Difference between revisions of "Journal Club"

From Bioinformatics Lab
Jump to: navigation, search
Line 6: Line 6:
 
!scope="col" style="padding:.4em" | Presenter
 
!scope="col" style="padding:.4em" | Presenter
 
!scope="col" style="padding:.4em" | Paper title
 
!scope="col" style="padding:.4em" | Paper title
 +
|-
 +
|style="padding:.4em;" rowspan=4|2015/02/23
 +
|style="padding:.4em;"|2014-67
 +
|style="padding:.4em;"|BH Kang
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]
 +
|-
 +
|style="padding:.4em;"|2014-66
 +
|style="padding:.4em;"|BH Kang
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]
 +
|-
 +
|style="padding:.4em;"|2014-65
 +
|style="padding:.4em;"|HH Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]
 +
|-
 +
|style="padding:.4em;"|2014-64
 +
|style="padding:.4em;"|HH Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]
 +
|-
 +
|style="padding:.4em;" rowspan=5|2015/02/16
 +
|style="padding:.4em;"|2014-63
 +
|style="padding:.4em;"|HH Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]
 +
|-
 +
|style="padding:.4em;"|2014-62
 +
|style="padding:.4em;"|HH Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]
 +
|-
 +
|style="padding:.4em;"|2014-61
 +
|style="padding:.4em;"|BH Kang
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]
 +
|-
 +
|style="padding:.4em;"|2014-60
 +
|style="padding:.4em;"|BH Kang
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]
 +
|-
 +
|style="padding:.4em;"|2014-59
 +
|style="padding:.4em;"|BH Kang
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]
 +
|-
 +
|style="padding:.4em;" rowspan=3|2015/02/09
 +
|style="padding:.4em;"|2014-58
 +
|style="padding:.4em;"|DS Bae
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]
 +
|-
 +
|style="padding:.4em;"|2014-57
 +
|style="padding:.4em;"|CY Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]
 +
|-
 +
|style="padding:.4em;"|2014-56
 +
|style="padding:.4em;"|ER Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]
 +
|-
 +
|style="padding:.4em;" rowspan=3|2015/02/02
 +
|style="padding:.4em;"|2014-55
 +
|style="padding:.4em;"|T Lee
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]
 +
|-
 +
|style="padding:.4em;"|2014-54
 +
|style="padding:.4em;"|CY Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]
 +
|-
 +
|style="padding:.4em;"|2014-53
 +
|style="padding:.4em;"|CY Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]
 +
|-
 +
|style="padding:.4em;" rowspan=3|2015/01/26
 +
|style="padding:.4em;"|2014-52
 +
|style="padding:.4em;"|ER Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]
 +
|-
 +
|style="padding:.4em;"|2014-51
 +
|style="padding:.4em;"|KS Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]
 +
|-
 +
|style="padding:.4em;"|2014-50
 +
|style="padding:.4em;"|JE Shim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]
 +
|-
 +
|style="padding:.4em;" rowspan=3|2015/01/12
 +
|style="padding:.4em;"|2014-49
 +
|style="padding:.4em;"|HJ Han
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]
 +
|-
 +
|style="padding:.4em;"|2014-48
 +
|style="padding:.4em;"|T Lee
 +
|style="padding:.4em;text-align:left"|
 +
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]
 +
|-
 +
|style="padding:.4em;"|2014-47
 +
|style="padding:.4em;"|ER Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]
 +
|-
 +
|style="padding:.4em;" rowspan=3|2015/01/05
 +
|style="padding:.4em;"|2014-46
 +
|style="padding:.4em;"|KS Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]
 +
|-
 +
|style="padding:.4em;"|2014-45
 +
|style="padding:.4em;"|DS Bae
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]
 +
|-
 +
|style="padding:.4em;"|2014-44
 +
|style="padding:.4em;"|DS Bae
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]
 +
|-
 +
|style="padding:.4em;" rowspan=2|2014/12/29
 +
|style="padding:.4em;"|2014-43
 +
|style="padding:.4em;"|HJ Han
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]
 +
|-
 +
|style="padding:.4em;"|2014-42
 +
|style="padding:.4em;"|HJ Han
 +
|style="padding:.4em;text-align:left"|
 +
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]
 +
|-
 +
|style="padding:.4em;" rowspan=2|2014/12/23
 +
|style="padding:.4em;"|2014-41
 +
|style="padding:.4em;"|CY Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]
 +
|-
 +
|style="padding:.4em;"|2014-40
 +
|style="padding:.4em;"|CY Kim
 +
|style="padding:.4em;text-align:left"|
 +
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]
 
|-
 
|-
 
|style="padding:.4em;" rowspan=4|2014/12/09
 
|style="padding:.4em;" rowspan=4|2014/12/09

Revision as of 17:41, 15 December 2014

2014
Date Paper
index 		Presenter Paper title
2015/02/23 2014-67 BH Kang

Relating the metatranscriptome and metagenome of the human gut.

2014-66 BH Kang

Alterations of the human gut microbiome in liver cirrhosis.

2014-65 HH Kim

An integrated catalog of reference genes in the human gut microbiome.

2014-64 HH Kim

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.

2015/02/16 2014-63 HH Kim

Computational meta'omics for microbial community studies.

2014-62 HH Kim

Functional profiling of the gut microbiome in disease-associated inflammation.

2014-61 BH Kang

Biodiversity and functional genomics in the human microbiome.

2014-60 BH Kang

Chapter 12: Human Microbiome Analysis.

2014-59 BH Kang

Conducting a Microbiome Study.

2015/02/09 2014-58 DS Bae

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.

2014-57 CY Kim

Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.

2014-56 ER Kim

The Genotype-Tissue Expression (GTEx) project.

2015/02/02 2014-55 T Lee

Genetic and epigenetic fine mapping of causal autoimmune disease variants.

2014-54 CY Kim

A general framework for estimating the relative pathogenicity of human genetic variants.

2014-53 CY Kim

A probabilistic model to predict clinical phenotypic traits from genome sequencing.

2015/01/26 2014-52 ER Kim

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

2014-51 KS Kim

Principles of regulatory information conservation between mouse and human.

2014-50 JE Shim

Conservation of trans-acting circuitry during mammalian regulatory evolution.

2015/01/12 2014-49 HJ Han

Practical guidelines for the comprehensive analysis of ChIP-seq data.

2014-48 T Lee

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.

2014-47 ER Kim

Rapid neurogenesis through transcriptional activation in human stem cells.

2015/01/05 2014-46 KS Kim

Small RNA changes en route to distinct cellular states of induced pluripotency.

2014-45 DS Bae

Genome-wide characterization of the routes to pluripotency.

2014-44 DS Bae

Divergent reprogramming routes lead to alternative stem-cell states.

2014/12/29 2014-43 HJ Han

Global view of enhancer-promoter interactome in human cells.

2014-42 HJ Han

Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.

2014/12/23 2014-41 CY Kim

Super-enhancers in the control of cell identity and disease.

2014-40 CY Kim

Master transcription factors and mediator establish super-enhancers at key cell identity genes.

2014/12/09 2014-39 HH Kim

Unraveling the biology of a fungal meningitis pathogen using chemical genetics.

2014-38 JE Shim

A proteome-scale map of the human interactome network.

2014-37 JE Shim

The role of the interactome in the maintenance of deleterious variability in human populations.

2014-36 HS Shim

Integrative annotation of variants from 1092 humans: application to cancer genomics.

2014/12/02 2014-35 HJ Han

Mapping functional transcription factor networks from gene expression data.

2014-34 KS Kim

In pursuit of design principles of regulatory sequences.

2014/11/25 2014-33 KS Kim

Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.

2014-32 HJ Han

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.

2014/11/18 2014-31 SM Yang

The 'dnet' approach promotes emerging research on cancer patient survival.

2014-30 HJ Han

Determination and inference of eukaryotic transcription factor sequence specificity.

2014/11/11 2014-29 DS Bae

Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.

2014-28 HH Kim

Dissecting engineered cell types and enhancing cell fate conversion via CellNet.

2014-27 HH Kim

CellNet: network biology applied to stem cell engineering.

2014/11/04 2014-26 HS Shim

Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.

2014-25 JH Shin

Phen-Gen: combining phenotype and genotype to analyze rare disorders.

2014/10/28 2014-24 HJ Han

A community effort to assess and improve drug sensitivity prediction algorithms.

2014-23 HS Shim

Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.

2014/09/30 2014-22 JE Shim

Network-based stratification of tumor mutations.

2014-21 KS Kim

Synonymous mutations frequently act as driver mutations in human cancers.

2014/09/23 2014-20 CY Kim

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.

2014-19 HJ Han

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.

2014/09/16 2014-18 JH Shin

Integrated analysis of recurrent properties of cancer genes to identify novel drivers.

2014-17 AR Cho

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.

2014/09/02 2014-16 JE Shim

A network module-based method for identifying cancer prognostic signatures.

2014-15 AR Cho

Realizing the promise of cancer predisposition genes.

2014/08/19 2014-14 JE Shim

Assessing the clinical utility of cancer genomic and proteomic data across tumor types.

2014-13 HS Shim

Mutational landscape and significance across 12 major cancer types.

2014/08/12 2014-12 HS Shim

Signatures of mutational processes in human cancer.

2014-11 HJ Kim

Discovery and saturation analysis of cancer genes across 21 tumour types.

2014/08/05 2014-10 CY Kim

Comprehensive identification of mutational cancer driver genes across 12 tumor types.

2014-9 JE Shim

IntOGen-mutations identifies cancer drivers across tumor types.

2014/07/29 2014-8 CY Kim

Computational approaches to identify functional genetic variants in cancer genomes.

2014-7 AR Cho

Mutational heterogeneity in cancer and the search for new cancer-associated genes.

2014-6 AR Cho

Cancer genomes: discerning drivers from passengers

2014/07/22 2014-5 AR Cho

The Cancer Genome Atlas Pan-Cancer analysis project.

2014-4 AR Cho

Cancer genome landscapes.

2014-3 AR Cho

Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.

2014/07/15 2014-2 HJ Han

A promoter-level mammalian expression atlas.

2014-1 HJ Han

An atlas of active enhancers across human cell types and tissues.

2013
Date Paper
index 		Presenter Paper title
2013/06/26 2013-31 HJ Han Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages
2013-30 YH Ko Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli
2013/06/04 2013-29 KS Kim Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding
2013-28 ER Kim Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
2013/05/28 2013-27 YH Ko Discovering statistically significant pathways in expression profiling studies
2013-26 JE Shim Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses
2013/05/21 2013-25 HJ Han Dynamic regulatory network controlling TH17 cell differentiation
2013-24 T Lee Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions
2013/05/14 2013-23 JE Shim Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci
2013-22 HJ Kim Chromatin marks identify critical cell types for fine mapping complex trait variants
2013/05/07 2013-21 ER Kim Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues
2013-20 HS Shim Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression
2013/04/09 2013-19 HJ Kim Annotation of functional variation in personal genomes using RegulomeDB
2013/04/02 2013-18 HJ Kim The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
2013/03/12 2013-17 ER Kim Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation
2013/03/05 2013-16 ER Kim ChIP–seq: advantages and challenges of a maturing technology
2013/02/21 2013-15 KS Kim Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density
2013-14 KS Kim A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells
2013-13 HJ Han Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.
2013/02/15 2013-12 HJ Han Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
2013-11 JE Shim, CY Kim Interpreting noncoding genetic variation in complex traits and human disease
2013-10 HJ Han, JH Kim Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
2013/02/08 2013-09 HJ Kim Widespread Site-Dependent Buffering of Human Regulatory Polymorphism
2013-08 JE Shim, CY Kim Linking disease associations with regulatory information in the human genome
2013-07 HJ Han, JH Kim Understanding transcriptional regulation by integrative analysis of transcription factor binding data
2013/01/25 2013-06 HJ Han, JH Kim The long-range interaction landscape of gene promoters
2013-05 ER Kim, HS Shim Landscape of transcription in human cells
2013-04 HJ Han, JH Kim Architecture of the human regulatory network derived from ENCODE data
2013/01/18 2013-03 KS Kim, TH Kim An expansive human regulatory lexicon encoded in transcription factor footprints
2013-02 HJ Han, JH Kim The accessible chromatin landscape of the human genome
2013/01/11 2013-01 JE Shim, CY Kim An integrated encyclopedia of DNA elements in the human genome

2012

Date Paper index Paper title
2013/01/11 2012-81 (TH Kim) MuSiC: identifying mutational significance in cancer genomes.
2012/12/04 2012-80 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation
2012/11/20 2012-79 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks
2012-78 (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins
2012/11/06 2012-77 (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
2012-76 (KS Kim) A public resource facilitating clinical use of genomes
2012/07/19 2012-75 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
2012-74 (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People
2012-73 (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes
2012-72 (SH Hwang) Network-based classification of breast cancer metastasis
2012-71 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants
2012-70 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
2012/07/16 2012-69 (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data
2012-66 (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools
2012-65 (ER Kim&TH Kim)The Variant Call Format and VCFtools
2012-64 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View
2012-63 (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions
2012-62 (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System
2012-61 (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome
2012-60 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective
2012/07/13 2012-59 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
2012-58 (JH Shin&HJ Kim)A framework for human microbiome research
2012-57 (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome
2012/07/12 2012-56 (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines
2012-55 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes
2012-54 (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity
2012-53 (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
2012/07/09 2012-52 (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
2012-51 (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells
2012-50 (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer
2012-49 (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism
2012-48 (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders
2012-47 (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
2012/07/06 2012-46 (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)
2012-45 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases
2012-44 (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners
2012-43 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans
2012-42 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes
2012-41 (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits
2012/07/02 2012-40 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions
2012-39 (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer
2012-38 (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas
2012-37 (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine
2012-36 (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype
2012-35 (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets
2012/03/05 2012-34 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.
2012-33 (11,Go&Ju)Differential expression analysis for sequence count data
2012-32 (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
2012/02/27
2012/02/28 		2012-31 (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics
2012-30 (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq
2012-29 (3,HJ Han)From RNA-seq reads to differential expression results
2012-28 (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods
2012-27 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq
2012-26 (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
2012-25 (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq
2012/02/06 2012-24 mirConnX: condition-specific mRNA-microRNA network integrator
2012-23 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
2012-22 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
2012-21 Reprogramming of miRNA networks in cancer and leukemia
2012-20 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma
2012/01/30 2012-19 Principles and Strategies for Developing Network Models in Cancer
2012-18 Reverse engineering of regulatory networks in human B cells
2012-17 Variations in DNA elucidate molecular networks that cause disease
2012-16 Harnessing gene expression to identify the genetic basis of drug resistance
2012-15 An Integrated Approach to Uncover Drivers of Cancer
2012/01/09 2012-14 Genetic variation in an individual human exome.
2012-13 Predicting phenotypic variation in yeast from individual genome sequences.
2012-12 Clinical assessment incorporating a personal genome.
2012/01/09
2012/01/16 		2012-11 Human allelic variation: perspective from protein function, structure, and evolution.
2012-10 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.
2012-09 Prediction of deleterious human alleles.
2012-08 Human non-synonymous SNPs: server and survey.
2012-07 A method and server for predicting damaging missense mutations.
2012-06 SNAP: predict effect of non-synonymous polymorphisms on function
2012/01/09
2012/01/16 		2012-05 Computational and statistical approaches to analyzing variants identified by exome sequencing.
2012-04 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.
2012-03 Targeted capture and massively parallel sequencing of 12 human exomes.
2012/01/09
2012/01/16 		2012-02 The distribution of fitness effects of new mutations.
2012-01 Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies

2011

Date Paper_index Paper_title
2011/11/28 2011-49 (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events
2011-48 (Shin)Network pharmacology: the next paradigm in drug discovery
2011-47 (Oh)Systematic exploration of synergistic drug pairs
2011-46 (Shim)Chemogenomic profiling predicts antifungal synergies
2011-45 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery
2011-44 (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines
2011/11/14 2011-43 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets
2011-42 Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole
2011-41 Analysis of multiple compound–protein interactions reveals novel bioactive molecules
2011/11/07 2011-40 Drug—target network
2011-39 A side effect resource to capture phenotypic effects of drugs
2011-38 Quantitative systems-level determinants of human genes targeted by successful drugs
2011-37 Drug Target Identification Using Side-Effect Similarity
2011/11/07 2011-36 Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data
2011-35 Exploiting drug–disease relationships for computational drug repositioning
2011-34 Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks
2011/10/05 2011-33 Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
2011-32 Quantifying environmental adaptation of metabolic pathways in metagenomics
2011-31 Quantitative assessment of protein function prediction from metagenomics shotgun sequences
2011/10/04 2011-30 A human gut microbial gene catalogue established by metagenomic sequencing
2011-29 Molecular eco-systems biology: towards an understanding of community function
2011-28 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
2011-27 Unravelling the effects of the environment and host genotype on the gut microbiome
2011/09/19 2011-26 independently evolved virulence effectors converge onto hubs in a plant immune system Network
2011-25 Evidence for network evolution in an arabidopsis interactome Map
2011/09/05 2011-24 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy
2011-23 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers
2011/09/22 2011-22 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks
2011-21 From expression QTLs to personalized transcriptomics
2011/06/20 2011-20 a user's guide to the encyclopedia of DNA elements(ENCODE)
2011/03/30 2011-19 enterotypes of the human gut microbiome
2011-18 toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data
2011/03/16 2011-17 variable pathogenicity determines individual lifespan in caenorhabditis elegans
2011-16 a high-resolution c.elegans essential gene network based on phenotypic profiling of a complex tissue
2011/04/25 2011-15 Hallmarks of Cancer : The next generation
2011-14 Mapping Cancer Origins
2011-13 Genetic Interactions in Cancer Progression and Treatment
2011/04/11 2011-12 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
2011-11 ***Changed!***

Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions

2011/03/28 2011-10 profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis
2011-09 cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
2011/03/14 2011-08 phenotypic landscape of a bacterial cell
2011-07 cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
2011/02/28 2011-06 genomic patterns of pleiotropy and the evolution of complexity
2011-05 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway
2011/02/21 2011-04 dynamic interaction networks in a hierarchically organized tissue
2011/02/14 2011-03 rewiring of genetic networks in response to DNA damage
2011/01/31 2011-02 Applying mass spectrometry-based proteomics to genetics, genomics and network biology
2011-01 Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

2010

Date Paper_index Paper_title
2010/12/27 2010-29 Functional_roles_fornoise_in_genetic_circuits
2010-28 Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries
2010/11/15 2010-27 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes
2010-26 It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks
2010/11/01 2010-25 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes
2010-24 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster
2010/10/11 2010-23 Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders
2010/09/13 2010-22 Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells
2010-21 Limits_of_sequence_and_functional_conservation
2010/05/26 2010-20 network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf
2010/05/19 2010-19 interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf
2010/04/21 2010-18 identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf
2010/04/14 2010-17 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man
2010/04/07 2010-16 systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes
2010-15 genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines
2010/03/31 2010-14 toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf
2010-13 systems_biology_of_stem_cell_fate_and_cellular_reprogramming
2010/03/24 2010-12 dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome
2010/01/18 2010-11 JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
2010/01/16 2010-10 systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
2010/01/15 2010-09 distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
2010/01/14 2010-08 chemogenomic_profiling_predicts_antifungal_synergies
2010/01/13 2010-07 edgetic_perturbation_models_of_human_inherited_disorders
2010/01/12 2010-06 analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
2010/01/11 2010-05 predicting_new_molecular_targets_for_known_drugs.pdf

Reference:SEA(Similarity Ensemble Approach)

2010/01/09 2010-04 harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
2010/01/08 2010-03 an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
2010/01/07 2010-02 a_phenotypic_profile_of_the_candida_albicans_regulatory_network
2010/01/06 2010-01 a_global_view_of_protein_expression_in_human_cells_tissues_and_organs



Retrieved from "https://netbiolab.org/wiki/index.php?title=Journal_Club&oldid=3386"
Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox