Laurana.pdf,20100317,MF,Staff,PDF file example of 3D object
gromacs4_manual.pdf,20100317,mf,Staff,test
a.ps,20100322,MF,STAFF,Test
006_worm_BNI_20100321.pptx,20100322,Chao,Nets,
20100322_worm_pgene.pdf,20100322,LH,Annotation,Transcribed pseudogenes
Worm PCA.pdf,20100322,RKA,Genome Tech,2 slides - Preliminary PCA of binding and expression in worm.
Worm PCA.pdf,20100322,RKA,Tech,
Worm_PCA.pdf,20100322,RKA,Tech,Blah
allele_sample.pdf,20100323,JJL,Allele,sample
human_tfbs_saturation.ppt,20100323,LL,Genome Tech,Saturation of human TFBS data from Yale ChIP-seq
007_worm_stage_specifc_genes.pptx,20100323,Chao,Genome-Tech,
Allele_Outline_010323.pptx,20100323,,Allele,
document_text.docx,20100323,,Allele,
updates0323.ppt,20100323,JCW,allele,updated tables
updates0323.ppt,20100323,JCW,Allele,
Worm_PCA.pdf,20100323,RKA,Tech,XYZ
miniJC_2010.03.23.pdf,20100323,ASB,Genome-TECH,mini JC on Montgomery et al and Prickell et al Nature 2010
GTEx (Gene-Tissue Expression) project.ppt,20100323,JCW,Tech,
miniJC_2010.03.23.pdf,20100323,ASB,Genome-TECH,
008_worm_smallRNA_signal.pptx,20100329,Chao,Genome-Tech,
TilingArrayPCATech.pdf,20100330,RKA,Tech,Initial Tiling Array PCA
Auerbach-WormPCA.pdf,20100401,RKA,Tech,
draft_v1_notes.pdf,20100401,,allele,
AlleleSeq_v1_27Mar.docx,20100401,,allele,
Allele_Outline_010331.pptx,20100401,,allele,
table2.xls,20100401,PA,Allele,table2
schematicRob.ppt,20100401,PA,Allele,Rob's Schematic
20100301SDR.ppt,20100401,MG,Nets (covar call w PK & Ben Turk),presentation by KY on covariation analysis
KKY_CC_miRNA_TF_net.pptx,20100401,KKY,Nets,
ACT_plots.rar,20100401,JJL,Allele,
allele_sample.pdf,20100407,JJL,Allele,sample
AlleleSeq_v2_April6.docx,20100407,,Allele,
AlleleSeq_v2_April6_marks_comments,20100407,,Allele,
Allele_Outline_100407.pptx,20100407,,Allele,
MiRNANet_040810.ppt,20100408,,,
iso.pdf,20100408,,,
iso.pdf,20100408,,,
iso.pdf,20100408,,,
iso.pdf,20100408,,,
iso.pdf,20100408,,,
isoform.pdf,20100408,,,
2010.4.8.TF QC and targets.pptx,20100408,ZL,tech,TFs
Supplementary_File1.Novel_ncRNA_Features_Part1.xls,20100412,zl,,
Pseudopipe Runs.ppt,20100413,YHL,Annotation ,Discrepancy of pseudogenes between different ensembl versions
Pseudopipe Runs.ppt,20100413,,,
structure_13Apr2010_EK.pptx,20100414,Ekta Khurana,Structure,Plan for studying genome variation at protein structure level
20100419_brainSeqUpdate.ppt,20100419,LH,genome-tech,BrainSeq Update
Brain_Atlas_Stage_v2.png,20100419,LH,genome-tech,RNA-Seq workflow (Ting Chen)
Slides_April19.pptx,20100419,,Allele,
TF-miRNA_042010.ppt,20100420,PA,Tech,TF-miRNA Network
20100420chromod.ppt,20100420,ky,GenomeTech,Human chromatin features and TF binding
NB_sin_motion.ppt,20100427,NB,Nets,protein motion and networks
NB_sin_motion.ppt,20100427,NB,Nets,
NB_sin_motion.ppt,20100427,NB,Nets,
TechUpdate04282010-RKA.ppt,20100428,RKA,Genome Tech,PCA Update-in-Progress
annotation4_28_10.pptx,20100428,RR,annotation,worm binding sites
2010.4.28.novel miRNA.pptx,20100428,zl,tech,
2010.4.29.novel miRNA.pptx,20100428,,,
miRNA_TF_Network_AWG_CALL_043010.ppt,20100429,PA,TECH,miRNA-TF Network
miRNA_TF_Network_AWG_CALL_043010.ppt,20100429,PA,TECH,Networks 9 slides
BiologyOfGenomes2010_FusionSeq.pdf,20100504,LH,genome-tech,BOG - FusionSeq poster
midL2-ws190_subsampling.pdf,20100504,ASB,Genome-TECH,RNASeq coverage
TechUpdate-05052010.ppt,20100505,RKA,TECH,Worm PCA Update
Group_meeting_May5.2010.ppt,20100505,AAN,All,Presentation for group meeting
midL2-ws190_subsampling.pdf,20100505,ASB,Genome-TECH,RNASeq coverage
earthsim.jpg,20100506,MF,Staff,Test
2010_05_06.ppt,20100506,NB,JC,Review on regulatory hierarchies
figure1.pdf,20100518,LH,genome-tech,RNA-Seq flow chart
20090518_454_data.pdf,20100518,LH,genome-tech,454 data
2010.5.20. Worm TFs - HOX.ppt,20100520,ZL,tech,TF worm
NB_sin_motion2.ppt,20100520,NB,Nets,updates on SIN+Motion
NB_sin_motion3.ppt,20100525,NB,Nets,Follow up of SIN + Motion
YHL_Defense_20100520.pptx,20100531,YHL,Theses,YHL's Thesis Defense
YHL_Thesis_20100525.pdf,20100531,YHL,Theses,YHL's Thesis
GenomeTech06012010.ppt,20100601,RKA,TECH,Follow-up on binding vs. expression (in progress)
GM20100526.ppt,20100601,KY,,Specificity Determining Residues & Human TF binding
BS_initial.pptx,20100602,AAN,Assembly,Initial analysis of CNV under balancing selection
figure1_v3.pdf,20100602,LH,Annotation,RSEQtools figure
NB_GrpMtg_20100607.ppt,20100607,NB,Group Meeting,SIN +  Motion
Project Outline.ppt,20100609,Declan,NETS/STRUCture/METAgenomics (META-mtg),Tentative Outline of Proposed Project
IQ_CUFF.odp,20100609,,,
Project Outline.ppt,20100609,Declan,NETS/STRUCture/METAgenomics (META-mtg),Tentative Outline of Proposed Project
Project Outline.ppt,20100609,Declan,Nets,
Project_Outline.ppt,20100609,,Nets,
IQ_CUFF.odp,20100609,,,
2010.6.23. SNPs in ncRNAs.ppt,20100623,ZL,,
gencode-variation.pptx,20100623,Ekta Khurana,annotation/assembly,gencode and variation
FinalmiRNATFNetworkSlides.ppt,20100624,PA,Nets,miRNA-TF nets
june25_2010_gencode_mtg_for_mark.ppt,20100625,SB,Annotation,For Mark's GENCODE presentation, June 2010
june8_2010_gencode_call.ppt,20100626,SB,GENCODE call presentation,Presented on June 8, 2010
final-jan19-2010-gencode.ppt,20100626,SB ,GENCODE call presentation,Presented on Jan 19, 2010
Berger_Manuscript_20100620_LAG.docx,20100628,ASB,RubinLab,main manuscript text
Berger_Supplement_20100620_MFB.docx,20100628,ASB,RubinLab,Prostate Cancer Genome Supplementary text
Berger_Figures_20100620.pdf,20100628,ASB,RubinLab,Prostate Cancer Genome Supplementary text
Berger_Figures_20100620.pdf,20100628,ASB,RubinLab,Prostate Cancer Genome Main figures
Berger_Supplementary_Figures_20100620.pdf,20100628,ASB,RubinLab,Prostate Cancer Genome Supplementary figures
Berger_Supplementary_Tables_20100620.xlsx,20100628,ASB,RubinLab,Prostate Cancer Genome Supplementary tables
Lucas_Genome_Tech_pres_2010-07-07.pptx,20100706,LL,Genome Tech,Slides showing a worm TF saturation plot and aggregation plots of input DNA from five labs
2010.7.8. SNPs in ncRNAs.ppt,20100707,zl,assemb,
July7.ppt,20100707,Declan,Nets/Structure,Project Updates & Questions
motifs070710,20100707,PA,NETS,Motifs
aag.ppt,20100726,Gang,Metagenomics/Net,Adopt a genome
aag.ppt,20100728,GF,Nets/Meta,Adopt a genome
RotTalk.ppt,20100805,Declan,JC,End-of-Rot
simulation_2010.08.04.pdf,20100805,ASB,genome-TECH,FusionSeq simulation
Wei5.pdf,20100805,zl,tech,
simulation_2010.08.04.pdf,20100805,ASB,genome-TECH,FusionSeq simulation
Spectral_methods_BBH.ppt,20100810,KKY,Nets,Spectral methods for BBH linkage network
WeiFinalv1.pdf,20100810,PA,Tech,Networks for Valerie
WeiFinalv2.pdf,20100810,PA,Tech,Networks for Valerie
WeiFinalv3.pdf,20100810,PA,Tech,Networks for Valerie
Spectral_methods_BBH.ppt,20100811,KKY,Nets,Spectral methods for BBH linkage network
metamembrane-cover-art.ai,20100816,mbg,misc,metamembrane cover art (archived)
modencode_AWG_fig5_PAv3.pdf,20100816,PA,Tech,New Figure 7
antibody_data.pptx,20100816,KKY,Nets,Epitope-Antibody Recognition 
gpmtg 2010.8.16. ncRNA and TF.pptx,20100816,ZL,gpmtg,Group meeting presentation 8.16.2010
Presentation1.ppt,20100824,PA,Nets,Dream5
ChainsPackingData.ppt,20100824,DC,Nets,Updates to Packing Data (Chain inclusion)
WormPCAUpdate.pdf,20100829,RKA,TECH,Worm PCA Update
JC_August_31,2010.pptx,20100901,AAN,Assembly,Journal club on September 1, 2010
009_worm_hot_pred.pptx,20100910,CC,Genome-Tech,hot region prediction
Li et al 2010 update.pdf,20100915,mbg,tech,Recent paper by Biggin et al. for discussion....
2010.9.16. HOT sites.ppt,20100915,zl,tech,
20100915_indelAnnotation.pdf,20100915,LH,tech,Indel Annotation
Supplementary Information and Figures.docx,20100915,mbg,tech,Mattick Suppl. Materials
Gersteinlab_gpmt_091510.key,20100916,,,
Lucas_group_meeting_Sept_21_2010.pptx,20100921,LL,Genome Tech,Group meeting presentation given Sept 21, 2010 covering my research spanning Nov 2009 to Sept 2010
EK-grpmtg-28Sep2010.pptx,20100928,EKta Khurana,Group Meeting,
2010_09_29.key.zip,20100928,BP,Genome Annotation,Repeat Mask
CBBRetreatPoster2010v3.pdf,20100928,PA,Nets,DREAM5
20101001_GersteinLabRNASeq.ppt,20100929,LH,tech,GersteinLab RNA-Seq pipeline
2010_09_22.key.zip,20100929,BP,Genome Annotation,Lost Pseudogenes
2010.9.29.TF coverage and length.pptx,20100929,zl,tech,
Peak_length_Peakseq_VS_MACS.pdf,20100929,,,
reoccuring_peak_motifs.pdf,20100929,mbg,tech,Lincoln & Brad's motif analysis doc. from my email
Gersteinlab_JC_092910.odp,20100930,,,
modencode-preedit_MGed_RAed.doc,20101005,RA,tech,Mark's markup of editor revisions to modENCODE submission
PolII_aggs.ppt,20101005,RKA,TECH,Aggregation plots of Pol II ChIP-Seq and ChIP-chip
LL_initial_findings_for_Genome_Tech.pptx,20101006,LL,Genome Tech,Identifying Novel Alternative Exons in Mouse (Mus musculus) DSCAM
Worm_TF_saturation_2010-10-06.pptx,20101006,LL,Genome Tech,Saturation of 28 Worm TF Binding Sites on Reduced WS190 Genome
LL_initial_findings_for_Genome_Tech.pptx,20101006,LL,Genome Tech,Identifying Novel Alternative Exons in Mouse (Mus musculus) DSCAM
annotation10_6_10.pptx,20101006,RR,Annotation,RNAi and pseudogenes
PolII_aggs.ppt,20101006,RKA,TECH,Aggregation plots of Pol II ChIP-Seq and ChIP-chip
6modencode_finalfigs.pdf,20101007,,Tech,6 main figures
7modencode_finalfigs.pdf,20101007,,,7 main figs
modENCODE_main_formatted_submittedtext_50refs.pdf,20101007,RA,tech,modENCODE draft; formated; submitted text; 6 figs; 50 refs; 15 pages
modENCODE_main_formatted_preedit_50refs.pdf,20101007,RA,tech,formatted modENCODE draft; preedit text; 6 figs; 50 refs; 11.5 pages
Chong_ModEncode_supp_table.xls,20101007,CS,Tech,ncRNA clustering transcripts GO analysis
WeiOld.pdf,20101007,PA,Tech,Wei Old
WeiNew.pdf,20101007,PA,Tech,Wei New
5way.pid,20101011,PA,ModEncode,miRNA-TF
TF-miRNA.novelcro.gene_id.txt,20101011,PA,ModEncode,TF-miRNA
TF-coding.novelcro.transcript_id.txt,20101011,PA,ModEncode,TF-coding
modENCODE_ENCODE_comp,20101012,jr,gtech,
modENCODE_ENCODE_comp.docx,20101012,jr,gtech,
wormNewFigure3A.pdf,20101012,RKA,TECH,New Figure 3A (now 2A)
KKY_JC_Oct10.pdf,20101013,KKY,JC,
KevinsFig.pdf,20101013,,Tech,Kevins Figure
HLH-1_TF_model_ver3.tif,20101013,,Tech,Chao's Figure 7D
2010-10-07_Figure_8_Revised.pdf,20101013,,,Jasons fig
ASB_gpmtg_2010.10.13.pdf,20101013,ASB,grpmtg,Playing with several RNA-Seq data; discovering new “things”
RNAi_20101018.pptx,20101019,,,
JC_101810.pptx,20101025,crystal,JC,
JC_101810.pptx,20101025,JCW,JC,JC_Oct25th_10
MG_JC_RA_adipo-epigenomics_11nov2010.ppt,20101111,RA,JC,epigenomics of adipogenesis (Cell 143: 156 2010)
MG_JC_RA_adipo-epigenomics_11nov2010.pdf,20101111,RA,JC,epigenomics of adipogenesis (Cell 143: 156 2010)
OctEx_Debrief.ppt,20101111,DC,Nets/Structure,ExamPoints
20101115_pseudoSeq.pdf,20101116,LH,mtg-anno,PseudoSeq
Trio_sequencing_slides_v2.pptx,20101116,AAN,Assembly,Deep trio sequencing slides for proposal v2
Trio_sequencing_aan_v2.docx,20101116,AAN,Assembly,Deep trio sequencing proposal v2
GM_PA.key,20101117,PA,GM,DREAM5
GM_PA.ppt,20101117,PA,GM,DREAM5
GM_PA.pdf,20101117,PA,GM,DREAM5
2010_11_17.pdf,20101117,BP,,Analysis of pseudopipe output
2010_11_17.pdf,20101117,BP,,Analysis of pseudopipe output
2010_11_17.pdf,20101117,BP,,Analysis of pseudopipe output
2010_11_17.pdf,20101117,BP,,Analysis of pseudopipe output
2010_11_17.pdf,20101117,BP,,Analysis of pseudopipe output
RPKM-Analysis-Nov23-Chen.pptx,20101123,ASB,Genome-TECH,Brainseq slides from USC
Mapping_to_splices.pptx,20101130,AAN,Annotation,Novel processed pgenes
JC_iPSCs.ppt,20101130,CS,JC,12/01/2010 JC
assembly_1Dec2010.pptx,20101201,EK,Annotation/assembly,conservation of var sites
fig3a.pdf,20101201,RR,,fig 3a
progress report.pptx,20101201,JCW,Genome Tech,species_specific_motifs
progress report.pptx,20101201,JCW,Tech,species_specific_motifs
progress report.pptx,20101201,JCW,Tech,species_specific_motifs
progress report.pptx,20101201,JCW,Tech,species_specific_motifs
progress report.pptx,20101201,JCW,Tech,species_specific_motifs
progress report.pptx,20101201,JCW,Tech,species_specific_motifs
progress report.pptx,20101201,Crystal,Tech,species_specific_motifs
progress report.pptx,20101201,Crystal,Tech,species_specific_motifs
progressReport.pptx,20101201,Crystal,Tech,species_specific_motifs
IQSeq_3slides.key,20101201,,,
IQSeq_3slides.ppt,20101201,,,
RNAseq-thoughts.ppt,20101201,mbg,,init. RNAseq thoughts
RNAseq-thoughts2.ppt,20101201,mbg,tech,Refined version for Friday's Transcriptome talk
RNAseq-thoughts-asb.ppt,20101201,mbg,tech,Version for ASB's MAQ talk
This file has a filename with spaces.rtf,20101202,mf,staff,test for spaces
This_file_has_a_filename_with_spaces.rtf,20101202,mf,staff,test for spaces
RNAseq-FusionSeq.ppt,20101202,ASB,TECH,RNASeq-FusionSeq-part summary slides
ACT_slides.pptx,20101202,jr,,act slides for worm/fly call
xiu_Dec2_2010_rot_presentation.pdf,20101202,SB,GM,Xiu rotation projet update
Bootstrapping.Dec012010.pptx,20101202,XJM,Annotation/Assembly,ncSNP_resampling
dec2-2010-sungrp-nmdanalysis.pdf,20101202,SB,Annotation,LOF update
Bootstrapping.Dec012010.pptx,20101202,XJM,Annotation/Assembly,ncSNP_resampling
20101203_RNAseq_analysis_pipeline.ppt,20101202,lh,tech,RNA-Seq 
20101203_RNAseq_analysis_pipeline.pdf,20101203,LH,tech,Yale RNA-Seq pipeline
20101203_RNAseq_analysis_pipeline.ppt,20101203,LH,tech,Yale RNA-Seq pipeline
RNAseq_data_mining_2010-12-02.pptx,20101208,LL,Genome Tech,Discovery of Novel DSCAM Exons Through RNAseq Data Mining
JC120810.ppt,20101208,Gang,JC,JC ppt Dec. 8, 2010
RNAseq_data_mining_2010-12-09.pptx,20101208,LL,Genome Tech,Discovery of Novel DSCAM Exons Through RNAseq Data Mining
Bootstrapping.Dec092010.pptx,20101209,XJM,Annotation/Assembly,ncSNP_resampling2
GM_net_rewiring_2.ppt,20101209,CS,gpmtg,
20101209_pseudoSeq.pdf,20101209,LH,tech,PseudoSeq Update - 11 slides
ASboner_RSEQtools_SEQC_20101206.pdf,20101214,ASB,TECH,RSEQtools presentation at MAQC/SEQC meeting [PDF]
ASboner_RSEQtools_SEQC_20101206.ppt,20101214,ASB,TECH,RSEQtools presentation at MAQC/SEQC meeting (PPT)
ASboner_RSEQtools_SEQC_20101206.odp,20101214,ASB,TECH,RSEQtools presentation at MAQC/SEQC meeting (ODP)
454_realign_on_known.58.pptx,20101215,AAN,Annotation,Breakpoint detection with 454+AGE
Known_breakpoints_NA12878.58.xlsx,20101215,AAN,Annotation,
assembly_13Dec2010.pptx,20101216,EK,annot/assem,snps str
KKY_GM_Dec2010.ppt,20101216,KKY,Group Meeting,
Sestan_Exon_array_ms_dec_2010.pdf,20110104,RA,tech,Sestan human brain exome manuscript (with main figs and supp text)
CNVnator_AGE.pptx,20110106,AAN,Annotation,HiSeq and 454 realign with AGE for NA12878
2011_01_11.pdf,20110111,BP,Annotation,Comparing human genome repeat annotations
jan11_2011_pten.ppt,20110111,SB,Annotation,PTEN update
20110111_VAT.pdf,20110111,LH,mtg-anno,Variation Annotation Tool
group_meeting.ppt,20110111,JCW,Group_meeting,Group_meeting
20110111_indelUpdate.pdf,20110111,LH,mtg-tech,Indel update
group_meeting.ppt,20110111,JCW,gpmtg,
CNV_in_conserved_regions.primates.pptx,20110118,AAN,Annotation,Overview of collaborative project with Charles Lee
20110118_LH_groupMeeting.pdf,20110119,LH,Group meeting,Group meeting
ASB-JC-20110118.key,20110119,ASB,JC,An Integrated Approach to Uncover Drivers of Cancer - Keynote
EncodeAWG20110120.pptx,20110119,CC,,
ASB-JC-20110119.pdf,20110119,ASB,JC,An Integrated Approach to Uncover Drivers of Cancer - PDF
EncodeAWG20110120.pdf,20110119,CC,,
EncodeAWG20110120.pdf,20110119,CC,,
EK-nets-24Jan2011.pptx,20110124,EK,Nets,Rotation project for Yao
Group_meeting_January25.2011.pptx,20110124,AAN,Group meeting,GM_Jan25
2011_01_25.pdf,20110125,BP,Annotation,Repeat annotation and blast
SNP_calling.pptx,20110125,JCW,Allele,UPdates
annote1_25_11.pptx,20110125,RR,,CMS
jan25-2011-subgrp.ppt,20110125,SB,Annotation,personal genomes
SNP_calling.pptx,20110125,JCW,Allele,UPdates
SNP_calling.pptx,20110125,JCW,Allele,SNP_calling
SNP_calling.pptx,20110125,,Allele,
SNP_calling.pptx,20110125,JCW,Allele,New_updates
SNPs.pptx,20110125,JCW,Allele,New_updates
EncodeAWG20110120.pptx,20110125,,,
BP_2011_01_25.pdf,20110126,BP,Journal Club,Carrier Testing for Severe Childhood Recessive Diseases by NGS
MG_gpmtg_RA_2011-02-02.pdf,20110202,RA,gpmtg,WNV RNA-seq
peak_width_presentation.pdf,20110203,AH,Tech,Presentation on PeakSeq updates
NovelTARs_2011.02.03.key,20110203,ASB,TECH,novel TARs update
gene_expression.ppt,20110203,,,
AH.JC.Feb.3.2011.Genome.Assembly.pdf,20110203,AH,all,gpmtg presentation
KKY_Nets_Feb_2011.pdf,20110203,KKY,Nets,Phenotypic profiling
2011_02_03.pdf,20110203,BP,Annotation,PseudoPipe vs. HAVANA
Gunel.ppt,20110203,PA,NETS,GUNEL
GrpTalk_Feb8.ppt,20110208,DC,GrpMtg,GrpMtg_Feb8
GrpTalk_Feb8.ppt,20110208,DC,GrpMtg,GrpMtg_Feb8
GrpTalk_Feb8.ppt,20110208,DC,GM,GM
DOE_grant_ACT_figure.doc,20110208,LL,Tech,Figure detailing ACT analyses for the DOE grant
Rozowsky_AlleleSeq_Response.r0.doc,20110208,,allele,
Genome_Res.-2010-Lalonde-gr.111211.110.pdf,20110208,,allele,
Bioinformatics-2009-Degner-3207-12.pdf,20110208,,allele,
ctcf_update.pptx,20110208,JCW,Allele,ctcf_update
20110208_VAT_update.pdf,20110208,LH,anno,VAT
feb08_2011_subgrp_updates.ppt,20110208,SB,Annotation,Updates
assembly_6Feb2011.pptx,20110208,EK,annot/str ?,ProSNP
MG_human_genome_next_10yrs_feb_2011.ppt,20110208,RA,ANNOT,pervasive transcription slide for JCVI genome-next-10 conf
AWG_followup_TFHM_models.pptx,20110208,CC,Genome-Tech,
positive_seleciton.key,20110208,Yao Fu,nets,positive selection
feb08_2011_subgrp_updates.ppt,20110209,SB,Annotation,Updates
feb08_2011_subgrp_updates_2.ppt,20110209,SB,Annotation,Updates
20110209_indelSeq_update.pdf,20110209,LH,tech,IndelSeq update
RenqiangMartinTalk.pdf,20110209,RM,JC,Introduction to Machine Learning
20110213_testSampleCall.pdf,20110214,LH,anno,TestSample
Nets_NB_20110208.ppt,20110214,NB,Nets,6 slides on Networks and phenotypes
GQ_for_SNPs.pptx,20110215,AAN,Annotation,Genotype quality for SNPs in G1K
KKY_Nets_20110215.pdf,20110215,KKY,Nets,3D yeast genome and citation network
KKY_Feb_2011_CNV_dist.pdf,20110215,KKY,Annotation,positional distribution of CNV 
Feb142011.block.bootstrapping.pptx,20110215,XJM,Annotation/Assembly,
presentation_2-15.pdf,20110215,yao fu,nets,network & snp
CircleTriangleNetworkFigure,20110215,PA,Nets,Circle/Triangle Network Figure
Hierarchy_slides.ppt,20110215,NB,Nets,slides on Hierarchy
MarkSlides.ppt,20110215,PA,Nets,Network
MarkSlides2.ppt,20110215,PA,NETS,Newest Network
Hierarchy_slides.ppt,20110216,NB,nets,updated slides for mark's presentation
20110216_JC_noisySplicing.ppt,20110216,LH,JC,Noisy splicing
20110216_JC_noisySplicing.pdf,20110216,LH,JC,
RA4MG_jcvigenomeat10_v2.ppt,20110217,RA,NETS,jcvigenomeat10 slides
Rozowsky_GM_110215.pptx,20110218,JR,,Group Meeting
LL_indel_caller_comparison_2011-03-01.pptx,20110228,LL,Genome Tech,A comparison of the output of two indel callers (Dindel, Broad GATK)
keyNet_2011_0301.pptx,20110301,CC,,
GrpMtg_JC_NB_20110302B.ppt,20110301,NB,GrpMtg and JC,Combined GrpMtg and JC presentation
1KG_phase1_initial.pptx,20110301,AAN,Annotation,Making CNV calls on 1KG phase 1 data
genomeAnnote3_2_10.pptx,20110302,RR,,
20110223_testSample_dindelGATK.pdf,20110302,LH,,TestSample: Dindel/GATK comparison
march2-test-sample.pdf,20110302,SB,Annotation/Assembly,test sample update
march2-test-sample.pdf,20110302,SB,Annotation/Assembly,test sample update
WhyManyPeaks_Min.pdf,20110302,RM,Genome Tech,Why so many peaks
KKY_Nets_20110302.pptx,20110302,KKY,Nets,update on keynet
JJW_ase_update.pptx,20110302,,Alllele,
JJW-CTCF.pptx,20110302,,Alllele,
Rozowsky_AlleleSeq_Response.rev1.doc,20110302,,,
assem-29Feb2011.pptx,20110302,EK,nets/str,structural conservation of SNPs
HGMD+TF_specificity.pdf,20110302,Yao Fu,nets,HGMD+TF specificity
eQTL.ppt,20110309,JCW,Genome Tech,eQTL_progress_report
eQTL.ppt,20110309,JCW,Genome Tech,eQTL_progress_report1
eQTL.ppt,20110309,JCW,Genome Tech,eQTL_progress_report1
eQTL.pdf,20110309,JCW,tech,eQTL pdf
test.vcf.txt,20110309,LH,,VCF test file
Yale_phase1_initial_CNV_calling.pptx,20110309,AAN,Annotation,1KG phase 1 initial CNV calling by CNVnator
BreakDancer_and_SV.pptx,20110309,AAN,Annotation,iPSC project update
prosnp-Mar8.pptx,20110309,EK,nets/str,str vs seq conservation
KKY_Nets_20110315_Ideas_Map.pdf,20110315,KKY,Nets,Ideas Map
CpG_2010_0315.pptx,20110315,,Genome-Tech,
JC_Mar15.ppt,20110315,DC,JC,JC_Mar15
mf-test1.txt,20110315,MF,STAFF,test for page numbering1
mf-test1.txt,20110315,MF,STAFF,test for page numbering 21
mf-test1.txt,20110315,MF,STAFF,test for page numbering 2,2
test.txt,20110315,AAN,Annotation,Test,125
Indel_figures_280211.pptx,20110315,,Annotation/Assembly,,
Presentation1.pptx,20110315,,,,
1KG_indel_DIvsAAFandDAF_031011.pdf,20110315,,,,
ZDZhang_SR-analysis_Feb28.pdf,20110315,,,,
nets-str-13Mar.pptx,20110315,EK,nets/str,prosnpnet,9
KKY_Mar_2011_FS_genome_structure.ppt,20110315,KKY,Tech,scaling,14
lab_meeting_.pdf,20110316,Yao Fu,nets,Rotation talk,27
CS_Thesis_2011.pdf,20110318,CS,Thesis,PhD thesis,
Variation_in_PPD.pptx,20110321,,Annotation,,
Variation_in_PPD.pptx,20110321,AAN,Annotation,Variation in pgenes,8
Update_in_March.2011.pptx,20110321,AAN,Annotation,Update on monkeys project,13
Disorder-JC-CSDS-full.pdf,20110321,CSDS,JC,Journal Club - Protein Disorder March2011,26
2011_03_22.pdf,20110322,BP,Annotation,GERP,6
03222011.ncSNP.ENCODE.AWG.pptx,20110322,,,,
SCOP_RM.pdf,20110322,RM,Nets/Structure,SCOP,4
RRgroupMeeting3_22_11.pdf,20110322,RR,Group Meeting,,
ModENCODE_net_comp.ppt,20110322,CS,nets,,22
ModENCODE_net_comp.ppt,20110323,CS,Nets,modENCODE call network comparison slides,14
ModENCODE_net_comp.ppt,20110324,CS,Nets,,16
Rozowsky_AlleleSeq_Response.rev3.doc,20110328,,,,
Rozowsky_AlleleSeq_Manuscript_MSB_rev3.docx,20110328,,,,
Rozowsky_AlleleSeq_Figures_MSB_rev3.pptx,20110328,,,,
Meeting_in_Lee_lab.03.31.2011.pptx,20110328,AAN,Annotation,Draft presentation for meeting in Lee lab on March 31,17
ModENCODE_net_comp.ppt,20110328,CS,modENCODE,modENCODE call network comparison slides,16
Pathway_variations.pptx,20110328,Jieming,Netz,,7
Pathway_variations.pptx,20110328,Jieming,Nets,,7
eQTL_update.pptx,20110328,JCW,Genome_tech,eqtl_update,
Pathway_variations.pptx,20110329,Jieming,Nets,pathways & snps,8
sb_bostonMeeting.pdf,20110329,SB,Annotation/Assembly,Charles Lee lab presentation,21
ENCODE_ChIP-Seq_Track_Combination.pptx,20110329,AH,Tech,,8
eQTL_update.pptx,20110329,JCW,Genome_tech,QTL_update,15
eQTL_update.pptx,20110329,JCW,Genome_tech,eqtl_update,15
ASboner_NovelTARs_brainseq_2011.04.08.pdf,20110329,ASB,TECH,Novel TARs for brainSeq,5
eQTL_update.pptx,20110329,JCW,Genome_tech,QTL_update,15
eQTL_update.pptx,20110329,JCW,Genome_tech,eqtl_update,16
Yifei_NETs_Mar29.ppt,20110329,Yifei Yang,NETS/STRUCture/METAgenomics,Subgm Mar 29,3
Yifei_NETs_Mar29.ppt,20110329,Yifei Yang,Nets,1000G AA substitution,3
Yifei_NETs_Mar29.ppt,20110329,Yifei Yang,Nets,1000G AA substitution,3
nets-str-29Mar2011.pptx,20110329,EK,nets/str,PRO-SNP-NET,7
Pathway_variations.pptx,20110329,Jieming,Nets,pathways & snps,8
MMDB_1.ppt,20110329,DC,Nets,Antithesis,5
FosmidPool.Phasing.XJM.JC.03302011.pptx,20110330,,,,
PPDs_in_pilots_of_1KG.pptx,20110404,AAN,Annotation,Variation in processed p-genes in Pilot 1,3,4 of 1KG,16
LL_gpmtg_pres_2011-04-04.pptx,20110404,LL,gpmtg,Group meeting presentation given April 4, 2011 covering DSCAM alternative splicing and cancer network dysregulation,37
Tech04032011.key,20110404,RKA,TECH,Slides for Initial Discussion of ChIP-Seq Toolset,14
Ant_Interaction_Network.ppt,20110404,KKY+NB,Nets,Intro to ants network and some prelim analysis,6
2011_04_05.pdf,20110405,BP,Annotation,Peptide mapping to pseudogenes,11
Sensitivity.Inter.elm.Apr052011.pptx,20110405,,,,
2011_04_05.pdf,20110405,,Annotation,,
2011_04_05.pdf,20110405,BP,Annotation,Peptide mapping to pseudogenes,11
Ant_Interaction_Network_Apr05.ppt,20110405,KKY,Nets,Social life of ants,20
Sensitivity.Inter.elm.Apr052011.pptx,20110405,,,,
ASboner_NovelTARs_brainseq_2011.04.08.pdf,20110406,ASB,brainseq,Novel TARs for brainSeq,7
Sensitivity.Inter.elm.Apr052011.pptx,20110406,,,,
Bias_in_RD_analysis.pptx,20110411,AAN,Annotation,Bias in RD analysis in 1KG project,23
3-conservation_issues.pptx,20110412,AAN,Annotation,Pgene 3'-end conservation,11
ASboner_NovelTARs_brainseq_2011.04.15.pdf,20110414,ASB,TECH,brainseq -- novel TARs,10
BrainSeq_ncRNA_Prediction_Overview.pdf,20110414,AH,Tech,BrainSeq ncRNA overview,2
LL_hub_GO_enrichment_2011-04-20.pptx,20110419,LL,Nets,GO Enrichments of Prostate Cancer-Associated Network Hubs,26
THE_Defense.ppt,20110419,CS,Thesis defense,Chong Shou thesis defense,40
ENCODE-TF-NETWORK_20110420.pptx,20110420,,,,
PPDs_in_pilots.stringent.pptx,20110420,AAN,Annotation,Update on pseudogene analysis,9
KKY_intrinsic_direction_human_reg_net.pdf,20110420,KKY,Tech,human TF reg network: intrinsic direction,10
sestan_whiteboardphoto_2011-04-19.JPG,20110421,RA,tech,Nenad Sestan's photo of whiteboard from brainseq mtg,1
GM_YifeiYang_Apr26.ppt,20110426,Yifei Yang,Group meeting,Group meeting, end of rotation talk,18
ATran_bias_aggregation.pptx,20110426,AAN,Annotation,ATran bias,3
pers-gen-table.xls,20110427,SB,Annotation/Assembly,Starting to fill NA12878 table,1
CC_20110426.pptx,20110427,,JC,,
ChIPseq_HM.pdf,20110427,RM,GenTech,ChIP_HM,3
Mark_Poster.ppt,20110427,PA,Poster,Mark's Poster,
KKY_ants_update_05022011.pdf,20110503,KKY,Nets,Ants upate,10
LL_pre-qualifying_presentation.pptx,20110503,LL,Nets,Presentation to be given before the qualifying committee for the pre-qualifying meeting,26
20110503_pseudoSeqUpdate.pdf,20110503,lh,anno,PseudoSeq Update ,21
2011_05_03.pdf,20110503,BP,Annotation,Pseudogenes in the ENCODE,7
SNP.indel.SV.AF.forIndelCompanion.May032011.pptx,20110503,,,,4
2011_05_03.pdf,20110503,BP,Annotation,Pseudogenes in the ENCODE,7
LL_pre-qualifying_presentation.pptx,20110503,LL,Nets,Presentation to be given before the qualifying committee for the pre-qualifying meeting,27
rotationtalk_gersteinlab.pptx,20110505,Jieming,Nets,EndOfRotationTalk,28
notes.txt,20110505,Jieming,Nets,post_meeting_discussion,1
1000g-may2011-prelim.ppt,20110507,sb,1000g,Rough slides for 1000g CSHL,14
LL_prostate_cancer_bottlenecks_2011-05-12.pptx,20110512,LL,Nets,Prostate Cancer-Associated Genes Mapped to HPRD: A Bottleneck Analysis,9
BrainSeq_ncRNAs.ppt,20110512,AH,Tech,,13
upstream_comp_tools.key,20110512,,,,
2011_05_12.pdf,20110512,BP,Annotation,Chromatin architecture of pseudogenes,4
Nets_Ensemble.ppt,20110512,PA,Nets,Ensembling,24
Annot12May2011.pdf,20110512,CSDS,Annotations,Chromatin and Pseudogene Update,8
upstream_comp_tools.key,20110512,,,,
Annot12May2011.pdf,20110512,CSDS,Annotation,Chromatin and Pseudogenes Update,8
upstream_comp_tools.pdf,20110512,,,,
Annot12May2011.pdf,20110512,CSDS,Annotation,Chromatin and Pseudogenes Update,8
Sboner_RSEQtools_ENCODE_May2011_Poster.pdf,20110516,ASB,TECH,Encode RSEQtools Poster May 2011,1
Net_modENCODE_2.ppt,20110517,CS,Nets,modENCODE,2
006_Encode_TF_profiles.pptx,20110517,CC,,,
CEU_denovo_CG.pptx,20110517,AAN,Annotation,Searching for de novo variants with CG data,20
PSO.ppt,20110517,PA,Nets,Particles,6
to_RA.ppt,20110517,KKY,Nets,mirnet,9
Phase1_results.pptx,20110518,AAN,Annotation,Initial analysis of p-genes using phase1 data,3
20110517_VAT_paper_update.pdf,20110518,LH,Anno,VAT Paper Update,4
Phase1_results.pptx,20110518,AAN,Annotations,Initial analysis of p-genes using phase1 data,4
stejustine.20May.pptx,20110523,EK,JC,practice for job talk,49
Gerstein_seminar.pptx,20110531,Ben Brown (submitted by DC),JC,Nonparametric Inference for Functional and Translational Genomics,54
LL_ICGC_on_HPRD_and_ENCODE_K562-2011-05-31.pptx,20110601,LL,Nets,A Network Perspective of ICGC Cancer SNVs,18
Phase1_update.pptx,20110601,AAN,Annotation,Update on Pgene calling in phase 1 data,2
modENCODE_DC_mtg_21_May_2011_notes.doc,20110602,RA,tech,Notes from mod/ENCODE DC mtg 21-25 May 2011,75
2011_06_02.pdf,20110602,BP,Annotation,Constraint regions in Pseudogene Annotations,10
Phase1_update.ppt,20110602,AAN,Annotation,Update on Pgene calling in phase 1 data,2
20110519ElementsNetworks_GSC_updated.ppt,20110602,KY/NB,Talk with Ben,Disc with Ben brown,
BenBrown_MG_JC_2011-05-31.pdf,20110602,RA,JC,Ben Brown on GSC (pdf),45
june02-2011-subgrp.ppt,20110602,SB,Annotation,This and that,7
Indel.filtered.vs.SNP.May252011.pdf,20110602,,,,
Trying_to_fix_seq_bias.pptx,20110608,AAN,Annotation,Trying to fix sequencing bias for CNV discovery,6
2011_06_07.pdf,20110608,BP,Annotation,Constraints regions in pseudogenes,3
Annot8June2011CSDS.pdf,20110608,CSDS,Annotation,Update on Pgenes and Chromatin,9
photo.JPG,20110608,DC,Annotation,Photos from Statistical Comparisons Debate,
photo(2).JPG,20110608,DC,Annotation,Photos from Statistical Comparisons Debate (Photo 2),1
varInNcRna.pdf,20110616,RM,Tech,variants in ncRNA ,1
TFncRNA.pdf,20110616,RM,Nets,ncRNA Net in ENCODE,3
LL_ENCODE_TF_disruption_2011-06-16.pdf,20110616,LL,Nets,ENCODE TF Hub and Bottleneck Disruption in Cancer,4
LL_ENCODE_TF_disruption_2011-06-16.pdf,20110616,LL,Nets,ENCODE TF Hub and Bottleneck Disruption in Cancer,5
KKY_Jun2011_K562_net.pdf,20110616,KKY,Nets,ENCODE network hierarchy/motifs,10
test.txt,20110616,,,,
KKY_Jun2011_K562_net.pdf,20110616,KKY,Nets,ENCODE network hierarchy/motifs,10
nets-tf-net-16Jun2011.pptx,20110616,EK,Nets,,5
evoFlex.JPG,20110618,DC,Nets,Evo-Structure Plasticity Picture 1,1
Figure2-Gerstein.png,20110618,NB,NSF grant,first figure for my parts,
types_motions.png,20110618,NB,NSF grant,Second figure for my parts,
Figure1-Gerstein.png,20110618,NB,NSF grant,first figure for my parts,
evoFlex.JPG,20110618,DC,Nets,Schematic for Grant: EvoFlex Pic 1,1
photo1DC.JPG,20110618,CSDS,NSF,Photo-1-DC-18thJune2011,1
photo2DC.JPG,20110618,CSDS,NSF,Photo-2-DC-18thJune2011,1
photo3DC.JPG,20110618,CSDS,NSF,Photo-3-DC-18June2011,1
photo4DCevoFlexSchematic.jpg,20110618,CSDS,NSF,Photo-4-DC-18June2011-EvolFlowSchematic,
PPDK_motions.png,20110618,AAN,Structure,Fig3 for NSF grant,1
CEU_denovo_CG.update.pptx,20110621,AAN,Annotation,Update on searching de novo variants in CEU family,8
TwittersStats.ppt,20110621,RR,Nets,Twitter,9
JC-6-21-11.ppt,20110621,PA,JC,Differential Networks,16
MG-NSF-2011-Figures.doc,20110621,CSDS,NSF,Figures NSF 2011,
Annot22June2011.pdf,20110622,CSDS,Annotation,Normalization of SegwayCounts on Pgene and Parent genes,4
2011_06_22.pdf,20110622,BP,Annotation,Effects of 2x mammal sequences on constraint elements in pgenes,7
june22_2011_subgrp.ppt,20110622,SB,Annotation,NA12878 indel RNASEQ analysis,3
june22_2011_subgrp.ppt.pdf,20110622,SB,Annotation,NA12878 indel RNASEQ analysis,4
june22_2011_subgrp.ppt.pdf,20110622,SB,Annotation,NA12878 indel RNASEQ analysis,4
RKA_GM-June_2011.pdf,20110622,RKA,GM,Group Meeting Presentation given 6-22-2011,42
mapping_structure.png,20110625,NB,NSF grant,combined figure for my parts,
F4Voss2010.jpg,20110625,CSDS,NSF-2011,Figure2-3V,1
Figure1-New.png,20110626,NB,NSF grant,another version of overall figure.,
JC_July29.2011.pptx,20110628,AAN,JC,RNA editing (journal club),15
JC_July29.2011.pptx,20110628,,,,1e+10
LL_Rubin_Gerstein_meeting_summary_2011-06-28.pdf,20110628,LL,Tech,Summary of Upcoming Work in the Rubin-Gerstein Collaboration,17
KKY_Jun_28_2011_ENCODE_network_update.pdf,20110628,KKY,Nets,update on encode net,9
ncRNA_Net.pdf,20110628,RM,Nets,ncRNA network,5
ncRNA_Net.pdf,20110628,RM,Nets,ncRNA network updated,6
notes-on-pot-encode-nets-paper-figs.doc,20110628,DC,Nets,Potential Nets-Encode Ppr Notes,1
MG-NSF-2011-Figures.doc,20110628,CSDS,NSF 2011,Figures NSF 2011,2
Fig1a.png,20110628,AAN,Structure,Fig1a,
Fig1b.png,20110628,AAN,Structure,Fig1b,
Fig2a.png,20110628,AAN,Structure,Fig2a,
Fig2b.png,20110628,AAN,Structure,Fig2b,
evoFlexNew.jpg,20110629,DC,NSF Grant,evoFlex,1
vectors.jpg,20110629,DC,NSF Grant,motion_evo_vectors,1
evoFlexNew.jpg,20110629,DC,NSF Grant,biophysical & evol flex schematic,1
vectors.jpg,20110629,DC,NSF Grant,correlation of vectors,1
VMoverview.jpg,20110629,DC,NSF Grant,Data Mngmnt Overview: AWS VMs,1
RDDs_and_pgenes.pptx,20110701,AAN,Annotation,Pgenes and RDDs,1
fig-cd4.tif,20110702,EK,nets/str,figure for 3Diii,1
hier_for_grant.pdf,20110702,NB,nets,hier figure for grant,
MG-NSF-2011-Figures-3rdJuly2011.doc,20110703,CSDS,NSF grant 2011,Figures so far NSF grant 2011,2
FlexSchematic.doc,20110704,DC,nets/str,biophysical & evol flexibility schematic (NSF-ABI grant),1
Figure1-New.png,20110704,NB,NSF grant,New overall figue,
Figure1-New.png,20110704,NB,NSF grant,New overall figue,
Pgenes_null_model.pptx,20110705,AAN,Annotation,Null model for pgene discovery,9
KKY_Jun_28_2011_ENCODE_network_update.pdf,20110706,KKY,Nets,,1
TF_vs_CellLine.xls,20110706,KKY,Nets,TF targets diff. cell lines,1
KKY_Jun_28_2011_ENCODE_network_update.pdf,20110706,KKY,Nets,ENCODE network hierarchy/motifs,2
MMDB_schematics.ppt,20110706,DC,nets/str,MolMovDB grant figs (AWS, MMDB organization),2
20110707_pseudoSeq.pdf,20110707,LH,Anno,PseudoSeq,127
Fig_packing_NSF.png,20110707,AAN,Structure,Packing figure for NSF grant 2011,1
2011_07_07.pdf,20110707,BP,Annotation,Conservation of pseudogenes,3
evoFlexMorph_New.jpg,20110707,DC,NSF 2011,Revised Biophysical & Evol Flexibility Fig,1
Grp.Mtg.June.2011.ppt,20110707,AH,GrpMtg,Group meeting presentation,30
types_motions.png,20110708,NB,NSF Grant,Figure 7,
MolMovDB_overview.jpg,20110708,DC,NSF 2011,Figure: MolMovDB Overview,1
AWS_overview.jpg,20110708,DC,NSF 2011,Cloud Computing Overview,1
NSF_DCfigures.ppt,20110708,DC,NSF 2011,Powerpoint Version of Figs (evoFlex, MMDB overview, & Cloud Computing),3
HappyHourExtra-8July2011.zip,20110708,CSDS,HappyHour,HappyHour-8July2011,
NSF-2011-Final-MBG-v02-MG-JC-NB-EK-DC-AAN-CSDS.doc,20110710,CSDS,NSF-2011,NSF-final version 10July2011,15
July5_2011_uorf.ppt,20110711,SB,JC,uORF July 2011 presentation,15
1KG_phase1_with_pe.pptx,20110712,AAN,Annotation,CNV calling in phase1 with PE support,6
FastLane-complete.pdf,20110712,CSDS,NSF,Completed Grant,54
comparing_Fi.pptx,20110713,AAN,Annotation,Comparing iPS and fibroblast sequencing,18
BP_GM_20110713.pdf,20110713,BP,Group Meeting,Chromatin features and evolutionary constraint of pseudogenes,32
comparing_Fi.pptx,20110713,,,,
20110712_pseudoSeqUpdate.pdf,20110713,LH,Anno,PseudoSeq Update ,11
mmdbFlex_Jul14.ppt,20110714,DC,Nets/Str,MolMovDB & IntrinsicFlexibility,3
HierNet.pptx,20110714,CC,,,8
BigAllele,20110714,PA,Nets,Big Allele,2
cancer_variants_on_personal_genome_table.pdf,20110714,LL,Nets,Cancer Variants in the Personal Genome Table,2
Update_7-14-11v2.ppt,20110719,PA,Nets,miRNA,30
for-nets-19Jul2011.pptx,20110719,EK,nets,netsnp,2
Pseudogene_Companion_Outline_0720.docx,20110720,BP,Annotation,Pseudogene Companion Outline,2
Figure_Slides.pdf,20110720,BP,Annotation,Pseudogene Companion Figure Slides,9
2011_07_20.pdf,20110720,BP,Annotation,Pseudogene preservation,3
Figure_Slides.pdf,20110720,BP,Annotation,Pseudogene Companion Figure Slides,9
2011_07_20.pdf,20110720,BP,Annotation,Pseudogene preservation,3
Annot20July2011CSDS.pptx,20110720,CSDS,Annotation,Chromatin and Pgenes,7
upstream_pgene_SD.pdf,20110720,,,,
disease_nc.pptx,20110720,JCW,Annotation,,
july20_complete_genomics.pdf,20110720,SB,Annotation,Complete genomics dataset,5
KKY_JC_July2011.pptx,20110720,KKY,JC,,16
july20_complete_genomics.pdf,20110720,SB,Annotation,Complete Genomics Dataset,5
Nets_motifs_corr.pptx,20110720,KKY,Nets,network motif vs expression,1
ALL_TF-TF_BIOGRID.txt,20110720,,,,
BigNetSpring.pdf,20110720,PA,,Big Allele,
BigNetOrganic.pdf,20110720,PA,,,
BigNetSpring.pdf,20110720,PA,,,
disease_nc(1).pptx,20110720,JCW,Annotation,,
MinGroupMeeting.pdf,20110727,RM,GroupMeeting,ncRNA_S3RBM,28
Pseudogene_Validations_07-27-2011.pptx,20110727,AAN,Annotation,Pseudogene prediction validation,5
2011_07_28.pdf,20110728,BP,Annotation,Case Study of Pseudogenes,16
20110728.Motif.TF.network.pptx,20110728,,,,
july28_2011_uorf_lof.pdf,20110728,SB,Annotation,LOF stuff,3
hs_enhancer.key,20110728,,,,
miRNA_pipeline_development_w.pdf,20110728,RK,Tech,miRNA BrainSeq pipeline,13
009_encode_TSS_models.pptx,20110728,,,,
BrainSeq_ncRNAs_July.29.ppt,20110728,AH,Tech,,
hs_enhancer.ppt,20110728,,,,
BrainSeq_ncRNA_updates.pdf,20110728,AH,Tech,,
BrainSeq_ncRNAs_July_29.pdf,20110728,AH,Tech,,
hs_enhancer.ppt,20110728,,,,
KKY_encode_hierarchy_update.pdf,20110728,KKY,Nets,encode network hierarchy updates,2
20110728.Motif.TF.network.v2.pptx,20110728,,,,
2011_05_05-Elements-TFAssociations.pdf,20110728,NB,Nets,Anshul and Manoj's first presentation,
02_24_11_TFCombn.pdf,20110728,NB,,Anshul and Manoj's first presentation,
20110728Nets_Figures.pptx,20110728,KY,,Plan for Downstream analysis,8
BigAllelev2.ppt,20110728,PA,Nets,The Big Allele,7
20110728.Motif.TF.network.v2.pptx,20110728,,,,
tf-nets-26Jul.pptx,20110728,EK,nets/str,tf nets selection,8
20110728Nets_Figures.pdf,20110728,KY,,Plan for Downstream analysis,8
Encode_TF_target_Symbol_Q01.txt,20110728,,,,
20110728.Motif.TF.network.v2.pptx,20110728,,,,
s1.pptx,20110728,,,,
for-oligo-EK-29Jul.pdf,20110729,EK,oligo call,selection on TFs and targets,
AlleleNetworksOligo.pdf,20110729,Pedro,oligo call,allele ,
KKY_CC_oligo.pdf,20110729,KKY,Oligo call,hierarchy and related,8
Downstream_analysis_Co-association_Kevin_Nitin.pdf,20110729,KY+NB,Oligo,Plan for Downstream analysis,
MPDegree.ppt,20110803,PA,Nets,New Big Allele,3
Summary_aug4.2011.pptx,20110803,AAN,Annotation,Summary of iPSC project,7
aug3RMSD.ppt,20110803,DC,Nets/Struct,RMSD Metric Comparisons,3
TF_ncRNA_Hierarchy.pptx,20110803,RM,Nets,ncRNA_hierarchy,5
20110803Nets_TFCoassociation.xlsm,20110803,KY,Nets,TF co-association figures and lists,
try.pdf,20110803,KKY,Nets,hierarchy and motifs,2
encode_figures_id_aug03.docx,20110803,KY,Nets,ENCODE integrative paper figures,
JC080311.ppt,20110803,Gang Fang,Metagenomics,JClub080311,15
TF_ncRNA_Hierarchy.pptx,20110803,RM,Nets,ncRNA_Hier,6
20110803.Favorable.SNP.motif.pptx,20110804,,,,
20110803.Favorable.SNP.motif.pptx,20110804,,,,
JointCall8_5_11.ppt,20110804,RR,Annote,Joint Call,
20110803.Favorable.SNP.motif.pptx,20110804,,,,
JointCall8_5_11.ppt,20110804,RR,,Joint Call,19
20110803.Favorable.SNP.motif.v2.pptx,20110804,,,,
20110803.Favorable.SNP.motif.v2.pptx,20110804,,,,
pgene_upstream.ppt,20110804,,,,
20110803.Favorable.SNP.motif.v2.pptx,20110804,,,,
20110803.Favorable.SNP.motif.v2.pptx,20110804,,,,
pgene_upstream.ppt,20110804,,,,
20110803.Favorable.SNP.motif.v2.pptx,20110804,,,,
20110803.Favorable.SNP.motif.v2.pptx,20110804,,,,
pgene_upstream.ppt,20110804,,,,
pgene_upstream.ppt,20110804,,,,
JointCall8_5_11_ver2.ppt,20110804,RR,Annote,joint call ver 2,
ASB_gpmtg_2011.08.04.key,20110807,ASB,gpmtg,BrainSpan overview,45
ASB_gpmtg_2011.08.04.ppt,20110809,ASB,,group meeting,
ASB_gpmtg_2011.08.04.pdf,20110809,ASB,,,
Pgenes_refine.pptx,20110809,AAN,Annotation,Refinement of pgene predictions,22
ASB_JC_2011.08.pdf,20110810,ASB,JClub,9th Annual Genome Technology Salary Survey,12
ASB_JC_2011.08.key,20110810,ASB,JClub,9th Annual Genome Technology Salary Survey,12
BigAllelev3.ppt,20110810,PA,Nets,,2
2011_08_10.pdf,20110810,BP,Annotation,Pgene TFBS,4
KKY_ENCODE_NET_AUG.pdf,20110810,KKY,nets,update on encode net,8
MEF2A_NFKB_examle.pptx,20110810,AAN,Nets,TF spacing on DNA (example),2
20110810.Heirachy.net.pptx,20110810,,,,
20110810.Heirachy.net.pptx,20110810,,,,
Downstream_analysis.ppt,20110810,NB,Nets,downstream analysis,10
Downstream_analysis.ppt,20110810,NB,Nets,downstream analysis,10
BN_ENCODE.pdf,20110810,RM,Nets,BayesianNet_TFInteractions,6
BN_ENCODE.pdf,20110810,RM,Nets,Bayesian Network,8
MG_gpmtg_RA_2011-08-11.pdf,20110811,RA,gpmtg,,43
JC.pdf,20110816,YF,JC,The landscape of recombination in African American,
JC.pdf,20110816,YF,JC,the landscape of recombination in African American,14
Annot17Aug2011CSDS.pptx,20110817,CSDS,Annotation,TF binding sites - pseudogenes,5
GIliNets.pdf,20110817,Gili,NETS/STRUCTURE,HierarchyGili,7
BiophysTF_Motifs.ppt,20110817,DC,Nets/Struct,Biophysical Basis of Motif Entropy,6
FigurePack.pptx,20110817,NB,Nets,Figures,7
Schematic.ppt,20110823,PA,Nets,figures for encode paper,3
twitter8_24_11.ppt,20110824,RR,Nets,Twitter,8
010_Gata1_knockdown.pptx,20110824,CC,Nets,,
011_miR_site_distance.pptx,20110824,CC,Nets,miR binding site distance,
FigS5.pdf,20110824,KKY,Nets,,
Figure6.pdf,20110824,CC,,mirNet motif Figure,
FigS5.pdf,20110824,CC,,all possible motifs ,
Figure6.pdf,20110824,KKY,Nets,,
photo8_24_11.JPG,20110824,,Nets,Photo minutes from 8-24-11,
photo8_24_11_two.JPG,20110824,,,Photo minutes from 8-24-11 part 2,
BayesianNet_ENCODE_Aug2011.pptx,20110824,RM,Nets,Bayesian Net,11
motifs_update.pdf,20110830,KKY,Nets,update on motifs analysis,4
NcrnaCodingRatio.pptx,20110830,RM,Nets,Tendency of TFs Regulating Ncrnas than Coding Genes,2
DistalRegulatoryModules.pdf,20110830,,,,
iPSC_analysis.Sep2011.pptx,20110831,AAN,Annotation,Update on F-to-i sequencing comparison,37
GroupMeeting22Aug2011_CSDSrecovered.pptx,20110831,CSDS,GPMTG,Group meeting,32
gencodeNotes.JPG,20110831,,Annote,,
AS_BrainSeq.pdf,20110831,,,,
ABCD.ppt,20110901,PA,Nets,figures for encodenets paper  schematic,5
NcRNANetworkMotif.pptx,20110901,RM,Nets,NcRNA Network Motifs,1
20110901.miRNA.target.SNP.compensation.pptx,20110901,,,,
BP_2011_09_01.pdf,20110901,BP,JC,Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism,15
twitter8_30_11.ppt,20110901,RR,Nets,Twitter,
GM_2.ppt,20110901,Gili,NETS/STRUCTURE,HierarchyGili_2,8
rotation_plan_090111.ppt,20110901,Darryl,Nets,Rotation Plan,5
rotation_plan_090111.ppt,20110901,Darryl,Nets,Rotation Plan,5
rotation_plan_090111.ppt,20110901,Darryl,Nets,Rotation Plan,5
regulusRX_top4_miRNAs_and_arabidopsisGWAS.ppt,20110901,PA,Nets,miRNA,17
Sept1data.ppt,20110901,DC,Nets/Struct,Sept1,2
Figure5B.pdf,20110909,KKY,nets,encode net update,2
iPSC_analysis.Sep2011.pptx,20110909,AAN,Annotation,iPS analysis,43
PCR_phase1_follow_up.pptx,20110913,AAN,Annotation,Follow up on PCR validation for deletions in phase 1,5
microRNA.pdf,20110913,YF,nets,microRNA co-localization,8
miRNA_SNP_analysis_Sept.14.2011.ppt,20110914,AH,Annotation,,5
20110914.miRNA.pptx,20110914,,,,
20110914.miRNA.pptx,20110914,,,,
012_TF_model.pptx,20110914,,Nets,TF model updates,4
encode_net_updates.pdf,20110914,KKY,Nets,,3
ChaoFeatures.pdf,20110914,PA,Nets,,1
drm.pdf,20110914,,,,
encode-nets_rankcalc_plots_RA_20110914.pdf,20110914,RA,nets,encode-nets rank calculations,16
MG_JC_RA_2011-09-14.pdf,20110914,RA,JC,Journal Club -- 3 interesting articles + human TFs,5
EncodeNcrnaSuppFigs_BN.pptx,20110914,RM,Nets,ENCODE Ncrna Supp Fig and BN ,8
EncodeNcrnaSuppFigs_BN.pptx,20110914,RM,Nets,Encode ncrna supp figs and BN analysis,9
LL_gpmtg_2011-09-14.pptx,20110915,LL,gpmtg,A Network Biology Approach to Cancer: Cancer Disruption Networks and Dysregulated Subnetwork Markers ,40
LL_gpmtg_2011-09-14.pptx,20110915,LL,gpmtg,A Network Biology Approach to Cancer: Cancer Disruption Networks and Dysregulated Subnetwork Markers,40
ENCODEnets_20110917-MG-edit-highlighted.doc,20110919,RA,nets,ENCODEnets draft highlighting MG's changes 20110917,
ENCODEnets_20110917-MG-edit-highlighted.doc,20110919,RA,nets,ENCODEnets draft highlighting MG's changes 20110917,
TFncRNACoding_OutDegreePlot.tif,20110919,RM,Nets,Supp_RM1,1
ncRNALevel_tif1.tif,20110919,RM,Nets,Supp_RM2,1
ncRNALevel_tif2.tif,20110919,RM,Nets,Supp_RM3,1
NcRNANetworkMotif.pptx,20110919,RM,Nets,Supp_RM4,1
TFncRNACoding_OutDegreePlot.tif,20110919,RM,Nets,Supp_RM1,1
DiamondNcRNAMotif.pptx,20110920,RM,Nets,4-way Motifs deleted--so not interesting,1
110920-Jclub1-Generating_Genome-Scale_Candidate_Gene_Lists_for_Pharmacogenomics.pptx,20110920,JC,Jclub,,16
GM_3_human.ppt,20110920,Gili,NETS/STRUCTURE,human coregulation,8
GM_3_human.ppt,20110920,Gili,NETS/STRUCTURE,human coregulation,8
CHI_gene_inac_pg_draft_v2.ppt,20110921,SB,GM,9/21/2011 grp meeting,27
Scoring_schematic.eps,20110921,JR,Allele,,
Scoring_schematic.eps,20110921,JR,Allele,,
Scoring_schematic_text,20110921,JR,Allele,,
rotation_presentation.09.21.11.ppt,20110921,Darryl,Nets,rotation progress,8
rotation_presentation.09.21.11.ppt,20110921,Darryl,Nets,rotation progress 9/21/11,8
drm.pdf,20110921,,,,
110930_genometech_ncVar_II_-_snps.pptx,20110930,JC,Annotation,allelespecificSNPs,4
ncVARII.Sep302011.pptx,20110930,,,,
110930_genomeannot_ncVar_II_-_snps.pptx,20110930,JC,Annotation,allelespecificSNPs,6
mirna_target_variation_analysis.ppt,20110930,AH,Annotation,miRNA targets vs. SNPs,4
Sep302011.Allelic.Score.pptx,20110930,,,,
110930_genomeannot_ncVar_II_-_snps.pptx,20110930,JC,Annotation,allelespecificSNPs,6
ncVARII.Sep302011.pptx,20110930,,,,
ncVARII.Sep302011.pptx,20110930,,,,
ncVARII.Sep302011.pptx,20110930,,,,
110930_genomeannot_ncVar_II_-_snps.pptx,20110930,JC,Annotation,allelespecificSNPs,6
updates_September_30.ppt,20110930,PA,Nets,,5
GM_5.ppt,20110930,Gili,NETS/STRUCTURE,human coregulation  seq,13
drm.pdf,20110930,,,,
Allelic.SNP.png,20111003,,,,
rotation_presentation.10.03.11.ppt,20111003,Darryl,Nets,Rotation progress 10/03/2011,10
Presentation3.ppt,20111003,PA,Encodenets,,13
TF_hierarchy_test.pdf,20111003,KKY,Nets,,2
mircoRNA-10-1.pptx,20111004,YF,Annotation,miRNA Targeting,8
RD_RP_for_pseudogenes.pptx,20111004,AAN,Annotation,Attempt to genotype pseudogenes,14
RRjournalClub10_4_11.ppt,20111004,RR,,Twitter predictions,
ncrna_variation_analysis.ppt,20111004,AH,Annotation,ncRNA variation,8
BP_PGENE_Figures_1004.pdf,20111004,BP,Annotation,Pseudogene Companion Figure Slides,12
pgene.pdf,20111004,,,,
ncrna_variation_analysis.ppt,20111004,AH,Annotation,ncRNA variation,8
fig-EK-3Oct2011.pptx,20111004,EK,annot,for 1KG,
VAT_on_AWS.ppt,20111004,DZC,Annotation,VAT on Amazon Web Services powerpoint,12
ncrna_variation_analysis.ppt,20111004,AH,Annotation,ncRNA variation,8
fig-EK-4Oct2011.v2.pptx,20111004,EK,annot,revised FIG slides,
Hier_miRNA.ppt,20111005,PA,Encode Nets,,3
Oct5.ppt,20111005,DC,Genome Tech,GSC,3
ChIPSeq.pptx,20111005,RKA,TECH,Overview of Pol 2 Signal Profile Research Idea,7
GrpMtg_NB_Oct5_2011.ppt,20111005,NB,GrpMtg,Last Group meeting,25
ncVARII.part3.pdf,20111005,,,,
drm.pdf,20111005,,,,
ncVARII.part3.pdf,20111005,,,,
Oct052011.Allele.selection.pptx,20111005,,,,
Oct052011.Allele.selection.pptx,20111005,,,,
CTCF_Fig.pdf,20111005,CC,,CTCF,
Allelic.peaks.SNP.density.png,20111007,,,,
GM_6.ppt,20111007,Gili,NETS/STRUCTURE,human coregulation  seq,9
iPSC_analysis.Oct2011.pptx,20111012,AAN,Annotation,Update on iPS project,11
Figure4_combined.pdf,20111012,NB,Nets,Update on Fig 4,2
Twitter9_29_11.ppt,20111012,RR,,Twitter mutations,12
Update_Oct-12-2011_Figures_3B_3C.ppt,20111012,PA,Encode Nets,,2
CEGS_2011_lighthning.abyzov.pptx,20111012,AAN,Annotation,Lightning talk for CEGS 2011,12
figure.ppt,20111012,Gili,NETS/STRUCTURE,encode figure,2
111013_genomeannot_ncVar_II_-_snps.pptx,20111013,JC,Annotation,allele SNPs in noncoding regions,13
Anno4Oct2011UpstreamElCSDS.pptx,20111013,CSDS,Annot,,6
Oct13.2011.ncVARII.pptx,20111013,,,,
6215687161_329e20f4b1_m.jpg,20111013,DC,ENCODE_Nets,img1,1
6215986378_f33e61f444_m.jpg,20111013,DC,ENCODE_Nets,img2,1
6216086202_8c18ee0b9c_m.jpg,20111013,DC,ENCODE_Nets,img3,1
6239155733_8a2f839eb1_m.jpg,20111013,DC,ENCODE_Nets,img4,1
6239156417_b21bf30047_m.jpg,20111013,DC,ENCODE_Nets,img5,1
6239674264_84c506e247_m.jpg,20111013,DC,ENCODE_Nets,img6,1
6239675550_ddcdde7c88_m.jpg,20111013,DC,ENCODE_Nets,img7,1
CEGS_2011_lighthning.abyzov.pptx,20111013,AAN,Annotation,,12
Cancer_variants_on_personal_genome_table_fixed_ncRNA_2011-10-12.pdf,20111013,LL,Tech,/Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_Atf3.txt /Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_Pax5_2.txt /Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_Pbx3.txt /Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_Batf.txt /Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_Pol2_1.txt /Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_Bcl11.txt 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/Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_Oct2.txt /Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_Zzz3.txt /Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_P300_1.txt /Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_P300_2.txt /Users/lucasl/Documents/Academics/Research/Projects/Cancer/CDN/Network_structure_\(curated_data\)/unmapped_to_nc/unmapped_vs_Pax5_1.txt,5
rotation_talk_oct_13.ppt,20111013,Gili,group meeting,rotation talk,31
111013_genomeannot_ncVar_II_-_snps.pptx,20111013,JC,Annotation,allele SNPs in noncoding regions,20
111013_genomeannot_ncVar_II_-_snps.pptx,20111013,JC,Annotation,allele SNPs in noncoding regions,20
ncVARII.637.Oct13.2011.AlleleSeq.peaks.v2.pdf,20111013,,,,
CEGS_2011_lighthning.abyzov.pptx,20111014,AAN,Annotation,Presentation for CEGS,14
CEGS_2011_lighthning.abyzov.pptx,20111014,,,,
ENCODE_TFAndTargetFunctions.pdf,20111019,RM,Nets,Brief functiona analysis of TFs and their targets in ENCODE,16
validations_1kg_pgenes_Oct2011.pdf,20111019,AAN,Annotation,Additional validation for novel pgenes,6
ENCODE_TFAndTargetFunctions.pdf,20111019,RM,Nets,8mins' Talk on Functional Analysis of ENCODE TFs and their Targets,24
K562_update.pdf,20111019,KKY,Nets,enodenet, k562,2
ncvar2_updates.oct.19.2011.ppt,20111019,AH,Annotation,ncVAR2 updates,15
Oct13.2011.ncVARII.pptx,20111019,,,,
Oct13.2011.ncVARII.pptx,20111019,,,,
rotation_presentation_1019.ppt,20111019,Darryl,group meeting,rotation presentation,47
Oct13.2011.ncVARII.pptx,20111019,,,,
Figure4_combined.pdf,20111019,NB,nets,,2
ENCODE_TFAndTargetFunctions.pdf,20111019,RM,Nets,8mins' talk on functional analysis of ENCODE TFs and their targets in different levels,25
K562_update.pdf,20111019,KKy,Nets,,
heatmaps.ppt,20111019,Gili,NETS/STRUCTURE,heat maps,7
FirstLook2.ppt,20111020,RKA,TECH,Kurtosis First Look,9
LL_JC_2011-10-20.pdf,20111020,LL,JC,Exploring PPI Networks for Disease-Associated Genes,20
ncvar2_updates.oct.19.2011.ppt,20111020,AH,Annotation,ncVAR2 updates,15
sup_figures.ppt,20111025,Gili,NETS/STRUCTURE,sup_figures_gili,3
heatmaps.ppt,20111025,Gili,NETS/STRUCTURE,גילי,12
111026_genomeannot_ncVar_II_-_snps.pptx,20111026,JC,Annotation,allele SNPs in noncoding regions (ncVarII),10
111026_genomeannot_ncVar_II_-_snps.pptx,20111026,JC,Annotation,allele SNPs in noncoding regions (ncVarII),10
mirna_target_variation_Oct.26.ppt,20111026,,Annotation,,
mirna_target_variation_Oct.26.ppt,20111026,AH,Annotation,mirna target variation,2
LL_dbGaP_initial_data_report_2011-10-26.pdf,20111027,LL,Tech,Report on dbGaP data recently approved for our use,9
Table-S4B-GenomicFeaturesFuncCat-RA.pdf,20111027,RA,encode-nets,table for data mining interesting features of TF families,1
JC_slides_RK_27072011.pdf,20111101,RK,JC,my first journal club by RK, aged 28,
EncodeNcrnaSuppFigs_BN.pptx,20111101,RM,Nets,First Part of BN on ENCODE Data,6
twitter11_1_11.ppt,20111101,RR,Nets,twitter,10
twitter11_1_11.ppt,20111101,RR,Nets,Twitter,10
111101_genomeannot_ncVar_II_reads_distrib_rnaseq.pptx,20111102,JC,Annotation,allele SNPs in RNAseq,8
LL_cancer_variants_2011-11-02.pdf,20111102,LL,Tech,Cancer Variants Mapping to Non-Genic TSS-Distal DHS Peaks,16
Selection.TF-sites.xlsx,20111102,,,,
111101_genomeannot_ncVar_II_reads_distrib_rnaseq.pptx,20111104,JC,Annotation,allele SNPs in RNAseq,8
GM_2011_ChaoCheng.pptx,20111113,CC,,Group Meeting,
qPCR_validation_update.Nov14.xlsx,20111118,AAN,Annotation,qPCR validation for iPSC project,1
11-11-16.pptx,20111122,YF,nets,coevolution between proteins,10
twitter11_20_11.pptx,20111122,RR,Nets,Twitter network,8
11-11-16.pdf,20111122,YF,nets,coevolution of proteins,10
20111130_VAT.pdf,20111130,LH,anno,VAT,5
nov30_2011_gencodestats_phase1_subgrp.ppt,20111130,SB,Annotation,Nov.30 subgrp ,7
Presentation1.pptx,20111201,RKA,Tech,Pol II Update,11
FutureMachines2011.pdf,20111201,RM,JC,Future Machine Learning,1
BP_2011_11_30.pdf,20111201,BP,Annotation,Pseudogene diversity and divergence,5
Pgene_Figures_1126.pdf,20111201,BP,Annotation,Pgene companion figures,23
LastENCODEnets.pptx,20111207,RM,Encode-nets,ncRNA,1
GroupMeetingDec2011.pptx,20111208,RM,GroupMeeting,ENCODE-nets ncRNA & gene-level co-association,34
JournalClub8Dec2011.pdf,20111208,CSDS,JournalClub,Journal Club 8 Dec 2011 ,16
20111208_VAT_figure.pdf,20111208,LH,Anno,VAT,1
FIguresU54.pptx,20111208,csds,u54,FiguresU54,
JC_MLTalkDec2011.pdf,20111213,RM,JournalClub,Advancement in Machine Learning,63
MinGroupMeetingDec2011.pdf,20111213,RM,Group Meeting,Deciphering function and regulation of coding genes and ncRNAs,35
for-analysis-call-20Dec2011.pptx,20111214,EK,annot/assem,preliminary version of slides for Analysis call,7
GTcall12_16_11.pptx,20111214,RR,,GT call slides,4
Dispersed_duplications.pptx,20111220,AAN,Annotation,Things to do for iPS project,5
MSKCC_December2011.pptx,20111220,AAN,Group meeting,Group meeting (job talk),53
Dispersed_duplications.pptx,20111220,,Annotation,,
DC_Jclub_Dec21.ppt,20111221,DC,Jclub,Journal Club: DC (12/21/2011),17
RK_GPMTG_Dec11.pdf,20111222,RK,Group Meeting,,49
CopyofApproach.doc,20120104,MG,Annotation,Grant with Church,10
Phase1_by_mechanism_and_aligner.xlsx,20120104,AAN,Annotation,Phase1 SVs by mechanism,3
flexScaleWSize.ppt,20120104,DC,Nets/Struct,degs. freedom scaled w/macromolecular size,5
flexScaleWSize_ii.ppt,20120110,DC,Nets/Struct,MMDB_intrinsFlex,4
figures.ppt,20120110,DC,Nets/Struct,rev figs,2
JC_Jan162012_XJM.pdf,20120116,,JC,,
120118-annot-ensemble_reg_build.pptx,20120118,JC,Annotation,Ensembl Regulatory Build,14
120118-annot-ensemble_reg_build.pptx,20120118,JC,Annotation,Ensembl Regulatory Build,17
AnnotRegulatorySeg18Jan2012.pptx,20120118,CSDS,Annotation,ENSEMBL Regulatory Segmentation,5
120118-annot-ensemble_reg_build.pptx,20120118,JC,Annotation,Ensembl Regulatory Build,16
120118-annot-ensemble_reg_build.pptx,20120118,JC,Annotation,Ensembl Regulatory Build,16
LL_nets_2012-01-17.pdf,20120123,LL,Nets,Subnetworks of Disrupted Genes in Cancer: A Preliminary Investigation,9
Ensembl_regulatory_build.pptx,20120124,YF,annotation,Ensembl regulatory build,9
Thurmanetal_23Jan2012.pdf,20120124,EK,Annotation,Summary of Thurman et al,
gerstein.nets.012312.pptx,20120124,DR,Nets,1.24.2012 arabidopsis networks,8
gerstein.nets.012312.pptx,20120124,DR,Nets,arabidopsis networks,8
12_23_11.pdf,20120124,PA,nets,Rubin,5
netsnp.24Jan2012.pdf,20120124,EK,Nets,netsnp,
JobTalk.pptx,20120124,KKY,JC,talk,
GO_enrichment.pptx,20120201,AAN,Annotation,Pseudogenes and cell cycle,9
gerstein.nets.020212.pptx,20120202,DR,Nets,arabidopsis network evolution,9
nets2_2_12.pdf,20120202,RR,Nets,Twitter Hmm,10
ChaoCheng_GTA.pptx,20120202,CC,Nets,,
ChaoCheng_GTA.pptx,20120203,CC,Nets,,
ChaoCheng_GTA.pptx,20120203,CC,Nets,,
20120123_DZC_gpmtg_Cloud_Computing.pptx,20120206,DZC,gpmtg,DZC Group Meeting 1/23/2012,23
GrpPrs_fb6_v8.ppt,20120206,DC,GrpMtg,GrpMtg,35
LL_protected_cancer_data_2012-02-07.pdf,20120207,LL,Tech,Gerstein Lab Protected Data Protocol and Summary of Protected Cancer Data,20
ortholog_triplets_mk_inp_and_prelim_WGCNA_02072012.pptx,20120207,DW,genome tech,ortholog triplets btw worm, fly and human from kellis and inparanoid, and some WGCNA analysis,5
2012-2-6.pptx,20120207,YF,Net,Cell Cycle regulated genes prediction,15
2012-2-6.pptx,20120207,YF,Nets,Cell Cycle regulated genes prediction,16
Phase1_map_to_breakpoints.initial.pptx,20120208,AAN,Annotation,Mapping reads to breakpoints in phase1,18
2012-2-6.pptx,20120208,YF,Nets,Cell Cycle regulated genes prediction,17
wordcount.xlsx,20120208,GZ,encode-nets,encode nets count,1
120202_GersteinLab+reganlab_group_meeting.pptx,20120209,JC,Group Meeting,ncVarII_23andMe_TPR_Mboo,43
ENCODE_rev_final.pdf,20120215,GZ,NETS/STRUCTURE,encode nets review summary,6
ENCODEnet_update_Feb20.pptx,20120220,KKY,encodenet,,15
Figure6B.AlleleSeq.variation.selection.Feb202012.pdf,20120220,,,,
Figure6B.AlleleSeq.variation.selection.Feb202012.v2.pdf,20120220,,,,
JR_Proposal_PG_Figure.docx,20120220,JR,ENCODE,,1
allele_fig.JPG,20120220,DC,Encode Nets,allele fig from whiteboard,1
JC_Feb_21_2012.pdf,20120221,DW,Journal Club,JC Feb 21 2012,
nets.02212012.pptx,20120221,DR,Nets,Plant Networks,17
encode-nets-revision_RA_2012-02-21.pdf,20120221,RA,encode-nets,I vs O plots; TF class stacked bar chart,3
netsnps-signalink.pptx,20120221,JC,Nets,NetSNPs-signalling,9
Pol2Tool02222012.ppt,20120221,RKA,TECH,Pol2 Discussion,1
2012-2-21.pptx,20120221,YF,Nets,Singlish Vs. Multiple hubs,5
netsFeb23.pdf,20120222,gf3,nets,Scott's biofuel genomes assembly,4
ortholog_prelim_WGCNA_net_analysis_02222012.pptx,20120222,DW,Tech,module comparison between worm and fly,
Figures-20Feb2012.pdf,20120222,EK,nets,,
new-supp-figs.pptx,20120229,EK,nets,reviewer responses for encodenets,2
New.Table.pdf,20120229,,,,
miRNA.eps,20120229,KKY,Nets,,
KKY_robust2.pptx,20120229,KKY,Nets,,2
JR_Network_Comparison.pdf,20120229,JR,,,1
Towards_gold_breakpoints.phase1.pptx,20120229,AAN,Annotation,Toward the gold set of breakpoints in phase1,10
Chao_response.docx,20120229,CC,Nets,,
FigS1D_new.xlsx,20120229,CC,Nets,Updated siRNA KO table .xls,
net_rev_sd.xlsx,20120229,CC,Nets,New Table- TF standard deviation,
New.Table.pdf,20120229,,,,
2012-2-6.pptx,20120301,YF,GM,Group Meeting,44
XGen.Xinmeng.Mu.Mar6.2012.v5.pptx.pdf,20120301,,,,
AlleleSeq.peak.Mar012012.pptx,20120301,,,,
LL_nets_presentation_2012-03-01.pdf,20120301,LL,Nets,Cancer Networks: miRNA-Disease Associations,13
JC_1_diabetes.pdf,20120302,GZ,group meeting,J club,33
120301-SignalSNPs.pptx,20120302,JC,Nets,signalSNPs,10
encodeNets_on_the_web.jpg,20120306,DC,Encode_Nets,Outline for exporting ENCODE-Nets data to the web,1
Network_Comparison.docx,20120306,JR,,,1
Network_Comparison.docx,20120306,JR,,,
new-supp-figs.6Mar2012.pptx,20120306,EK,Encodenets,reviewer responses for encodenets,6
Encode-nets_fig4BC_REV2.pdf,20120306,,Nets,Figure 4B,
Figure5_rev.pptx,20120306,KKY,encodenet,,1
Condition_Network_-_3.6.2012.pptx,20120307,YF,Annotation,condition-specific network,3
Mar5_dyn_net_StatPot.pptx,20120307,DC,Nets/Struct,Pairwise Potentials,4
ortholog_prelim_analysis_03092012.pptx,20120307,dw,ENCODE,,
2012_03_14.pdf,20120314,BP,Annotation,Pseudogene conservation,3
2012_03_14.pdf,20120314,BP,Annotation,Pseudogene conservation,3
20120314_VAT_reviews.pdf,20120314,lh,anno,VAT reviews,3
Condition_Network_-_3.6.2012.pptx,20120314,YF,Anno,condition specific network,3
DAF.ALL_NCRNA.FOR_ANNOTATION.13Mar2012.pdf,20120314,EK,annot/assem,FIG- DAF spectrum,1
JianrongWang_presentation_March2012.pdf,20120314,RK,JobTalk,JobTalk_JianrongWang,89
Nets3_15_12.pptx,20120315,RR,Nets,DIffusing Tweet ,12
Two_examples_details_of_1-to-1_orthologs_between_worm,_fly_and_human.pdf,20120319,DW,Tech,Two examples details of 1-to-1 orthologs between worm, fly and human,
KKY_GM_Mar2012.pptx,20120320,KKY,GM,,30
Table.21Mar2012.xlsx,20120321,EK,Encodenets,table with O, I, O+I,1
JC_March26.2012.pptx,20120326,AAN,JC,Paper about chromothripsis,30
SAV_properties.pptx,20120326,AAN,Annotation,Properties of SAV validation,13
Selection_pressure_is_on_gene_network,_not_on_singleton_protein_outline_Mar_27_2012.pdf,20120327,DW,Genome Tech,Outline: Selection pressure is on gene network, not on singleton protein,
Selection_pressure_is_on_network,_not_on_singleton_protein_04032012.pdf,20120403,DW,gpmtp,Selection pressure is on network, not on singleton protein,30
120409-annot-Condition-specificity_and_Allele-specificity.pptx,20120410,JC,Annotation,Allele-specific and condition-specific,7
LL_gpmtg_2012-04-10.pdf,20120410,LL,gpmtg,Subnetworks of Disrupted Genes in Cancer,30
120409-annot-Condition-specificity_and_Allele-specificity.pptx,20120410,JC,Annotation,Allele-specific and condition-specific,6
KKY_Noise_vs_Nets_Apr2012.pdf,20120411,KKY,Nets,Noise vs metabolic network,12
Human_co-expression_network_analysis_for_strong_1-1-1_orthologs.pdf,20120417,DW,Tech,Human co-expression network analysis for strong 1-1-1 orthologs,2
Apr172012.GoupMeeting.pptx,20120417,,,,
Apr172012.GoupMeeting.pptx,20120417,,,,
modEncode_miRNA_Comparison.pptx,20120417,AH,Tech,modEncode miRNAs preliminary comparison,2
Pgene_genotyping_by_junctions.pptx,20120417,AAN,Annotation,Genotyping PPGs by splice-junctions,4
netsnp.16April2012.pdf,20120418,EK,nets,netsnp,20
GZ_junctions.pptx,20120424,GZ,annotation,deletion_junction_seq,15
mark_1stSlide.pptx,20120424,JC,slides,beginning slide,3
Global_co-expression_network_analysis_for_orthologs,_species-specific_genes_and_small_RNAs_in_modENCODE.pdf,20120424,dw,tech,Global co-expression network analysis for orthologs, species-specific genes and small RNAs in modENCODE,6
Potts_couple.pdf,20120424,KKY,Nets,modules in co-expression nets,10
TIP_ChaoCheng.pptx,20120424,,Nets,slides on TIP,3
Talk_med_school.pptx,20120425,KKY,GM,for SB,
Fig4d.pdf,20120425,BP,Annotation,Sequence identity to parents,1
Fig4d.pdf,20120425,BP,Annotation,Sequence identity to parents,1
pnps.13May.pptx,20120514,EK,Encodenets,pn/ps calcn,3
pnps.13May.pptx,20120514,EK,Encodenets,pn/ps caln,3
pnps.13May.pptx,20120514,EK,Encodenets,pn/ps calcn,4
Global_co-expression_network_analysis_for_orthologs,_species-specific_genes_and_small_RNAs_in_modENCODE_May_14_2012.pdf,20120514,DW,Genome tech,global co-expression network and clustering,8
human_Boston_Data_carriedavis.pdf,20120514,RA,tech,human dataset slides from Carrie Davis,7
fly_tars_presentation.pptx,20120514,AH,Tech,Fly TARs,7
MGed--ENCODEnets_maintext_final_0514.Eked.doc,20120515,EK,Encode nets,edited main text,
MGed--ENCODEnets_supptext_final_0514-1.EKed.doc,20120515,EK,Encode nets,edited supp text,
MGed--ENCODEnets_maintext_final_0514.XJMed.doc,20120516,,,,
MGed--ENCODEnets_supptext_final_0514.XJMed.doc,20120516,,,,
may16_evoFlex.ppt,20120516,DC,Nets/Struct,EvoFlex,4
KKY_nets_May2012.pptx,20120516,KKY,nets,modules, and R_net,10
TR_PH_integration.pptx,20120612,KKY,Nets,TR+PH,4
pos-sel.EK.pptx,20120612,EK,nets,,4
contMapSeqVar.ppt,20120613,DC,Annot,Contact Maps for Morphs,4
Figures.pdf,20120618,BP,Annotation,Pgene figures,12
LL_cancer_subnets_2012-06-18.pdf,20120618,LL,Annote,Disrupted PPI Subnetworks in Cancer: Analysis of Prostate Cancer Subtype Expression Data and TCGA Cancer Mutation Data,10
tech.pdf,20120619,,,,
ncrna_clustering_20120619.pdf,20120619,dw,tech,clustering ncrnas and genes,1
Worm-Fly_Small_RNA-seq.pptx,20120619,AH,GT,modencode ncRNAs,5.23
BP_GM_20120619.pdf,20120619,BP,Group Meeting,Gencode pseudogene resource,26
tech.pdf,20120620,,,,
FAQ_guidlines.pdf,20120622,GZ,group meeting,FAQ posting guidlines,1
faq_JC.pptx,20120627,Gili,JC,FAQ_JC,7
CAPE-Tech06282012.ppt,20120628,RKA,TECH,CAPE Test Data Overview,8
modENCODE_Small_RNA-Seq_data_Processing.pptx,20120702,AH,GM,Group Meeting presentation,20
6-28-2012.pptx,20120703,YF,Anno,DHS & SNPs,7
LL_cancer_subnets_2012-06-18.pdf,20120704,LL,Annote,Summary of TCGA Cancer Mutation Metadata & Intersection of TCGA Cancer Variants with 1KG Variants,8
master_tcga_sample_spreadsheet.xlsx,20120710,LL,,Master TCGA sample spreadsheet,1
120710-annot-1KGphase1_allelicSNPs.pptx,20120710,JC,Annotation,FIG-allelicSNPs ,5
120710-annot-1KGphase1_allelicSNPs.pptx,20120710,JC,Annotation,FIG-allelicSNPs ,5
embStudy.ppt,20120710,RKA,TECH,Draft Slides for Txn Call,10
Fly-Human-Worm_TARs.pptx,20120711,AH,Tech,,6
xSpecies_miRNAplan_RK.pdf,20120711,RK,TECH,xSpecies_miRNA,25
modENCODE_joint_AWG_txn_2012-07-13.pdf,20120711,RA,tech,draft slide pack for Friday modENCODE txn call,33
official_maf_vital_stats.txt,20120711,LL,,A comprehensive summary of our TCGA cancer metadata,1
official_maf_vital_stats.txt,20120711,LL,,A comprehensive summary of our TCGA cancer metadata,1
modENCODE_joint_AWG_txn_2012-07-13.pdf,20120712,RA,tech,,
nature11245_proof1.pdf,20120717,DC,ENCODE-Nets,Proofs,20
embUpdate07172012.ppt,20120717,RKA,Tech,emb Analysis Update,5
july.17.hfw_tars.pptx,20120717,AH,Tech,,2
modencode_network_analysis_20120717.pdf,20120717,DW,Tech,Network analysis of modENCODE gene co-expression networks,12
PseudogeneHumanWormFly-CSDS-RolOn201217July.pptx,20120717,CSDS,Tech,Worm Fly Pgene,4
july.17.hfw_tars.pptx,20120717,AH,Tech,,3
july.17.hfw_tars.pptx,20120717,AH,Tech,,4
modencode_network_analysis_20120717.pdf,20120717,DW,Tech,Network analysis of modENCODE gene co-expression networks ,12
GP0717MG.pptx,20120717,gf3,,group meeting ,25
mm_vital_stats.txt,20120719,LL,,Summary of dbGaP multiple myeloma variant data,1
mm_vital_stats.txt,20120719,LL,,Summary of dbGaP multiple myeloma variant data,1
embSchematic.ppt,20120724,RKA,Tech,Draft Figure,1
modencode_short-TARs.pptx,20120724,AH,Tech,short-TARs,3
JC_7-22.pptx,20120724,YF,GM,miRNA and its impact on mRNA expression variability,24
120724-annot-1KGphase1_allelicSNPs_2.pptx,20120724,JC,Annotation,allelicSNPs,4
LL_tcga_mm_vs_1kg_intersection_2012-07-23.pdf,20120724,LL,Annote,TCGA and MM exome variants vs. 1KG coding variants,11
july24_swedish.ppt,20120724,SB,Annotation,Swedish exome stats,1
7-16-2012.pptx,20120724,YF,Annotation,cell line specific DHS sites,4
20120724.FIG.CellLineSpec.partII.pptx,20120724,,,,
120724-annot-1KGphase1_allelicSNPs_2.pptx,20120724,JC,Annotation,allelicSNPs,4
20120724.FIG.CellLineSpec.partII.pptx,20120724,,,,
FIG_pic.jpg,20120724,DC,Annotation,FIG pic from whiteboard,1
embUpdate08012012.ppt,20120801,RKA,Tech,Update of emb figure,1
FIG-7-30-2012.pptx,20120801,YF,Annotation,DHSs,3
LL_cancer_variants_and_tcga_report.pdf,20120801,LL,Annote,Cancer Variant Intersections with 1KG Coding Variants and TCGA Dataset Report,8
aug1_subgrp.ppt,20120801,SB,Annotation,Swedish exome stats,3
august.1.wfh_tar_update.pptx,20120801,AH,Tech,Modencode TAR classifications,5
aug1_subgrp.ppt,20120801,SB,Annotation,Swedish exome stats,3
networks.EK.31Jul2012.pdf,20120801,EK,annot,FIG networks call,6
LL_prostate_variant_mapping.pdf,20120807,LL,Annotation,Cancer Variant Mapping, Cancer Driver Selection,5
2012_08_07.pdf,20120808,BP,Annotation,Pseudogenes v7 and v10,4
modEncode-GroupMeeting8AUG2012.pdf,20120808,CSDS,GPMTG,Group meeting - modEncode 8th Aug 2012,25
xSpecies_miRNAs.pdf,20120814,RK,Tech,miRNAs,6
LL_cancer_variants_int_1kg_coding_variants.pdf,20120814,LL,Annotation,Cancer Exome Variant Intersections with 1KG Coding Variants,10
ALL.merged_5_crossmatch_stringent_bps.20101123.svs.low_coverage.sites.breakpoint.uniq.sim.GA.all.stat.table.xlsx,20120814,,,,
ALL.merged_5_crossmatch_stringent_bps.20101123.svs.low_coverage.sites.breakpoint.uniq.sim.GA.all.stat.table.xlsx,20120814,,,,
ALL.merged_5_crossmatch_stringent_bps.20101123.svs.low_coverage.sites.breakpoint.uniq.sim.GA.all.stat.table.xlsx,20120814,,,,
LL_addendum.pdf,20120814,LL,Annotation,Extra slides,1
for-fig.14Aug2012.pptx,20120814,EK,Annot,FIG,3
CSHL_poster.pptx,20120822,BP,Annotation,Poster for cold spring harbor non-coding RNA meeting,1
CSHL_poster.pptx,20120822,BP,Annotation,Poster for cold spring harbor non-coding RNA meeting,1
orthologous_ncRNAs_20120823.pdf,20120823,DW,tech,Identification of “orthologous” ncRNAs,15
FIguresPGeneModENcodeAUG2012v04.pdf,20120823,CSDS,GeneTech,Figure for Transcription Paper,1
August.24.modencode_tx_update.pptx,20120823,AH,Tech,modencode tx,10
MG_gpmtg_RA_2012-08-23.pdf,20120823,RA,gpmtg,mod/ENCODE comparative transcriptome project -- biological background on worm, fly, and human,71
JournalClub.CancerDriverMutation.Aug292012.pptx,20120829,,,,
LL_cancer_vs_population_variation_2012-09-06.ppt,20120906,LL,Annotation,Melanoma driver/passenger intersection analysis with 1KG,8
9-4.pptx,20120906,YF,Annotation,negative selection on non-coding region,9
RK_GPMTG_07-09-2012.pdf,20120907,RK,GPMTG,Group meeting PDF,45
RK_GPMTG_07-09-2012.mov,20120907,RK,GPMTG,Group meeting- video for rotating brain etc,45
Jclub.ppt,20120910,DC,JC,Jclub - sept 10,18
120911-annot-eQTL.pptx,20120911,JC,Annotation,eQTL,4
SV.mode.enrichment.pdf,20120911,,,,
120911-annot-eQTL.pptx,20120911,JC,Annotation,eQTL,4
120911-annot-eQTL.pptx,20120911,JC,Annotation,eQTL,4
120911-annot-eQTL.pptx,20120911,JC,Annotation,eQTL,4
120911-annot-eQTL.pptx,20120911,JC,Annotation,eQTL,4
120911-annot-eQTL.pptx,20120911,JC,Annotation,eQTL,4
120911-annot-eQTL.pptx,20120911,JC,Annotation,eQTL,4
120911-annot-eQTL.pptx,20120911,JC,Annotation,eQTL,4
LL_cancer_variant_intersections_2012-09-19.pdf,20120918,LL,Annotation,Cancer Variant Intersection Analysis: Additional Datasets,8
GroupMeeting_09.18.2012.pptx,20120919,AAN,Group meeting,Slides for group meeting ,46
120919-eQTL_II.pptx,20120919,JC,Annotation,eQTL,4
120919-eQTL_II.pptx,20120919,JC,Annotation,eQTL,4
call_comparison.pptx,20120926,AAN,Annotation,Retroduplication call comparison,10
LL_pres_2012-09-27.pptx,20120927,LL,Annotation,Cancer micro-presentation,3
KKY_Tech_Potts.pptx,20120928,KKY,tech,,9
FIguresPGeneModENcodeSept2012v03.pptx,20120928,CSDS,GTech,Updated - PGene modEncode,1
orthologous_ncRNAs_20120928.pdf,20120928,dw,tech,clustering ncrna,1
tech.key,20120928,,,,
LL_more_cancer_stuff_2012-10-02.pdf,20121002,LL,Annotation,Cancer variant overlap work figure mockup stuff,4
orthologous_ncRNAs_20121003.pdf,20121003,dw,tech,orthologous ncrnas,1
mir150_ENCODEtracks_big.png,20121003,RA,tech,exRNA ENCODE mir-150 example ,1
KKY_Tech_Potts.pptx,20121010,KKY,tech,,6
KKY_Tech_Potts.pptx,20121010,KKY,tech,,6
MG_jclub_RA_2012-10-10.pdf,20121010,RA,Jclub,Stam DNase papers,30
MG_jclub_RA_2012-10-10.pdf,20121010,,,,
JC-Oct2012-Exosomes.pdf,20121010,CSDS,JournalClub,Exosome & exRNA,27
RSEQtools.jpeg,20121010,CSDS,exRNA-grant,RSEQtools-figure,1
exRNA_grant.pdf,20121012,,,,
TAR_Update.pdf,20121015,AH,Tech,,3
CeleDmelHsap_hoxclusters.pdf,20121015,RA,tech,Cele Dmel Hsap Hox clusters,1
Fig1-D-galas-Pipeline.png,20121015,CSDS,GeneTech,Figure 1. Initial pipeline for mapping exogenous RNA in plasma.,1
PrelimRes-PipelineDGalas.png,20121015,CSDS,GeneTech,Figure 2.  Mapped reads to microbial genera, using initial pipeline.,1
exRNA_Galas_figure.pdf,20121015,RA,tech,Galas figure for exRNA grant proposal,1
modENCODE_txncomp_19Oct2012.pptx,20121017,JR,gtech,,
LL_latest_variant_work_2012-10-17.pptx,20121017,LL,Annotation,Latest cancer variant work,2
mirna_update.pptx,20121017,AH,Annotation,,5
mir150_figure_pagefit_upperleft_2.pdf,20121022,RA,tech,mir150 figure for exRNA grant; ~1/4 page,1
mir150_figure_pagefit_upperleft.pdf,20121022,RA,tech,mir150 figure for exRNA grant;  exactly 1/4 page (text too small?),1
exRNA_clustering_network_figure_from_encodenet.ppt,20121024,DW,exRNA,sample figure for clustering&network in exRNA grant,1
exRNA-Pipelinev02.pptx,20121024,CSDS,exRNA-grant,Figure1-pipeline,1
exRNA-Pipelinev02.pdf,20121024,CSDS2,exRNA-grant,Figure1-pipeline-pdf,1
FigurePage-exRNA2012.pdf,20121024,CSDS,exRNA-grant,FigurePage,1
dmel_shortRNA_mir10.png,20121025,RA,tech,IGV view of Dmel mir10 locus in many short RNA-seq datasets,1
dmel_shortRNA_novel_miRNA.png,20121025,RA,tech,IGV view of novel miRNA in Dmel near mir100 in many short RNA-seq datasets,1
Oct.25.TAR_IDR.pptx,20121025,AH,Tech,6,6
GATK_on_NA12878.pptx,20121025,AAN,Annotation,GATK,3
LL_cancer_variants_pN_2012-10-25.pptx,20121025,LL,Annotation,Cancer variants: Part N,7
FigurePage-exRNA2012-v02withSpaceforGanttChart.pdf,20121027,CSDS,exRNA-grant,Total Figure with space for Gantt chart as well.,1
FigurePage-exRNA2012-v03.pdf,20121027,CSDS,exRNA-grant,Figure with Gantt chart,1
exRNA_Gantt.pdf,20121027,BP,,exRNA gantt chart,1
FigurePage-exRNA2012-v04.pdf,20121027,CSDS,exRNAgrant,Figure page with Gantt Chart,1
FIG_contribution_by_gersteinlab.pptx,20121031,AAN,Annotation,Draft of slides for FIG premeeting in San Francisco,4
SV_contribution_by_gersteinlab.pptx,20121031,AAN,Annotation,Draft slides for SV premeeting in San Francisco,10
FigurePage-exRNA2012-v06.pdf,20121031,CSDS,exRNA-grant,Figure page with Captions,1
LL_noncoding_elements_pres_2012-10-29.pptx,20121101,LL,Annotation,Patterns of noncoding cancer variation,13
FigurePage-exRNA2012-v06.pdf,20121103,CSDS,exRNA-grant,Figure page with Captions FINAL,1
Kbase.pdf,20121105,gf3,P1,kbase brief,2
Command_line_scripts_for_gene_co-expression_networks_and_clustering_(Gerstein_Lab_in_Yale).pdf,20121105,dw,network,kbase network clustering,5
LL_sample_frequency_cancer_data_2012-11-05.pptx,20121105,LL,Annotation,Sample Frequency of Mutated Genes and TFBSes in WGS Cancer Datasets,9
Yan_GM_Nov2012.pptx,20121106,KKY,group meeting,,28
presentation_11-9_3.pptx,20121106,KKY,Tech,Steven Braun rotation,20
v2-cshl-pergen-2012-lof.ppt,20121113,SB,Annotation,Personal genomes talk,15
FIG_hivePlots.ppt,20121113,DC,Annot,hivePlots,5
FIG_hivePlots.ppt,20121113,DC,Annot,FIG hive graphs,5
PersonalGenomes_2012.abyzov.pptx,20121113,AAN,Annotation,Draft slides for Personal Genomes meeting,17
LL_cancer_driver_genes_2012-11-13.pptx,20121113,LL,Annotation,Putative cancer driver genes,4
ncRNA_table_update.Nov.14.pptx,20121114,AH,Tech,ncrna update,2
LL_JC_2012-11-14.pptx,20121114,LL,JC,Towards the Development of a “Cancerpedia”: Cataloguing Useful Drug-Gene Interactions in Cancer Tissue,18
RNAradialPlot.pptx,20121114,CSDS,GeneTech,RNA radial plot,1
TAR_update_exon_rpkms_Nov.19.pptx,20121119,AH,tech,presentation,2
11-19-2012.pptx,20121119,YF,Annotation,Sensitive region Vs. HGMD,2
Cancer.motif.Nov19.2012.pptx,20121119,,,,
Cancer.motif.Nov19.2012.pptx,20121119,,,,
Cancer.motif.Oct18.2012.pptx,20121119,,,,
Figure_1_mockup_v4.pptx,20121127,BP,Tech,Transcriptome paper Figure 1 mockup,1
tar_update_Nov.28.2012.pptx,20121128,ah,tech,,1
FigurePack_modENCODE_txncomp_30Nov2012.pdf,20121128,JR,tech,latest cmptxn figure pack,23
LL_pol2_reg_genes_breast_cancer_2012-11-28.pptx,20121128,LL,Annotation,Multiply mutated annotations in breast cancer,3
TxnSuppFigures20121211.pptx,20121211,YZ,,TxnSuppFigs20121211,18
TxnSuppTables20121211.docx,20121211,YZ,,TxnSuppTables20121211,2
Human_RNAseq_datasets_for_modencode.xls,20121211,YZ,,HumanDataset,1
mod%2FENCODE_trancription_datasets.xlsx,20121211,YZ,,WormDataset,1
RotationTalk-HeZhu_RA.pptx,20121217,He,tech,Rotation Talk,24
modENCODE_txn_clustering_201201217.pdf,20121217,dw,tech,txn clustering figure 7 dec172012,2
Figure1_Version2.pdf,20121217,EK,Annot,current figure1-17Dec2012,1
figure2.pdf,20121217,EK,Annot,current figure2-17Dec2012,1
figue4.low-res-network.pdf,20121217,EK,Annot,current figure4-17Dec2012,1
FIG-companion.supplement.EK.17Dec2012.pdf,20121217,EK,Annot,current supplement-17Dec2012,28
figure5.pdf,20121217,EK,Annot,current figure5-17Dec2012,1
figure5.pdf,20121217,EK,Annot,current figure5-17Dec2012-new,1
figure3.pdf,20121217,EK,Annot,current Figure3-17Dec2012,1
figure5.18Dec2012.pdf,20121218,EK,Annot,update Figure 5,1
figure5.18Dec2012.pdf,20121218,EK,Annot,updated Figure 5,1
Figure2.pdf,20121218,YF,Anno,update Figure1 (now Figure2),1
Figure1.pdf,20121218,YF,Annotation,updated Figure 1 (current Figure 1),1
fly_consortium_productionGerstein.xls,20121221,YZ,,FlyDataset,1
MG-edit--FigurePgene20Decv03.pdf,20130103,CSDS,Cmp Tnx,Figure Pgene 30Dec2012.pdf,1
MG-edit--FigurePgene30Decv02.pptx,20130103,CSDS,Cmp Tnx,Figure Pgene 30Dec2012.pptx,1
MG-edit--FigurePgene30Decv02.pdf,20130103,CSDS,Cmp Tnx,Figure Pgene 30Dec2012.pdf,1
MG-edit--FigurePgene30Decv02.pdf,20130103,CSDS,Cmp Txn,Figure Pgene 30Dec2012.pdf,1
MG-edit--FigurePgene30Decv02.pptx,20130103,CSDS,Cmp Txn,Figure Pgene 30Dec2012 .pptx,1
modENCODE_txn_clustering_20130108.pptx,20130110,dw,tech,modencode clustering figure,
20130110.pptx,20130110,BP,Genome Tech,Pseudogene transcription,7
modENCODE_txn_clustering_20130108.pptx,20130110,dw,tech,modencode clustering figure,
20130110.pptx,20130110,BP,Genome Tech,Pseudogene transcription,13
modENCODE_txn_clustering_20130115.pptx,20130115,dw,tech,modencode clustering figure,10
uniquely_mapped_tars.pptx,20130115,ah,tech,,1
modENCODE_txn_clustering_20130115.pptx,20130115,dw,tech,modencode clustering figure,10
uniquely_mapped_tars.pptx,20130115,AH,Tech,,2
Exhibit2_radar_CSDS.pdf,20130115,CSDS,tech,radar plots of cmptxn exhibit 2,1
modENCODE_txn_clustering_20130115.pptx,20130115,dw,tech,modencode clustering figure,10
modENCODE_txn_clustering_20130115.pptx,20130115,dw,tech,modencode clustering figure,10
modENCODE_txn_clustering_20130115.pptx,20130115,dw,tech,modencode clustering figure,10
MODENCODEncRNAanalysis.pdf,20130115,RK,Tech,,4
Cluster-Human-Fly-HenryZheng.pdf,20130115,KKY,GeneTech,Henry - Clustering GO- Human-Worm,3
heat_map_ortho.png,20130115,KKY,Tech,,
20130115.pptx,20130115,BP,Annotation,Pseudogene transcription,13
modENCODE_txn_clustering_20130121.pptx,20130121,dw,tech,modencode clustering figure,
txncmp_ncRNA_21Jan.pptx,20130121,JR,tech,,
txncmp_ncRNA_21Jan.pptx,20130121,JR,tech,,
modencode_ncrnas.pptx,20130121,AH,tech,,2
cmptxn-exhibit2-2012-01-21.pptx,20130121,RA,tech,cmptxn exhibit 2,8
cmptxn-exhibit2-2012-01-21.pptx,20130121,,,,
modENCODE_nets.pptx,20130121,KKY,tech,,2
gunel-glioma-variants-mappings_2013-01-21_v2.pptx,20130121,LL,Annotation,Mapping Glioma Variants to Genome Feature Annotations,9
cmptxn_word_counts_2013-01-26.xlsx,20130126,RA,tech,cmptxn word counts,2
CmpTxnSupp20130129.docx,20130129,YZ,mtg-tech,CmpTxnSupp20130129,
modENCODE_txn_clustering_20130130.pptx,20130131,dw,tech,modenocde clustering figure for new modules,
txncmp_ncRNA_30Jan.pptx,20130131,,,,
Exhibit6_panelB_RKA_v2.pdf,20130131,JR,,,
Cmp_Txn_author.docx,20130131,JR,,,
KKY_Potts_clustering_update.pptx,20130131,KKY,tech,Potts model update,6
TARvsMS20130131_v2.pptx,20130131,YZ,mtg-tech,Tar vs Peptides identified by MSMS,7
AnnotationEvolution.pptx,20130131,CSDS,Gene-tech,Evolution of Annotation in in human, worm, fly,1
RPKM-Pseq-TARs-HWF-Jan2013.pptx,20130131,CSDS,Gene-tech,RPKM-TAR-PseudoSeq,1
MG-edit--FigurePgene31Jan13.pptx,20130131,CSDS,Gene-tech,PgeneFigure-CmpTxn,2
gunel-glioma-variants-mappings_2013-01-31.pptx,20130131,LL,Annotation,Mapping Glioma Variants to Genome Feature Annotations,18
20130129.pptx,20130131,BP,Tech,Tissue specificity of pgenes,5
20130129.pptx,20130131,BP,Tech,Tissue specificity of pgenes,5
Corelation-Results-Worm.pptx,20130131,CSDS,Pgene,Worm-Coexpression Correlation,
cancer_variants_vs_tfs_2013-02-05.pptx,20130206,LL,Annotation,Cancer Variants and TFBSes: A Mixed Bag,5
Retrodus_from_exome.1KG.pptx,20130206,AAN,Annotation,First look at retrodups from exome sequnecing,10
modENCODE_txn_clustering_20130206.pptx,20130206,dw,tech,modencode clustering figure,
tar_specs.zip,20130206,AH,Tech,,3
hwf_tar_exon_rpkms.pptx,20130206,AH,tech,,1
KKY_Tech_Feb6.pptx,20130206,KKY,tech,,7
AnnotationEvolution.pptx,20130206,CSDS,Gene-TECH,Protein Coding Gene Annotation Evolution,
JC_02.12.2013.pptx,20130211,AAN,all,Journal Club -- relation of APOBEC to clustered mutations in cancer,29
modENCODE_txn_clustering_20130208.pptx,20130212,dw,tech,modencode clustering figure,
Olfactory-Ribo-Age.pdf,20130212,CSDS,Gene-TECH,Olfactory vs Ribosomal Pseudogene,1
AnnotationEvolutionRv05.pdf,20130212,CSDS,Gene-TECH,AnnotationEvolution.pdf,1
cancer_variants_tfs_and_sliding_windows_2013-02-11.pptx,20130212,LL,Annotation,Cancers Variant Intersections with TFBSes, and Recurrently Mutated Regions,13
PgenePerChrom.pdf,20130219,CSDS,pgene-TECH-Annot,PseudogenesPerChrom,7
NewpgeneFigure-18Fen2013.pptx,20130219,CSDS,Gene-TECH,New Pgene Figure 18 Feb2013,2
modENCODE_txn_clustering_20130220.pptx,20130220,dw,tech,mod clustering figure,
FigurePack_modENCODE_cmptxn_20130222.pdf,20130220,,,,
Tar&pgeneVsMS20130220.pptx,20130220,YZ,tech,Pgene&TARs vs MS peptides,
Figure.pptx,20130220,KKY,Tech,regulation figure,1
table_v1.xlsx,20130220,GF,Tech,Modencode_bigtable,4
table_v1.xlsx,20130220,GF,Tech,bigtable,4
LL_gpmtg_2013-02-11.pptx,20130220,LL,Group meeting,Cancer Variant Intersections,66
Figure.pptx,20130220,KKY,tech,,1
modENCODE_txn_clustering_20130306.pptx,20130306,dw,tech,modencode clustering figure,
FigurePack_modENCODE_cmptxn_20130308.pptx,20130306,,,,
Splicing_Figure_030413.pdf,20130306,JR,,,
FigurePack_modENCODE_cmptxn_20130301.pdf,20130306,JR,,,
modENCODE_txn_clustering_20130306.pptx,20130306,dw,tech,modencode clustering figure,
WormAllVsMS20130306_concise.pptx,20130306,YZ,mtg-tech,Worm all pgenes/TARs/ncRNA predictions vs MS peptides,6
WormAllVsMS20130306_concise.pptx,20130306,YZ,mtg-tech,Worm all pgenes/TARs/ncRNA predictions vs MS peptides,6
table_v2.xlsx,20130308,GF,tech,big table Version 2,4
COmparison.pdf,20130308,CSDS,,HWF comparison,
PgeneFigure-5March2013.pdf,20130308,CSDS,,PGeneOLD,
table_v3.xlsx,20130311,GF,tech,Big table version 3,4
cmptxn_TFHMexhibit_20130306_RA.pdf,20130312,RA,tech,cmptxn TFHM figure,1
cmptxn_ex8panelC_20130306.pdf,20130312,dw,tech,cmptxn_ex8panelC_20130306,
cmptxn_ex8panelC_boxes_20130306.pdf,20130312,dw,tech,cmptxn_ex8panelC_boxes_20130306,
cmptxn_ex8panelC_box_20130306.pdf,20130312,dw,tech,cmptxn_ex8panelC_box_20130306,
cmptxn_ex8panelC_shade_20130306.pdf,20130312,dw,tech,cmptxn_ex8panelC_shade_20130306,
TRG_&_BRG&SEC_&_RHW_edits_to_revies_nc_parts_3-10-13.doc,20130312,JR,,,
Worm_CompareUnique_20130312.pptx,20130312,YZ,mtg-tech,ncRNA-derived peptide unique?,
unique_ncRNAmatches_both05.xlsx,20130312,YZ,mtg-tech,3 unique TAR-derived peptides? ,
LL_prostate_variants_percent_increase_2013-03-12.pptx,20130312,LL,Annotation,Cancer Somatic Variant Percent Increase over Germline,6
Total_and_polyA_RNA_counts.pptx,20130320,AH,Tech,,1
Doolittle_ENCODE_critique_PNAS_AOP_2013-03-11.pdf,20130320,RA,tech,RA's highlights in Doolittle's PNAS ENCODE critique,
LL_glioma_variants_2013-03-20.pptx,20130320,LL,Annotation,New Glioma Variant Analyses,11
2pg-research-summary-1jan13.doc,20130324,,,Research Summary,
exRNA-Critique-Response.docx,20130325,CSDS,Gene-TECH,exRNA-critique-response,13
unique_ncRNAmatches_bothall.xlsx,20130326,YZ,mtg-tech,unique ncRNA in worm,1
unique_pgene-MS_matches.pptx,20130327,YZ,mtg-tech,unique pgenes having MS matches,2
LL_glioma_variant_findings_2013-03-27.pptx,20130327,LL,Annotation,Glioma Variant Findings,15
FigurePack_modENCODE_cmptxn_20130327.pdf,20130327,JR,,,
de_novo_SNPs_in_03.pptx,20130402,AAN,Annotation,De novo SNP predictions in 03 family,9
cmptxn_authorlist.docx,20130403,JR,,,
FigurePack_modENCODE_cmptxn_20130403.pdf,20130403,JR,,,
cmptxn_diff_8apr.docx,20130409,JR,,,
LL_recurrent_glioma_variants_2013-04-10.pptx,20130410,LL,Annotation,Recurrent Glioma Variants and Annotations,10
presentation.pdf,20130412,Emre Guney,Ally,Job talk,152
addition_to_cell_cycle.pptx,20130415,AAN,Annotation,Additional analysis of cell cycle and retroduplication relation,9
peakseq_2.2.pptx,20130416,ah,tech,,1
modENCODE_hourglass_companion.pptx,20130424,dw,tech,hourglass companion,
modENCODE_hourglass_companion.pptx,20130424,dw,tech,hourglass companion,
LL_larva_analyses_2013-04-24.pptx,20130424,LL,Annotation,Introducing LARVA: Large-Scale Analysis of Recurrent Variants and Annotations,10
hgmd.vs.phase1.pptx,20130424,YF,Annotation,FunSEQ,5
LL_2013-04-30.pptx,20130430,LL,Annotation,FIG stuff,2
LL_2013-05-01.pptx,20130501,LL,Annotation,Top 100 DAF Graph,1
cross-validation.pdf,20130501,YF,Anno,AUC graph,1
LL_2013-05-01_p2.pptx,20130501,LL,Annotation,Top 100 DAF Graph p2,1
repeats.xlsx,20130514,,,,
repeats.xlsx,20130514,,,,
LL_DAF_slides_2013-05-13.pdf,20130514,LL,Annotation,DAF sensitivity cutoff analysis,2
LL_FIG_slides_2013-05-14.pptx,20130514,LL,Annotation,LL FIG slides,5
modENCODE_Potts_clustering_Figures_05122013.pptx,20130515,KKY,tech,Potts model,10
plots.ppt,20130515,DC,Annot,Prcntg Genome Cutoffs,7
Figure2.May11.pdf,20130515,YF,,,
Figure2.May13.pdf,20130515,YF,,,
FunSeq_sample_variant_tables.xlsx,20130515,AH,Annotation,,2
FIG-companion_miscEdits.pdf,20130515,DC,Annot,Misc FIG paper corrections,24
BP_2013_05_15.pdf,20130515,BP,JClub,Extensive transcriptional heterogeneity revealed by isoform profiling,18
LL_FIG_slides_2013-05-14_(2).pptx,20130515,LL,Annotation,DAF cutoff analysis followup,2
LL_larva_analyses_2013-05-10.pptx,20130515,LL,Annotation,The latest recurrent variant analyses with LARVA,17
pgenes_by_chrom.pptx,20130522,AAN,Annotation,Distribution of p-genes by chromosomes,8
LL_grasso_exome_intersections_2013-05-22.pptx,20130522,LL,Annotation,Grasso cancer exome variant intersections with 1KG,3
Lupski_figs.pdf,20130522,AH,Annotation,,2
psychENCODe_overview.pptx,20130522,AAN,Annotation,psychENCODE figure schematics,1
Lupski_Figure_venn.pdf,20130522,AH,Annotation,Lupski Venn,1
Rozowsky_GPMTG_22May2013.pptx,20130523,JR,,,
ProteogenomicMappingNiche20130523.pptx,20130523,YZ,mtg-tech,Mapping MS - ENCODE,
AS.key,20130523,,,,
venter_venn.pdf,20130523,AH,Annotation,Venter genome Venn Diagram,1
DAC_overview_at_ENCODE_mtg--20130529-i0enc13-draft-CSDS.pptx,20130527,CSDS,DAC,,32
as13-YaleSeminar.pdf,20130605,SB,,AS13 postdoc candidate slides,100
JC_RK.pdf,20130605,RK,JC,Journal club on CLASH,30
SeekPeak_June_4.pptx,20130605,ah,tech,,6
BP_TG_2013_presentation.pdf,20130605,BP,Pgene,NLM traning grant meeting presentation,15
de_novo_SNP_validation.pptx,20130605,AAN,Annotation,Validation of de novo SNPs in trios with autism,17
LL_prostate_cancer_stuff_2013-06-11.pptx,20130612,LL,Annotation,New Cancer Datasets, Prostate Cancer LARVA Results,6
ProteogenomicMappingNiche20130613.pptx,20130613,YZ,mtg-tech,Proteogenomics - update,1
NIH-CEGS-MSKCC-AlleleSeqExtensions.docx,20130613,JR,,NIH-CEGS-MSKCC alleleseq extensions,1
Tech_Figures.pdf,20130613,KKY,tech,for Pottie,2
JJL_AS.pdf,20130613,,,,
RK_BSpanNorm.pdf,20130613,RK,Tech,BrainSpan_normalisation,9
BP_NLM_ITC_2013_presentation.pdf,20130613,BP,Pgene,Transcribed pseudogenes in human genome,16
2013_06_25.pdf,20130625,BP,Tech,Mouse pseudogene conservation,6
PseudogeneLocalization20130625.pdf,20130625,,mtg-tech,Pseudogene localization,
MiSeq_for_NA12878.pptx,20130626,AAN,Annotation,MiSeq data for NA12878,4
LLs_LARVA_prostate_cancer_results.pptx,20130626,LL,Annotation,LARVA Prostate Cancer Results: Deluxe Sample Size Edition,10
LLs_LARVA_prostate_cancer_results.pptx,20130626,LL,Annotation,LARVA Prostate Cancer Results: Deluxe Sample Size Edition,12
jun_26pftvo.ppt,20130626,DC,Annot,6_26_2013,3
AS.pdf,20130702,,,,
dup.pdf,20130710,,,,
PseudogeneLocalization20130710_sh.pptx.pdf,20130710,YZ,mtg-tech,pgene loc cross-species,
PGENE_10July.pdf,20130710,CSDS,pgene,,
SeekPeak_Benchmarks_July_10.pptx,20130711,ah,tech,SP,4
gtex-july11-SB-JClub.pptx,20130711,SB,JC,GTex,
AS.pdf,20130717,,,,
Mining_ENCODE_publications.pptx,20130717,dw,tech,encode lit.,5
ASPB2013_daifengwang_gersteinlab_v4.pptx,20130717,dw,tech,kbase aspb 2013,1
GP0718MG.pptx,20130718,GF,GP,Group meeting,20
PseudogeneLocalization20130716.pdf,20130718,YZ,mtg-tech,Pgene loc,
170717-allele-STAR_v_TopHat2.pptx,20130723,JC,Allele,,10
Pgene_20130724.pdf,20130724,BP,Pgene,Human pgenes orthologous to mouse genes,5
Pgene_20130724.pdf,20130724,BP,Pgene,Human pgenes orthologous to mouse genes,5
GenomeSeek.pptx,20130724,AH,Tech,,3
GenomeSeek.pptx,20130724,,Tech,,3
PseudogeneLocalization20130724.pdf,20130724,YZ,mtg-tech,pseudo loc,
PseudogeneLocalization20130724.pdf,20130724,YZ,mtg-tech,pseudo loc,
redund_mdls.ppt,20130725,DC,Annot,redn,5
kinases.ppt,20130725,DC,Annot,kin,5
SpliceCode.pdf,20130725,,,job talk - Splice Code,
JC_Sept2013.pdf,20130725,KKY,JC,,16
LL_cancer_recurrence_results_and_stats_2013-07-25.pptx,20130725,LL,Annotation,Cancer Mutation Recurrences and Calculating their Statistical Significance,14
SurvivalGuide.pptx,20130730,MF,Wheel,Short Term Survival Kit,18
title.pptx,20130730,KKY,Tech,,1
PseudogeneLocalization20130730_sh.pdf,20130730,YZ,mtg-tech,pseudo loc,
IMG_2464.MOV,20130730,RK,JC,Mihali server presentation (part 1),NA
LL_pathway_and_network_analysis_2013-07-31.pptx,20130731,LL,Annotation,Pathway and Protein Interaction Network Analysis with LARVA,10
jul_31_kns.ppt,20130731,DC,Annot,kn,3
title.pptx,20130731,KKY,tech,,1
GENCODE__GPMTG_Update_PGENE-07Aug2013.pptx,20130807,CSDS,GM,Group meeting pseudogenes,51
Letter_to_Magdalena.doc,20130814,JR,,,
Minutes_from_ModENCODE_PI_Call_on_August_14.doc,20130814,JR,,,
kn_cnt.ppt,20130815,DC,Annot,kn,3
Pgene_20130815.pdf,20130815,BP,Tech,Transcribed mouse pseudogenes,5
PseudogeneLocalization20130815_ToBeUpdated.pdf,20130815,YZ,mtg-tech,primates pseudogene loc,
tr_jclub_jul17_v.ppt,20130819,DC,jclub,jclub,1
PseudogeneLocalization20130820.pdf,20130820,YZ,mtg-tech,Pseudo loc primates,
kn22.pptx,20130821,dc,annot,kn,
DC-GPMTG-Aug2013_v2.pptx,20130821,dc,grpmtg,grpmtg,25
JournalClub-Aug2013.pdf,20130821,CSDS,Jclub,exRNA Journal Club,28
PseudogeneLocalization20130815_20130826.pdf,20130826,YZ,mtg-tech,Pseudo loc primates,
GENCODE__GPMTG_Update_PGENE-14Aug2013MEGA.pptx,20130826,CSDS,Pgene,Pgene  Mega Pack,
PseudogeneLocalization20130820_20130826.pdf,20130827,YZ,mtg-tech,Pseudo loc primates,
flktor12.pptx,20130827,dc,annot,en,9
en3.pptx,20130828,dc,annot,en,9
CNVnator_on_phase3.prelim.pptx,20130903,AAN,Annotation,Applying CNVnator to phase3 data,23
de_novo_SNP_validation_update.pptx,20130903,AAN,Annotation,Update on de novo SNP validation,21
modENCODE_txn_clustering_20130903_genometech.pptx,20130903,dw,tech,cmptxn clustering figure,3
Figure_1_mockup_20130903.pptx,20130903,BP,Tech,Figure 1 mockup,3
Archive.zip,20130903,,,,
Presentation_20130902.pptx,20130903,BP,Pgene,Mouse pgene orthologs,5
pgene_cancer_130902.pptx,20130903,MRS,pgenes,cancer_pgenes_090313,~10
pgene_cancer_130902.pptx,20130903,MRS,pgenes,cancer_pgenes_090313,~10
pgene_cancer_130902.pptx,20130903,MRS,pgene,cancer_pgenes_090313_MRS,10
pgene_cancer_130902.pptx,20130903,MRS,Tech(pgene),cancer_pgenes_090313_MRS,
pgene_cancer_130902.pptx,20130903,MRS,Tech(pgene),cancer_pgenes_090313_MRS,
pgene_cancer_130902.pptx,20130903,MRS,Tech(pgene),cancer_pgenes_090313_MRS,
PseudogeneLocalization20130903.pdf,20130904,YZ,mtg-tech,X Y autosome exchange,
CNVnator_on_phase3.prelim.pptx,20130909,AAN,Annotation,Applying CNVnator to phase3 data,25
de_novo_SNP_validation_update.pptx,20130909,AAN,Annotation,AAN - Update on de novo SNP validation,25
Retrodup_summary_future.pptx,20130909,AAN,Pseudogenes,Project about variable retroduplications: summary and future directions,15
modENCODE_txn_clustering_201309010_genometech.pptx,20130910,dw,tech,cmptxn clustering,6
Figure_1_mockup_20130910.pptx,20130910,BP,Tech,Figure 1,1
cmptxn_clustering_data_files.zip,20130910,dw,tech,cmptxn clustering stats (genes, GOs),4
stages_aligned_hg.xls,20130910,kky,Tech,stage aligned hg genes,
stages_aligned_hg.xls,20130910,kky,Tech,stage aligned hg genes,
Archive.zip,20130911,,,,
FigurePack_modENCODE_cmptxn_20132609.pptx.pdf,20130918,JR,,,
DMRR-DIAC-2013-09-23_JR.pptx,20130918,JR,,,
tar_classifications.pptx,20130919,ah,tech,,1
Archive.zip,20130919,,,,
ncRNAdynamics_26Aug2013.pptx,20130919,AS,Journal Club,Mechanism and applications of chromosome inactivation by Xist,25
FigurePack_modENCODE_cmptxn_20130924.pptx,20130924,,,,
tar_classifications.pptx,20130924,ah,tech,,1
SNPs_around_breakpoints.initial.pptx,20130925,AAN,Annotation,First looks at SNP aggregation around SV breakpoints,7
dsflvro.pptx,20130925,dc,annot,,3
dsflvro.pptx,20130925,dc,annot,,3
fig.pptx,20130925,YF,anno,figure update,
personalCancerGenomicsSlide.pptx,20130925,JC,Annotation,intro slides,12
YZ_Figure_Update_Human_20130924.pdf,20130925,YZ,mtg-tech,YZ Figure Update,
YZ_Figure_Update_Human_20130924.pdf,20130925,YZ,mtg-tech,YZ Figure Update,
YZ_Figure_Update_Human_20130924.pdf,20130925,YZ,mtg-tech,YZ Figure Update,
HumanUniquePgenes_20130924_sh.pdf,20130925,YZ,mtg-tech,Human Unique MS-Pgene,
FunSeq-for-Encode-n-cancer.25Sep2013.pdf,20130928,EK,Annot,slides shown in annot,32
FigurePack_modENCODE_cmptxn_20131003.pptx.pdf,20131003,JR,,,
ComparativePaper_CZ_20130905.xlsx,20131003,BP,Tech,Data sets,1
SNP_aggregation.part2.pptx,20131003,AAN,Annotation,SNP aggregation about breakpoints,8
phylo_trees_Oct3_flvt.pptx,20131003,dc,annot,oct3,7
personalCancerGenomicsSlide.pptx,20131004,JC,Annotation,intro slides updated,12
personalCancerGenomicsSlide.pptx,20131004,JC,Annotation,intro slides updated,12
SNP_aggregation.part3.pptx,20131008,AAN,Annotation,SNP aggregation about breakpoints (part 3),13
FigurePack_modENCODE_cmptxn_20131008.pptx.pdf,20131008,JR,,,
StructuralVariation_YZ_20131008.pptx,20131008,YZ,,Journal Club - YZ,
StructuralVariation_YZ_20131008.pptx,20131008,YZ,,Journal Club - YZ,
SV_DISCOVERY.pdf,20131008,YZ,,UM CMG Lecture,
StructuralVariation_YZ_20131008.pptx,20131008,YZ,,Journal Club - YZ,
StructuralVariation_YZ_20131008.pptx,20131008,YZ,,Journal Club - YZ,
FigurePack_modENCODE_cmptxn_20131017.pptx.pdf,20131017,JR,,,
ED_Figures_ALL.pdf,20131017,JR,,,
SNP_aggregation.part4.pptx,20131017,AAN,Annotation,SNP aggregation about breakpoints (part 4),5
KKY_GM_Oct2013.pptx,20131017,kky,GM,,30
FigurePack_modENCODE_cmptxn_20131028.pptx.pdf,20131026,JR,,,
FigurePack_modENCODE_cmptxn_20131028.pptx.pdf,20131026,JR,,,
SNP_aggregation.part5.pptx,20131027,AAN,Annotation,SNP aggregation about breakpoints (part 5),4
worm_hourglass_correlation.pptx,20131028,dw,tech,cmptxn: schematic explanation and network visualization for worm hourglass,
Oct28.pptx,20131028,STL,Annotation,SV breakpoints and fragile sites,3