bioRxiv Channel: International Human Epigenome Consortium (IHEC) https://biorxiv.org This feed contains articles for bioRxiv Channel "International Human Epigenome Consortium (IHEC)" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ ChromGene: Gene-Based Modeling of Epigenomic Data ]]> https://biorxiv.org/cgi/content/short/2022.05.24.493345v1?rss=1" Jaroszewicz, A. Ernst, J. 2022-05-25 doi:10.1101/2022.05.24.493345 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ A framework for summarizing chromatin state annotations within and identifying differential annotations across groups of samples ]]> https://biorxiv.org/cgi/content/short/2022.05.08.491094v1?rss=1" Vu, H. T. Koch, Z. Fiziev, P. Ernst, J. 2022-05-08 doi:10.1101/2022.05.08.491094 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Universal chromatin state annotation of the mouse genome ]]> https://biorxiv.org/cgi/content/short/2022.12.19.521116v1?rss=1" Vu, H. T. Ernst, J. 2022-12-20 doi:10.1101/2022.12.19.521116 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Universal annotation of the human genome through integration of over a thousand epigenomic datasets ]]> https://biorxiv.org/cgi/content/short/2020.11.17.387134v1?rss=1" Ernst, J. Vu, H. T. 2020-11-19 doi:10.1101/2020.11.17.387134 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Chromatin state modeling across individuals reveals global patterns of histone modifications ]]> https://biorxiv.org/cgi/content/short/2022.08.02.502571v1?rss=1" Zou, J. Ernst, J. 2022-08-03 doi:10.1101/2022.08.02.502571 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types ]]> https://biorxiv.org/cgi/content/short/2023.07.14.549056v1?rss=1" Dincer, T. U. Ernst, J. 2023-07-15 doi:10.1101/2023.07.14.549056 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Synovial Sarcoma Chromatin Dynamics Reveal a Continuum in SS18:SSX Reprograming ]]> https://biorxiv.org/cgi/content/short/2024.05.14.594262v1?rss=1" Hofvander, J. Qiu, A. Lee, K. Bilenky, M. Carles, A. Cao, Q. Moksa, M. Steif, J. Su, E. Sotiriou, A. Goytain, A. Hill, L. Singer, S. Andulis, I. Wunder, J. Mertens, F. Banito, A. Jones, K. B. Underhill, T. M. Nielsen, T. Hirst, M. 2024-05-17 doi:10.1101/2024.05.14.594262 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Regulatory roles of three-dimensional structures of topologically associating domains ]]> https://biorxiv.org/cgi/content/short/2022.07.22.501196v1?rss=1" Li, K. Y. Cao, Q. Wang, H. Leung, D. C. Y. Yip, K. Y. 2022-07-23 doi:10.1101/2022.07.22.501196 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data ]]> https://biorxiv.org/cgi/content/short/547596v1?rss=1" Nordström, K. Schmidt, F. Gasparoni, N. Salhab, A. Gasparoni, G. Kattler, K. Müller, F. Ebert, P. Costa, I. G. DEEP consortium, Pfeifer, N. Lengauer, T. Schulz, M. H. Walter, J. 2019-02-13 doi:10.1101/547596 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ SARS-CoV-2 impacts the transcriptome and epigenome at the maternal-fetal interface in pregnancy ]]> https://biorxiv.org/cgi/content/short/2022.05.31.494153v1?rss=1" Gao, L. Mathur, V. Tam, S. K. M. Zhou, X. Cheung, M. F. Chan, L. Y. Estrada-Gutierrez, G. Leung, B. W. Moungmaithong, S. Wang, C. C. Poon, L. Leung, D. C. Y. 2022-05-31 doi:10.1101/2022.05.31.494153 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection ]]> https://biorxiv.org/cgi/content/short/2022.05.10.491413v1?rss=1" Aracena, K. A. Lin, Y.-L. Luo, K. Pacis, A. Gona, S. Mu, Z. Yotova, V. Sindeaux, R. Pramatarova, A. Simon, M.-M. Chen, X. Groza, C. Lougheed, D. Gregoire, R. Brownlee, D. Li, Y. He, X. Bujold, D. Pastinen, T. Bourque, G. Barreiro, L. B. 2022-05-11 doi:10.1101/2022.05.10.491413 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Transposable elements are associated with the variable response to influenza infection ]]> https://biorxiv.org/cgi/content/short/2022.05.10.491101v1?rss=1" Chen, X. Pacis, A. S. Aracena, K. A. Gona, S. Kwan, T. Groza, C. Lin, Y. L. Sindeaux, R. H. M. Yotova, V. Pramatarova, A. Simon, M.-M. Pastinen, T. M. Barreiro, L. B. Bourque, G. 2022-05-10 doi:10.1101/2022.05.10.491101 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Genome graphs detect human polymorphisms in active epigenomic states during influenza infection ]]> https://biorxiv.org/cgi/content/short/2021.09.29.462206v1?rss=1" Groza, C. Chen, X. Pacis, A. Simon, M.-M. Pramatarova, A. Aracena, K. A. Pastinen, T. Barreiro, L. B. Bourque, G. 2021-10-01 doi:10.1101/2021.09.29.462206 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ The adapted Activity-By-Contact-model for enhancer-gene assignment and its combination with transcription factor affinities in single cell data ]]> https://biorxiv.org/cgi/content/short/2022.01.28.478202v1?rss=1" Hecker, D. Behjati Ardakani, F. Schulz, M. H. 2022-01-28 doi:10.1101/2022.01.28.478202 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ TF-COMB - discovering grammar of transcription factor binding sites ]]> https://biorxiv.org/cgi/content/short/2022.06.21.496953v1?rss=1" View larger version (23K): org.highwire.dtl.DTLVardef@e37cccorg.highwire.dtl.DTLVardef@1165241org.highwire.dtl.DTLVardef@725a2corg.highwire.dtl.DTLVardef@17e1893_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bentsen, M. Heger, V. Schultheis, H. Kuenne, C. Looso, M. 2022-06-22 doi:10.1101/2022.06.21.496953 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ FORGEdb: systematic analysis of candidate causal variants to uncover target genes and mechanisms in complex traits. ]]> https://biorxiv.org/cgi/content/short/2022.11.14.516365v1?rss=1" Breeze, C. E. Haugen, E. Gutierrez-Arcelus, M. Yao, X. Teschendorff, A. Beck, S. Dunham, I. Stamatoyannopoulos, J. Franceschini, N. Machiela, M. Berndt, S. 2022-11-16 doi:10.1101/2022.11.14.516365 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ EpiVar Browser: advanced exploration of epigenomics data under controlled access ]]> https://biorxiv.org/cgi/content/short/2023.08.03.551309v1?rss=1" Lougheed, D. R. Liu, H. Aracena, K. A. Gregoire, R. Pacis, A. Pastinen, T. Barreiro, L. B. Joly, Y. Bujold, D. Bourque, G. 2023-08-05 doi:10.1101/2023.08.03.551309 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Robust chromatin state annotation ]]> https://biorxiv.org/cgi/content/short/2023.07.15.549175v1?rss=1" Foroozandeh Shahraki, M. Farahbod, M. Libbrecht, M. W. 2023-07-17 doi:10.1101/2023.07.15.549175 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ A statistical approach to identify regulatory DNA variations ]]> https://biorxiv.org/cgi/content/short/2023.01.31.526404v1?rss=1" Baumgarten, N. Rumpf, L. Kessler, T. Schulz, M. H. 2023-02-03 doi:10.1101/2023.01.31.526404 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ ChromBERT: Uncovering Chromatin State Motifs in the Human Genome Using a BERT-based Approach ]]> https://biorxiv.org/cgi/content/short/2024.07.25.605219v1?rss=1" Lee, S. Lin, C. Chen, C.-Y. Nakato, R. 2024-07-26 doi:10.1101/2024.07.25.605219 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Epigenetic control of metabolic identity across cell types ]]> https://biorxiv.org/cgi/content/short/2024.07.24.604914v1?rss=1" Pacheco, M. P. Gerard, D. Mangan, R. J. Chapman, A. R. Hecker, D. Kellis, M. Schulz, M. H. Sinkkonen, L. Sauter, T. 2024-07-24 doi:10.1101/2024.07.24.604914 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Transposable elements impact the regulatory landscape through cell type specific epigenomic associations ]]> https://biorxiv.org/cgi/content/short/2024.08.07.606967v1?rss=1" Hyacinthe, J. Bourque, G. 2024-08-07 doi:10.1101/2024.08.07.606967 Cold Spring Harbor Laboratory Press 2024-08-07 <![CDATA[ Revisiting Evidence for Epigenetic Control of Alternative Splicing ]]> https://biorxiv.org/cgi/content/short/2024.08.30.610315v1?rss=1" Manz, Q. List, M. 2024-09-01 doi:10.1101/2024.08.30.610315 Cold Spring Harbor Laboratory Press 2024-09-01 <![CDATA[ Epigenomic analysis of hepatocellular carcinoma reveals aberrant cis-regulatory changes and dysregulated retrotransposons with prognostic potentials ]]> https://biorxiv.org/cgi/content/short/2024.09.16.613254v1?rss=1" Cheng, C. C. Y. Cheung, M. F. Lee, A. Y. Wu, Q. Chow, S. H.-C. Ang, J. Y. J. Riquelme Medina, I. Lo, G. Wu, H. Yang, W. Lai, P. B. S. Yip, K. Cheng, A. Leung, D. C. Y. 2024-09-20 doi:10.1101/2024.09.16.613254 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci ]]> https://biorxiv.org/cgi/content/short/2025.02.20.639228v1?rss=1" Hecker, D. Song, X. Baumgarten, N. Diagel, A. Katsaouni, N. Li, L. Li, S. Kumar Maji, R. Behjati Ardakani, F. Ma, L. Tews, D. Wabitsch, M. Björkegren, J. L. M. Schunkert, H. Chen, Z. Schulz, M. H. 2025-02-21 doi:10.1101/2025.02.20.639228 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Pan-cell type continuous chromatin state annotation of all IHEC epigenomes ]]> https://biorxiv.org/cgi/content/short/2025.02.06.636950v1?rss=1" Daneshpajouh, H. Moghul, I. Wiese, K. C. Libbrecht, M. W. 2025-02-08 doi:10.1101/2025.02.06.636950 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ GIMMEcpg: Global Imputation of Mean CpG MEthylation in Real-time ]]> https://biorxiv.org/cgi/content/short/2025.03.17.643746v1?rss=1" Moghul, I. Chai, N. Pontikos, N. Hardcastle, A. Herrero, J. Beck, S. 2025-03-18 doi:10.1101/2025.03.17.643746 Cold Spring Harbor Laboratory Press 2025-03-18 <![CDATA[ Systematic comparison of dCas9-based DNA methylation epimodifiers over time indicates efficient on-target and widespread off-target effects ]]> https://biorxiv.org/cgi/content/short/2025.03.15.641804v1?rss=1" Pahlevan Kakhki, M. Rangani, F. Ewing, E. Starvaggi Cucuzza, C. Zheleznyakova, G. Kalomoiri, M. v, T. V. S. Covacu, R. Andreou, I. Needhamsen, M. Kular, L. Jagodic, M. 2025-03-16 doi:10.1101/2025.03.15.641804 Cold Spring Harbor Laboratory Press 2025-03-16 <![CDATA[ Cell type-specific epigenomic variation and its association with genotype in the human breast ]]> https://biorxiv.org/cgi/content/short/2025.04.16.648998v1?rss=1" Hauduc, A. Steif, J. Bilenky, M. Moksa, M. M. Cao, Q. Ding, S. Eaves, C. J. Hirst, M. 2025-04-20 doi:10.1101/2025.04.16.648998 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ EpiSegMix: A Flexible Distribution Hidden Markov Model with Duration Modeling for Chromatin State Discovery ]]> https://biorxiv.org/cgi/content/short/2023.09.07.556549v1?rss=1" Schmitz, J. E. Aggarwal, N. Laufer, L. Walter, J. Salhab, A. Rahmann, S. 2023-09-07 doi:10.1101/2023.09.07.556549 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Harnessing machine learning models for epigenome to transcriptome association studies ]]> https://biorxiv.org/cgi/content/short/2025.05.09.653095v1?rss=1" Behjati ardakani, F. Ashrafiyan, S. Rumpf, L. Hecker, D. Schulz, M. H. 2025-05-15 doi:10.1101/2025.05.09.653095 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations ]]> https://biorxiv.org/cgi/content/short/2025.06.18.660301v1?rss=1" Quon, J. Reynolds, A. P. Tripician, N. Rynes, E. T. Teodosiadis, A. Kellis, M. Meuleman, W. 2025-06-23 doi:10.1101/2025.06.18.660301 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Integrated flexible DNA methylation-chromatin segmentation modelingenhances epigenomic state annotation ]]> https://biorxiv.org/cgi/content/short/2025.07.25.666820v1?rss=1" Aggarwal, N. Schmitz, J. E. Laufer, L. Rahmann, S. Walter, J. Salhab, A. 2025-07-27 doi:10.1101/2025.07.25.666820 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Leveraging the largest harmonized epigenomic data collection for metadata prediction validated and augmented over 350,000 public epigenomic datasets ]]> https://biorxiv.org/cgi/content/short/2025.09.04.670545v1?rss=1" Raby, J. Frosi, G. White, F. Laperle, J. Jacques, P.-E. 2025-09-04 doi:10.1101/2025.09.04.670545 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Learning a Pairwise Epigenomic and Transcription Factor Binding Association Score Across the Human Genome ]]> https://biorxiv.org/cgi/content/short/2024.12.19.629547v1?rss=1" Kwon, S. B. Ernst, J. 2024-12-22 doi:10.1101/2024.12.19.629547 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ GECSI: Large-scale chromatin state imputation from gene expression ]]> https://biorxiv.org/cgi/content/short/2025.10.02.679828v1?rss=1" Fu, J. Ernst, J. 2025-10-04 doi:10.1101/2025.10.02.679828 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Whole-genome profiling of native 5-hydroxymethylation in human neurons with long-read sequencing ]]> https://biorxiv.org/cgi/content/short/2026.01.11.695537v1?rss=1" 60%) were enriched in neuron-related terms, with functional variety when stratifying across chromatin states. Analysis of transcription factor motifs in highly methylated regions, demonstrated 5hmC- and 5mC-specific enrichment affecting downstream regulatory networks. Altogether, our study demonstrates the potential of ONT to characterize whole-genome, native 5hmC and 5mC DNA modifications in human neurons, specifically highlighting the enrichment of 5hmC in actively transcribed regions and enhancers in the human brain. ]]> Klose, D. Sepehri, M. H. Olsen, R.-A. Vu, H. Ernst, J. Kular, L. Needhamsen, M. Jagodic, M. 2026-01-12 doi:10.64898/2026.01.11.695537 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ TEExplorer: A Web Portal to Investigate TE-Epigenome Associations Across Human Cell Types ]]> https://biorxiv.org/cgi/content/short/2026.02.18.706470v1?rss=1" Hyacinthe, J. Lougheed, D. R. Bourque, G. 2026-02-19 doi:10.64898/2026.02.18.706470 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Histone Modification Metapeaks are Epigenetic Landmarks Predictive of Cell State ]]> https://biorxiv.org/cgi/content/short/2026.03.31.715657v1?rss=1" Tanner, R. M. Perkins, T. J. 2026-04-02 doi:10.64898/2026.03.31.715657 Cold Spring Harbor Laboratory Press 2026-04-02