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1Big Data Systems
A. Davoudian, and M. Liu. ACM Computing Surveys, 53 (5): 1--39 (October 2020)
3 years ago by @analyst
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software
machine-learning
acm
2020
softwaremachine-learningacm2020
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2MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
P. Jia, X. Yang, L. Guo, B. Liu, J. Lin, H. Liang, J. Sun, C. Zhang, and K. Ye. Genomics, Proteomics & Bioinformatics, 18 (1): 65-71 (2020)
4 years ago by @marcsaric
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shouldread
software
cancer-research
immunology
shouldreadsoftwarecancer-researchimmunology
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1Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
K. Ellrott, M. Bailey, G. Saksena, K. Covington, C. Kandoth, C. Stewart, J. Hess, S. Ma, K. Chiotti, M. McLellan and 730 other author(s). Cell Systems, 6 (3): 271--281.e7 (March 2018)
4 years ago by @marcsaric
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shouldread
wxs
exome
software
cancer-research
variant-calling
pan-cancer
fulltext
shouldreadwxsexomesoftwarecancer-researchvariant-callingpan-cancerfulltext
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1Statistical significance for hierarchical clustering
P. Kimes, Y. Liu, D. Neil Hayes, and J. Marron. Biometrics, 73 (3): 811-821 (September 2017)
5 years ago by @marcsaric
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shouldread
software
methods
clustering
r-language
statistics
fulltext
bioconductor
shouldreadsoftwaremethodsclusteringr-languagestatisticsfulltextbioconductor
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1Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue
D. Sinicropi, K. Qu, F. Collin, M. Crager, M. Liu, R. Pelham, M. Pho, A. Rossi, J. Jeong, A. Scott and 7 other author(s). PLOS ONE, 7 (7): 1-10 (July 2012)
5 years ago by @marcsaric
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shouldread
software
cancer-research
ffpe
rna-seq
fulltext
shouldreadsoftwarecancer-researchffperna-seqfulltext
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1IGSA: Individual Gene Sets Analysis, including Enrichment and Clustering
L. Wu, X. Chen, D. Zhang, W. Zhang, L. Liu, H. Ma, J. Yang, H. Xie, B. Liu, and Q. Jin. PLoS One, (2016)
6 years ago by @marcsaric
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enrichment
shouldread
gene-set
comparison
software
GSEA
fulltext
benchmark
enrichmentshouldreadgene-setcomparisonsoftwareGSEAfulltextbenchmark
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1MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
J. Kultima, S. Sunagawa, J. Li, W. Chen, H. Chen, D. Mende, M. Arumugam, Q. Pan, B. Liu, J. Qin and 2 other author(s). PLOS ONE, 7 (10): e47656+ (Oct 17, 2012)
6 years ago by @karthikraman
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software
metagenomics
softwaremetagenomics
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1Prediction of genome-wide DNA methylation in repetitive elements
Y. Zheng, B. Joyce, L. Liu, Z. Zhang, W. Kibbe, W. Zhang, and L. Hou. Nucleic Acids Res, 45 (15): 8697-8711 (September 2017)
6 years ago by @marcsaric
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illumina
microarray
software
methylation
cancer-research
SHOULDREAD
r-language
fulltext
illuminamicroarraysoftwaremethylationcancer-researchSHOULDREADr-languagefulltext
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2Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data
X. Ma, Z. Liu, Z. Zhang, X. Huang, and W. Tang. BMC Bioinformatics, 18 (1): 72-72 (January 2017)
7 years ago by @marcsaric
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software
methylation
network-analysis
SHOULDREAD
R-project
rna-seq
softwaremethylationnetwork-analysisSHOULDREADR-projectrna-seq
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1A pathology atlas of the human cancer transcriptome
M. Uhlen, C. Zhang, S. Lee, E. Sjöstedt, L. Fagerberg, G. Bidkhori, R. Benfeitas, M. Arif, Z. Liu, F. Edfors and 17 other author(s). Science, (August 2017)
7 years ago by @marcsaric
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database
software
cancer-research
SHOULDREAD
fulltext
databasesoftwarecancer-researchSHOULDREADfulltext
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1Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
K. Bradnam, J. Fass, A. Alexandrov, P. Baranay, M. Bechner, I. Birol, S. Boisvert, J. Chapman, G. Chapuis, R. Chikhi and 81 other author(s). Gigascience, 2 (1): 10 (July 2013)
7 years ago by @peter.ralph
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software
genome_assembly
softwaregenome_assembly
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1AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm
Y. Wang, X. Liu, K. Robbins, and R. Rekaya. BMC Research Notes, 3 (1): 117 (2010)
9 years ago by @uga.abgg
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software
genomics
2010
methodology
softwaregenomics2010methodology
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1SNPxGE2: a database for human SNP–coexpression associations
Y. Wang, S. Joseph, X. Liu, M. Kelley, and R. Rekaya. Bioinformatics, 28 (3): 403-410 (2012)
9 years ago by @uga.abgg
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software
genomics
2012
softwaregenomics2012
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1The iRoCS Toolbox – 3D analysis of the plant root apical meristem at cellular resolution
T. Schmidt, T. Pasternak, K. Liu, T. Blein, D. Aubry-Hivet, A. Dovzhenko, J. Duerr, W. Teale, F. Ditengou, H. Burkhardt and 2 other author(s). The Plant Journal, 77 (5): 806--814 (2014)
10 years ago by @alex_ruff
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biology
to_READ
software
plants
segmentation
registration
filtering
biologyto_READsoftwareplantssegmentationregistrationfiltering
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1A Multi-Agent Framework for Software Dynamic Configuration
Z. du Liu, X. dang Cheng, and H. sheng Liao. Education Technology and Computer Science (ETCS), 2010 Second International Workshop on, 1, page 602-605. (March 2010)
11 years ago by @timfan3939
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agent
software
configuration
dynamic
agentsoftwareconfigurationdynamic
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3Using the k-core decomposition to analyze the static structure of large-scale software systems
H. Zhang, H. Zhao, W. Cai, J. Liu, and W. Zhou. The Journal of Supercomputing, 53 (2): 352--369 (2010)
11 years ago by @jaeschke
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core
software
network
graph
structure
coresoftwarenetworkgraphstructure
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1ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains
O. Ronneberger, K. Liu, M. Rath, D. Rueβ, T. Mueller, H. Skibbe, B. Drayer, T. Schmidt, A. Filippi, R. Nitschke and 3 other author(s). Nat Methods, 9 (7): 735-742 (July 2012)
12 years ago by @alex_ruff
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biology
visualization
software
segmentation
registration
biologyvisualizationsoftwaresegmentationregistration
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2Specification of Non-functional Requirements for Contract Specification in the NGOSS Framework for Quality Management and Product Evaluation
X. Liu, M. Azmoodeh, and N. Georgalas. Fifth International Workshop on Software Quality, 2007. WoSQ'07: ICSE Workshops 2007, page 7--7. IEEE, (May 2007)
12 years ago by @fritzsolms
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computing;
Application
chain
product
contract
{NGOSS}
Telecommunications
evaluation;
industry;
formal
application;
quantitative
service
Software
software;
operation
support
architecture;
requirements;
Supply
science;
specification;
telecommunication
framework;
Heart;
management;
qualitative
nonfunctional
Quality
Computer
system;
telecom
quality;
Communication
Contracts;
computing;Applicationchainproductcontract{NGOSS}Telecommunicationsevaluation;industry;formalapplication;quantitativeserviceSoftwaresoftware;operationsupportarchitecture;requirements;Supplyscience;specification;telecommunicationframework;Heart;management;qualitativenonfunctionalQualityComputersystem;telecomquality;CommunicationContracts;
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2Model Driven Development with non-functional aspects
L. Zhu, and Y. Liu. ICSE Workshop on Aspect-Oriented Requirements Engineering and Architecture Design, 2009. EA '09, page 49--54. IEEE, (May 2009)
12 years ago by @fritzsolms
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Context
Australia;
development
Architecture
programs;
Unified
modeling;
system
compositional
Architecture;
Model
diagnostics;
Software
compilers;
generation;
driven
code
modeling
reasoning
languages;
software
language
development;
architecture;
analysis;
about
science;
life
program
framework;
Natural
description
Programming;
cycle;
nonfunctional
aspect
Computer
systems;
ContextAustralia;developmentArchitectureprograms;Unifiedmodeling;systemcompositionalArchitecture;Modeldiagnostics;Softwarecompilers;generation;drivencodemodelingreasoninglanguages;softwarelanguagedevelopment;architecture;analysis;aboutscience;lifeprogramframework;NaturaldescriptionProgramming;cycle;nonfunctionalaspectComputersystems;
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2Symbolic computation of analytic approximate solutions for nonlinear differential equations with initial conditions
Y. Lin, Y. Liu, and Z. Li. Computer Physics Communications, 183 (1): 106 - 117 (January 2012)
13 years ago by @drmatusek
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adomain
dynamics
method
software
ODEs
decomposition
adomaindynamicsmethodsoftwareODEsdecomposition
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publications (hide)26
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