Payne
Laura Wiley
ClarLynda Williams-DeVane
Integrating community-level data resources for precision medicine research
618(5)
William S. Bush
Dana C. Crawford
Farren Briggs
Darcy Freedman
Machine learning and deep analytics for biocomputing: Call for better explainability
623(5)
Dragutin Petkovic
Lester Kobzik
Christopher Re
Methods for examining data quality in healthcare integrated data repositories
628(6)
Vojtech Huser
Michael G. Kahn
Jeffrey S. Brown
Ramkiran Gouripeddi
Erratum
Erratum: Identifying mutation specific cancer pathways using a structurally resolved protein interaction network
634
H. Billur Engin
Matan Hofree
Hannah Carter