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Last UpdatedAuthors or LabsTitleAnticipated/Actual Publication DateJournalStatus (Pulldown menu) Url
(doi or draft)
Consideration for Coordination with Encyclopedia Publication Consider for Coordination with Other Publications SPECIFYNotesMain or Companion journal, Encyclopedia group? (Dropdown menu) Main or Companion journal, EN-TEx group? (Dropdown menu) Do not deleteAdded on Portal
2
ENC0015/23/2016Akilesh (Stamatoyannopoulos lab)Regulatory Genomic Phenotyping Reveals Key Drivers of Renal Cell Carcinoma2016TBDIn Preparation
3
ENC0021/30/2016Anshul Kundaje, Youngsook L Jung, Qunhua Li, Nathan Boley, Jin-Wook Lee, Peter Kharchenko, Seth Strattan, Joel Rozowsky, James B. Brown, Ben Hitz, Serafim Batzoglou, Arend Sidow, Michael Cherry, Barbara Wold, Peter Bickel, Peter ParkAutomated quality control, reproducibility analysis and scoring of transcription factor ChIP-seq datasetsDec 2017Nature ProtocolsIn Revision
4
ENC00311/4/2016Beer labPredicting Enhancer Activity and Variant Impact using gkm-SVMJan 2017Human MutationPublished
5
ENC0047/7/2016Burge and Yeo labsSequence context effects on RBP binding to RNA motifs
6
ENC00510/14/2015Dekker, Gilbert, Yue and Noble groupsAn Integrative Method for Detecting Structural Variations in Cancer GenomesDecember, 2016Nature BiotechIn PreparationNo
7
ENC0061/19/2016Dobin, Dreszer, Hitz, RNA Working GroupRNA-Seq pipeline2016In Preparation
8
ENC0077/23/2015Ecker, Pennacchio, Visel, Ren and Wang labsDynamic methylome remodeling throughout mammalian post-implantation fetal development2017In PreparationNoyes (mouse papers)
9
ENC0085/9/2016Ecker, Pennacchio, Visel, Ren and Wang labs
Improved regulatory element prediction based on tissue-specific local epigenomic signatures
2017PNASPublished
10.1073/pnas.1618353114
NoNo
10
ENC00911/18/16Feng Yue and Li Lab
HiRep: A Stratification-Aggression method to evaluate the Reproducibility of Hi-C experiment
Dec 2016Genome BiologyIn Preparation
11
ENC01012/16/2016Ferhat Ay, Peter Bickel, Job Dekker, David Gifford, Anshul Kundaje, Bryan R. Lajoie, Christina Leslie, Qunhua Li, William Noble, Doug Phanstiel, Michael Sauria, Mike Snyder, Maryna Taranova, Oana Ursu, Gurkan Yardimci, Feng Yue, Lee ZamparoQC metrics for Hi-C datasetsIn PreparationNo3D nucleome subgroup
12
ENC0117/7/2016Fu and Burge labsPromoter-directed loading of RNA processing machineries
13
ENC012Gerstein & White LabsComparison of the ENCODE regulatory network with that of model organismsx
14
ENC0136/10/16Gerstein LabENGINE - a method for linking enhancers to genesIn Preparationx
15
ENC0146/10/16Gerstein LabEnsemble methods for predicting enhancers2016/2017In PreparationIn Revision
16
ENC0157/1/16Gerstein LabAllelic analysis of ENCODE elements2016 submissionIn Preparationx
17
ENC016Gerstein LabUsing pattern recognition of epigenetic signals for supervised enhancer prediction2016 submissionNature MethodIn Preparation
18
ENC0177/8/2016Gerstein, Weng, Len, etc. labsBlind test of enhancer prediction algorithms using mouse transgenic data2016/2017 submissionIn PreparationNoNo
19
ENC0183/18/2016Gifford LabDifferential chromatin profiles partially determine transcription factor binding2016Submitted
20
ENC0198/27/2016Gifford LabK-mer Set Memory (KSM) motif representation enables accurate prediction of the impact of regulatory variants2017 Jan submissionCell SystemsIn Preparationyes, novel motif representation and motif discovery method, ENCODE3 TF motifs
21
ENC0208/27/2016Gifford LabAccurate eQTL prioritization with an ensemble-based framework2016 submissionHuman MutationIn Revisionhttp://www.biorxiv.org/content/early/2016/08/16/069757
22
ENC0218/27/2016Gifford LabModeling Trends in Distributions2015 submissionSubmitted
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ENC02210/20/2016Gifford LabDiscovering DNA motifs and genomic variants associated with DNA methylationSubmittedGenome ResearchSubmittedhttp://www.biorxiv.org/content/early/2016/09/06/073809
24
ENC0239/18/2015Gingeras Lab, Gerstein LabPrecision-STAR: allele aware mapping and expression analysisIn Preparationyes Mapping RNA-seq to personal genomes
25
ENC0249/18/2015Gingeras Lab, Guigo LabCircular RNA in human cell lines and tissues.In Preparationyes Method for detecting cricular RNAs. Circular RNAs in Gingeras Lab total RNA-seq data (ENCODE2/3).
26
ENC0259/18/2015Gingeras Lab, Guigo Lab, Gerstein LabAllele specific expression, splicing, and promoter usage in human tissuesIn Preparationyes Analysis of allele-specific expression in EN-TeX human tissues.EN-TEx
27
ENC02610/28/16Graveley, Yeo, Burge labsGlobal analysis of RBP KD/RNA-seq dataNov 2016 submissionTBD - Genome ResearchIn PreparationCompanion Journalx
28
ENC0278/7/2015Graveley, Yeo, Burge, Fu, Lecuyer, XiaoIntegrated Analysis of ENCODE RNA Binding Protein Datasets (eCLIP, RNAi/RNA-seq, RBNS, ChIP-seq, Imaging)Nature or CellIn PreparationYesWill serve as primary paper for the RNA binding protein data production (Graveley project)
29
ENC028July 2016Grubert, Srivas, Spacek, Snyder (+others in Snyder Lab)Landscape of Long-Range Interactions in the Human Genome Across Multiple Cell Types2016/2017In PreparationMaybe
30
ENC0291/27/2016Guigo and Gingeras LabsPrimary cell expression profiling reveals cell type clustering over tissue of origin and embryological lineage2016Submission 2016Science / NatureIn PreparationIt could
31
ENC0307/5/2016Guigo/Harrow (GENCODE)Adding thousands of full-length long noncoding RNAs to the GENCODE catalogue using RNA Capture Long-read Sequencing (CLS)Submission 2016
Nature BiotechnologyIn PreparationIt could
32
ENC03112/6/16HardisonA guide to translation of research results from model organisms to human (Research Highlight of Breschi et al. 2016 Genome Biology)July 2016Genome BiologyPublishedhttps://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1026-9
33
ENC0321/8/2016Hardison and collaborating labsDynamics and stability of regulatory landscape in mouse hematopoiesis2016In Preparationnono
34
ENC0331/19/2016Hitz, DCC, DACENCODE Uniform Pipelines2016In Preparation
35
ENC0344/13/2017Hitz, et. alSnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata2017PLoS OnePublishedhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0175310
36
ENC0353/27/2015Jill Moore and Zhiping WengFunctional annotation of noncoding variants reveals role of neural and immune pathways in genetic foundation of psychiatric disordersPLoS OneIn RevisionENCODE2 and REMC data
37
ENC0369/18/2015Ke Lui, Peter Bickel, Haiyan Huang, Ben BrownTranscriptional status of active enhancers depends on epigenetic contextIn Preparationyes Our companion paper emerging from the Enhancer Competition
38
ENC0377/7/2016Keles and Ay GroupsMapping long range interactions in repetitive regions of the genome2016 submissionIn PreparationYesThis is our multi-read mapper for Hi-C data with applications to ENCODE3 data
39
ENC0389/2/2015Keles GroupFunctional mediation analysis In Preparation
40
ENC0399/25/2015Keles GroupAn empirical Bayes test for detecting Allelic Imbalance in ChIP-seqJASASubmittedNo
41
ENC0407/7/2016Keles GroupatSNP DB: a web resource for quantifying impact of dbSNP SNPs on transcription factor binding2016 submissionNAR Database issueIn Preparationatsnp.biostat.wisc.eduNo
42
ENC0415/17/2016Klein Lab(tentative) Genetic variation in prostate-specific enhancers contributes to prostate cancer risk but not prostate eQTLs in general2016/2017In Preparation
43
ENC04210/21/2016Koon-Kiu Yan, Gerstein MrTADFinder: A network-based approach to identify topologically associating domains in multiple resolutionsDec 2016 submissionPLoS CBSubmittedhttps://doi.org/10.1101/097345
44
ENC04312/16/2016Koon-Kiu Yan, Gerstein lab, Noble labHiC-Spector: A matrix library for spectral analysis and reproducibility of Hi-C contact mapsNov 2016 submissionBioinformaticsSubmittedhttp://biorxiv.org/content/early/2016/11/21/088922#page
45
ENC04412/15/2016
Kundaje + DREAM Challenge Team
A systematic comparison of methods for predicting in-vivo transcription factor binding profiles across diverse cell lines and tissues
Nov 2017 SubmissionCellIn PreparationYes (if possible)
46
ENC0459/24/2015Kundaje labDeep learning the relationship between chromatin architecture and chromatin stateDec 2017 submissionNature BiotechIn PreparationNoNo
47
ENC0469/24/2015Kundaje labDeep learning models for predicting transcription factor bindingDec 2017 submissionNature BiotechIn PreparationNoNo
48
ENC0479/24/2015Kundaje labIntegrative models of transcriptional regulation across diverse human cell types and tissuesMay 2017 submissionTBAIn PreparationNoNo
49
ENC0489/24/2015Kundaje labRegulatory drivers of chromatin state dynamics in hematopoetic differentiation and leukemogenesisTBATBAIn PreparationNoNo
50
ENC0491/30/2016Kundaje labMulti-scale comparisons of 3D chromatin contact mapsDec 2017SubmittedNoYes (3D group)
51
ENC0504/11/2016Kundaje labDeepLIFT: A novel interpretation engine for deep learning models for regulatory genomicsOct 2017Publishedhttp://proceedings.mlr.press/v70/shrikumar17a.html
52
ENC0518/10/2016Kundaje labDeep learning models for context-specific regulatory variant predictionTBAIn PreparationNoYes (ENCODE GWAS group)
53
ENC0528/10/2016Kundaje labHow to train your DRAGONN (Deep regulatory genomic neural network)Nov 2017 submissionNature MethodsIn PreparationNoNo
54
ENC0531/30/2016Kundaje lab, Kellis labDe-novo inference of enhancer-gene networks in diverse cellular contexts reveals the long-range regulatory impact of disease-associated variantsDec 2017Nature GeneticsIn RevisionNoNo
55
ENC0549/5/2016Kundaje, Snyder, Hughes labsA comprehensive regulatory lexicon of C2H2 Zinc Finger transcription factorsDec 2017 submissionIn PreparationNoNo
56
ENC0551/19/2016Kundaje, Strattan, Hitz, DCCChIP-Seq pipelinesTBAIn Preparation
57
ENC05611/13/2015Liu LabModeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles2016Genome ResearchSubmittedyes http://cistrome.org/MARGE/
58
ENC0579/2/2015Matthew Maurano, Eric Haugen, Richard Sandstrom, Jeff Vierstra, Anthony Shafer, Rajinder Kaul, John StamatoyannopoulosLarge-scale identification of sequence variants impacting human transcription factor occupancy in vivoNature GeneticsIn RevisionDNase data
59
ENC0587/14/2015Mingxiang Teng, Rafa and othersA benchmark for RNA-seq quantification pipelines based on a minimal datasetGenome BiologyPublishedPMID: 27107712 PMCID: PMC4842274 DOI: 10.1186/s13059-016-0940-1
60
ENC05912/20/2016Mortazavi, Guigo, Gingeras, Wold, Myers labsComparative dynamics of microRNAs during mammalian developmentJanuary 2017 submissionIn PreparationyesyesMain Journal
61
ENC06012/7/16Myers LabA genome-wide interactome of DNA-binding regulatory proteins in the human liverJuly 2016Genome ResearchIn preparation
62
ENC06111/1/2016Noble labSoftware tools for visualizing Hi-C data2017Genome BiologyIn Revisionhttp://biorxiv.org/content/early/2016/11/07/086017
63
ENC06211/17/2016Noble labImputation of genomics data sets using a tensor factorization modelEarly 2017TBDIn Preparation
64
ENC06312/16/2016Noble lab
A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.
2016Genome ResearchSubmittedhttp://biorxiv.org/content/early/2016/11/07/086025No
65
ENC06412/16/2016Noble labChoosing panels of genomics assays using submodular optimizationGenome BiologyPublishedhttp://www.genomebiology.com/2016/17/1/229
66
ENC0657/7/2016Nussbacher et al (Yeo and Graveley Labs)MicroRNA regulation by RBPs2016 submissionIn Preparation
67
ENC0667/7/2016Nussbacher et al (Yeo Lab)RNA modifications and RBP binding2016 submissionIn Preparation
68
ENC067July 2106Ouyang maybe others (Snyder)TF knockdowns2016 submissionGenome Research?In Preparation
69
ENC0687/7/2016Peng Liu, Emery H. Bresnick, Colin N. Dewey, and Sündüz KelesIntegrative Analysis of RNA-seq with ChIP-seq Discovers Novel Transcripts in Hematopoietic Differentiation2016/2017In Preparation
70
ENC06912/1/16Pennacchio LabLimb-Enhancer Genie: an accessible resource of accurate enhancer predictions in the developing limbsEarly 2017PLOS Comp BioSubmitted
71
ENC0707/7/2016Pratt et al (Yeo Lab)Standards and automatic quality control methods for eCLIP analysis (DNAnexus pipeline)2016 submissionGenome Research?In Preparation
72
ENC0713/17/2016Pritchard LabLeafCutter: Annotation-free quantification of RNA splicing. 2016In Preparationhttp://biorxiv.org/content/early/2016/03/16/044107
73
ENC0727/7/2016Pritchard LabLeveraging GWAS to identify disease-relevant functional annotations2016 submissionIn Preparation
74
ENC073July 2016Regulation Subgroup (Mishra)Cool Regulaiton Stuff2016 submissionWith main paperthinking
75
ENC0747/23/2015Ren lab (in collaboration with Dahl, Klungland labs)Broad histone H3K4me3 domains in mouse oocytes modulate maternal to zygotic transition Published online September 14, 2016NaturePublishedPMID: 27626377nono
76
ENC0759/24/2016Ren lab and collaborating labsLandscapes of chromatin accessibility in the mouse genome during embryogenesisNov 2016 submissionTBDIn PreparationYesMouse papersWill primarily use ATAC-seq datasets generated for 12 embryonic tissues over 8 developmental stages
77
ENC0769/24/2016Ren lab and collaborating labsSingle cell analysis of regulatory landscapes during mouse forebrain development Nov 2016 submissionTBDIn PreparationyesMouse papersWill primarily use single cell ATAC-seq datasets generated for mouse forebrain tissues over 8 developmental stages
78
ENC07712/15/2015Rinn labWidespread RNA binding by chromatin-associated proteins2016Genome BiologyIn RevisionIt is one of the mouse papers
79
ENC0789/14/2015RNA Working GroupENCODE RNA-Seq PipelinesIn PreparationTo describe the RNA-Seq pipelines that are implemented at the DCC
80
ENC0799/18/2015RNA-Chromatin Interaction Working GroupCo-transcriptional regulation at the RNA-Chromatin inferfaceIn PreparationRNA-chromatinPlace-holder for the primary publication of the RNA-Chromatin Interactions Working Group
81
ENC0809/16/16Sauria et al (Taylor)Assessing HiC dataset qualityDec 2016 submissionTBDIn Preparation
82
ENC08110/18/2016Shoresh and colleagues (Bernstein groupGenetic similarity measures for quality control of epigenetic profilesNov 2016 submissionTBDIn Preparation
83
ENC0827/7/2016Stamatoyannopoulos[Mouse regulatory DNA during development and differentiation]2017 submissionMouse group coordinatedIn PreparationMouse
84
ENC0837/7/2016Stamatoyannopoulos / Funnell[Analysis of regulatory DNA knockouts]2017 submissionIn Preparation
85
ENC0847/7/2016Stamatoyannopoulos / MauranoLarge-scale identification of functional regulatory variants in the mouse genome2017 submissionMouse group coordinatedIn PreparationMouse
86
ENC0857/7/2016Stamatoyannopoulos / Vierstra[Nano-DNaseI]2017 submissionIn Preparation
87
ENC0867/7/2016Stamatoyannopoulos / Vierstra[Quantitative genomic footprinting]2017 submissionIn Preparation
88
ENC0879/18/2015Sumanta Basu, Bin Yu, Ben BrownIntrospective Learning Machines: an iterative approach to feature interaction detection and mappingPNASIn PreparationMethods paper introducing the ILM methodology
89
ENC088Tak, .....FarnhamDeletion of a single enhancer can cause widespread changes in the transcriptome and epigenome of human cellsGenome BiologyIn Revision
90
ENC0899/14/16Vierstra et al (Stamatoyannopoulos/Vierstra)Nano-DNaseI2017 submissionTBDIn Preparation
91
ENC0909/14/16Vierstra et al (Stamatoyannopoulos/Vierstra)A new framework for genomic footprinting2017 submissionTBDIn Preparation
92
ENC0919/14/16Vierstra et al (Stamatoyannopoulos/Vierstra)Fine-scale mapping of regulatory pathways controlling differentiation2017 submissionTBDIn Preparation
93
ENC0927/5/2016Visel/PennacchioExtensive Enhancer Redundancy Assures Phenotypic Robustness in Mammals2017 submissionNatureIn Revision
94
ENC0939/14/16Wang et al. (Stamatoyannopoulos)Genome-wide analysis of TF affinity2017 submissionTBDIn Preparation
95
ENC0947/1/16Wang labIdentification of key transcription factors during developmentIn Preparation
96
ENC0957/6/16Wang labIdentification of cis-regulatory elements for histone modifications in mouseIn Preparation
97
ENC0967/23/2015Wang lab, Ren lab, Pennacchio, Visel and Ecker(tentative) Dynamic chromatin landscapes durign embryonic developmentIn PreparationYesMouse papers
98
ENC097wengWeng/Fu and KundajeComparison of altorighms for calling peaks in DNase-seq and histone mark ChIP-seq data for enhancer and promoter predictions2016 submissionBriefings of BioinformaticsSubmittedNoNo
99
ENC0987/8/2016Weng/MooreIdentifying Stop Codon Readthrough in Human Ribosomal Profiling Data2016 submissionNARIn PreparationNoNo
100
ENC0997/8/2016Weng/van der VeldeDynamics of chromosome states during mouse development2016 submissionIn PreparationYesmouse papersChromHMM analysis of Chromatin states of the mouse developmental progression matrix
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