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| Line 14: |
Line 14: |
| | |[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ] | | |[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ] |
| | |- | | |- |
| − | |rowspan = "7" |2012/02/27<br />~2012/02/28 | + | |rowspan = "7" |2012/02/27<br />2012/02/28 |
| | | | | | |
| | |[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics] | | |[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics] |
| Line 68: |
Line 68: |
| | |[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer] | | |[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer] |
| | |- | | |- |
| − | |rowspan = "3" | | + | |rowspan = "3" |2012/01/09 |
| − | |rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012
| + | | |
| − | |rowspan = "3" |
| + | |
| | |[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.] | | |[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.] |
| | |- | | |- |
| | + | | |
| | |[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.] | | |[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.] |
| | |- | | |- |
| | + | | |
| | |[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.] | | |[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.] |
| | |- | | |- |
| − | |rowspan = "6" | | + | |rowspan = "6" |2012/01/09<br />2012/01/16 |
| − | |rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012
| + | | |
| − | |rowspan = "6" |
| + | |
| | |[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.] | | |[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.] |
| | |- | | |- |
| | + | | |
| | |[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.] | | |[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.] |
| | |- | | |- |
| | + | | |
| | |[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.] | | |[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.] |
| | |- | | |- |
| | + | | |
| | |[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.] | | |[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.] |
| | |- | | |- |
| | + | | |
| | |[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.] | | |[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.] |
| | |- | | |- |
| | + | | |
| | |[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function] | | |[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function] |
| | |- | | |- |
| Date
|
Paper_index
|
Paper_title
|
| 2012/03/05
|
|
(8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.
|
|
|
(11,Go&Ju)Differential expression analysis for sequence count data
|
|
|
(12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
|
2012/02/27
2012/02/28
|
|
(1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics
|
|
|
(2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq
|
|
|
(3,HJ Han)From RNA-seq reads to differential expression results
|
|
|
(4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods
|
|
|
(5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq
|
|
|
(6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
|
|
|
(7,So&Shin)TopHat: discovering splice junctions with RNA-Seq
|
| 2012/02/06
|
|
mirConnX: condition-specific mRNA-microRNA network integrator
|
|
|
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
|
|
|
A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
|
|
|
Reprogramming of miRNA networks in cancer and leukemia
|
|
|
An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma
|
| 2012/01/30
|
|
Principles and Strategies for Developing Network Models in Cancer
|
|
|
Reverse engineering of regulatory networks in human B cells
|
|
|
Variations in DNA elucidate molecular networks that cause disease
|
|
|
Harnessing gene expression to identify the genetic basis of drug resistance
|
|
|
An Integrated Approach to Uncover Drivers of Cancer
|
| 2012/01/09
|
|
Genetic variation in an individual human exome.
|
|
|
Predicting phenotypic variation in yeast from individual genome sequences.
|
|
|
Clinical assessment incorporating a personal genome.
|
2012/01/09
2012/01/16
|
|
Human allelic variation: perspective from protein function, structure, and evolution.
|
|
|
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.
|
|
|
Prediction of deleterious human alleles.
|
|
|
Human non-synonymous SNPs: server and survey.
|
|
|
A method and server for predicting damaging missense mutations.
|
|
|
SNAP: predict effect of non-synonymous polymorphisms on function
|
|
|
January 9 Mon, 2012
January 16 Mon, 2012
|
|
Computational and statistical approaches to analyzing variants identified by exome sequencing.
|
| Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.
|
| Targeted capture and massively parallel sequencing of 12 human exomes.
|
|
|
January 9 Mon, 2012
January 16 Mon, 2012
|
|
The distribution of fitness effects of new mutations.
|
| Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies
|
|
|
November 28 Mon, 2011
|
TY Oh,
SH Hwang,
JE Shim,
S Beck,
JH Shin
|
(Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events
|
| (Shin)Network pharmacology: the next paradigm in drug discovery
|
| (Oh)Systematic exploration of synergistic drug pairs
|
| (Shim)Chemogenomic profiling predicts antifungal synergies
|
| (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery
|
| (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines
|
|
|
November 14 Mon, 2011
|
HH Kim & AR Cho
|
Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets
|
| Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole
|
| Analysis of multiple compound–protein interactions reveals novel bioactive molecules
|
|
|
November 7 Mon, 2011
|
YH Ko
|
Drug—target network
|
| A side effect resource to capture phenotypic effects of drugs
|
| Quantitative systems-level determinants of human genes targeted by successful drugs
|
| Drug Target Identification Using Side-Effect Similarity
|
|
|
November 7 Mon, 2011
|
JW Song
|
Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data
|
| Exploiting drug–disease relationships for computational drug repositioning
|
| Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks
|
|
|
October 5 Mon, 2011
|
HH Kim
|
Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
|
| Quantifying environmental adaptation of metabolic pathways in metagenomics
|
| Quantitative assessment of protein function prediction from metagenomics shotgun sequences
|
|
|
October 4 Mon, 2011
|
S Beck
|
A human gut microbial gene catalogue established by metagenomic sequencing
|
| Molecular eco-systems biology: towards an understanding of community function
|
| Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
|
| Unravelling the effects of the environment and host genotype on the gut microbiome
|
|
|
September 19 Mon, 2011
|
TY Oh
|
independently evolved virulence effectors converge onto hubs in a plant immune system Network
|
| Evidence for network evolution in an arabidopsis interactome Map
|
|
|
September 5 Mon, 2011
|
SG Ji
|
Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy
|
| SH Hwang
|
Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers
|
|
|
August 22 Mon, 2011
|
ER Kim
|
Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks
|
| T Lee
|
From expression QTLs to personalized transcriptomics
|
|
|
June 20 Mon, 2011
|
JH Shin
|
a user's guide to the encyclopedia of DNA elements(ENCODE)
|
|
|
May 30 Mon, 2011
|
HH Kim
|
enterotypes of the human gut microbiome
|
| toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data
|
|
|
May 16 Mon, 2011
|
AR Cho
|
variable pathogenicity determines individual lifespan in caenorhabditis elegans
|
| a high-resolution c.elegans essential gene network based on phenotypic profiling of a complex tissue
|
|
|
April 25 Mon, 2011
|
S Beck
|
Hallmarks of Cancer : The next generation
|
| Mapping Cancer Origins
|
| Genetic Interactions in Cancer Progression and Treatment
|
|
|
April 11 Mon, 2011
|
JE Shim
|
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
|
| T Lee
|
***Changed!***
Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions
|
|
|
March 28 Mon, 2011
|
TY Oh
|
profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis
|
| cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
|
|
|
March 14 Mon, 2011
|
JW Song
|
phenotypic landscape of a bacterial cell
|
| cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
|
|
|
February 28 Mon, 2011
|
KS Kim
|
genomic patterns of pleiotropy and the evolution of complexity
|
| HJ Han
|
simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway
|
|
|
February 21 Mon, 2011
|
MH Lee
|
dynamic interaction networks in a hierarchically organized tissue
|
|
|
February 14 Mon, 2011
|
AR Cho
|
rewiring of genetic networks in response to DNA damage
|
|
|
January 31 Mon, 2011
|
JW Song
|
Applying mass spectrometry-based proteomics to genetics, genomics and network biology
|
| Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
|
|
|
December 27 Mon, 2010
|
ER Kim
|
Functional_roles_fornoise_in_genetic_circuits
|
| T Lee
|
Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries
|
|
|
November 15 Mon, 2010
|
AR Cho
|
Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes
|
| SG Ji
|
It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks
|
|
|
November 1 Mon, 2010
|
HH Kim
|
A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes
|
| JH Shin
|
A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster
|
|
|
October 11 Mon, 2010
|
JE Shim
|
Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders
|
|
|
September 13 Mon, 2010
|
SH Hwang
|
Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells
Limits_of_sequence_and_functional_conservation
|
|
|
May 26 Wed, 2010
|
AR Cho
|
network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf
|
|
|
May 19 Wed, 2010
|
SG Ji
|
interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf
|
|
|
April 21 Wed, 2010
|
JH Shin
|
identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf
|
|
|
April 14 Wed, 2010
|
TY Oh
|
an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man
|
|
|
April 7 Wed, 2010
|
HHkim
|
systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes
|
| T Lee
|
genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines
|
|
|
Mar 31 Wed, 2010
|
JE Shim
|
toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf
systems_biology_of_stem_cell_fate_and_cellular_reprogramming
|
|
|
Mar 24 Wed, 2010
|
SH Hwang
|
dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome
|
|
|
Jan 18 Mon, 2010
|
TY Oh(T Lee)
|
JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
|
|
|
Jan 16 Sat, 2010
|
JE Shim(MH Lee)
|
systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
|
|
|
Jan 15 Fri, 2010
|
SG Ji
|
distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
|
|
|
Jan 14 Thu, 2010
|
HH kim
|
chemogenomic_profiling_predicts_antifungal_synergies
|
|
|
Jan 13 Wed, 2010
|
JH Shin(ER Kim)
|
edgetic_perturbation_models_of_human_inherited_disorders
|
|
|
Jan 12 Tue, 2010
|
TY Oh(T Lee)
|
analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
|
|
|
Jan 11 Mon, 2010
|
JE Shim(MH Lee)
|
predicting_new_molecular_targets_for_known_drugs.pdf
Reference:SEA(Similarity Ensemble Approach)
|
|
|
Jan 09 Sat, 2010
|
SG Ji
|
harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
|
|
|
Jan 08 Fri, 2010
|
AR Cho
|
an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
|
|
|
Jan 07 Thu, 2010
|
HH Kim
|
a_phenotypic_profile_of_the_candida_albicans_regulatory_network
|
|
|
Jan 06 Wed, 2010
|
JH Shin(ER Kim)
|
a_global_view_of_protein_expression_in_human_cells_tissues_and_organs
|
