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2012 Journal Club

Presenting Date Presenter Paper
Jan 04 Graham Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions
Jan 11 Shihong Detecting Novel Associations in Large Data Sets
Jan 18 William DNA-binding factors shape the mouse methylome at distal regulatory regions
Jan 25 Arko* A Novel Sperm-Delivered Toxin Causes Late-Stage Embryo Lethality and Transmission Ratio Distortion in C. elegans
Feb 01 Graham Sperm-borne microRNA-34c is required for the first cleavage division in mouse
Feb 08 Edward Genomewide characterization of non-polyadenylated RNAs
Feb 22 Luan* Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells
Feb 29 Balreet* Lead exposure suppressed ALAD transcription by increasing methylation level of the promoter CpG islands
Mar 07 Graham Reprogramming within hours following nuclear transfer into mouse but not human zygotes
Mar 28 Luan* Experimental selection of hypoxia-tolerant Drosophila melanogaster
Apr 04 Shihong Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
Apr 11 Graham High order chromatin architecture shapes the landscape of chromosomal alterations in cancer
Apr 18 Graham DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes
Apr 25 Shihong Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
May 02 Dr Ruden* Non-CG Methylation and Cytosine Hydroxymethylation Differences in European and Africanized Honey Bees
May 09 Balreet* Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution
May 30 Edward The 1000 Genomes Project: data management and community access
Jun 06 Graham Dynamic reconfiguration of long human genes during one transcription cycle
Jun 13 Luan* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome
Jun 20 Nan** Isoform-level microRNA-155 target prediction using RNA-seq
Jul 11 Graham Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
Jul 25 Graham Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm
Aug 01 Shihong Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
Aug 08 Edward Determinants of nucleosome organization in primary human cells and Micrococcal nuclease does not substantially bias nucleosome mapping and The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning
Aug 15 Luan* Nuclear Exclusion of TET1 Is Associated with Loss of 5-Hydroxymethylcytosine in IDH1 Wild-Type Gliomas
Aug 22 Ester Embryonic stem cell potency fluctuates with endogenous retrovirus activity
Aug 29 Dr Luca Marchetti Applications of the MP theory to model signaling circuits from gene expression data
Sept 19 Graham An integrated encyclopedia of DNA elements in the human genome
Sept 26 Tin** Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
Oct 3 Arko* Loss of 5-Hydroxymethylcytosine Is an Epigenetic Hallmark of Melanoma
Oct 10 Selva Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility
Oct 31 Edward Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Nov 7 Graham Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
Nov 14 Arko* Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase
Nov 28 Wen* More than the Sum of its Parts: A Complex Epistatic Network Underlies Natural Variation in Thermal Preference Behavior in Caenorhabditis elegans.
Dec 05 Meritxell AZFc Deletions and Spermatogenic Failure: A Population-Based Survey of 20,000 Y Chromosomes
Dec 12 Thair** TEAK: Topology Enrichment Analysis frameworK for detecting activated biological subpathways

*: from Ruden's lab
**: from Zhu's lab

Previous Journal Clubs:

Journal club 2011

Journal club 2010

Last updated: Nov 01, 2012

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