The BLUEPRINT Data Analysis Portal

Fernández, José María, de la Torre, Victor, Richardson, David, Royo, Romina, Puiggròs, Montserrat, Moncunill, Valentí, Fragkogianni, Stamatina, Clarke, Laura, Flicek, Paul, Rico, Daniel, Torrents, David, Carrillo de Santa Pau, Enrique, Valencia, Alfonso·2016·Cell Systems
DOI 10.1016/j.cels.2016.10.021

Cited by (164)

Items 101–164 of 164

  1. Single‐Cell Multiomics Reveals TCR Clonotype‐Specific Phenotype and Stemness Heterogeneity of T‐ ALL Cells
    Songnan Sui, Xiaolei Wei, Yue Zhu, Qiuyue Feng, Xianfeng Zha, Lipeng Mao, Boya Huang, Wen Lei, Guobing Chen, Huien Zhan et al. · 2024 · Cell Proliferation
  2. Epigenetic Variation Taking Center Stage in Immunological Research
    Simone Ecker, Stephan Beck · 2017 · Epigenomics
  3. Cell-free DNA Profiling Informs Major Complications of Hematopoietic Cell Transplantation
    Alexandre Pellan Cheng, Matthew Pellan Cheng, Conor James Loy, Joan Sesing Lenz, Kaiwen Chen, Sami Smalling, Philip Burnham, Kaitlyn Marie Timblin, José Luis Orejas, Emily A. Silverman et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  4. A local sequence signature defines a subset of heterochromatin-associated CpGs with minimal loss of methylation in healthy tissues but extensive loss in cancer
    Dror Bar, Lior Fishman, Yueyuan Zheng, Irene Unterman, Devorah Schlesinger, Amir Eden, De‐Chen Lin, Benjamin P. Berman · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  5. Histone modification clocks for robust cross-species biological age prediction and elucidating senescence regulation
    Zhixin Niu, Chang Liu, Yurong Fan, Lei Gu · 2026 · Proceedings of the National Academy of Sciences
  6. cellsig plug-in enhances CIBERSORTx signature selection for multidataset transcriptomes with sparse multilevel modelling
    Md. Abdullah‐Al‐Kamran Khan, Wu Jian, Yuhan Sun, Alexander D. Barrow, Anthony T. Papenfuss, Stefano Mangiola · 2023 · Bioinformatics
  7. Genome-wide association analysis of neutrophil granularity identifies CDK6 as a regulator of primary granules
    Kathryn Fleming, Kate Burley, Fernando M. Ponce-Garcia, Parsa Akbari, Claire A. Naveh, Chris Rice, Przemysław Zakrzewski, Willem Gibbs, Sarah Groves, Drinalda Cela et al. · 2025 · iScience
  8. sciMET-cap: High-throughput single-cell methylation analysis with a reduced sequencing burden
    Sonia N. Acharya, Ruth V. Nichols, Lauren E. Rylaarsdam, Brendan L. O’Connell, Theodore P. Braun, Andrew Adey · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  9. Reversal of inflammatory reprogramming by vasodilator agents in pulmonary hypertension
    Anna Kirillova, Meena Sethuraman, Xishuang Dong, Almina Kirdar, Gil Speyer, Yassmin Al Aaraj, Annie M.M. Watson, Lily K. Schneider, Michael D. Creager, Robert Lafyatis et al. · 2024 · ERJ Open Research
  10. Artificial intelligence meets epigenetics: a new frontier in precision oncology
    Ruby Srivastava · 2026 · Epigenetics Reports
  11. Epioncogene Networks: Identification of Epigenomic and Transcriptomic Cooperation by Multi-omics Integration of ChIP-Seq and RNA-Seq Data
    Fabian V. Filipp · 2018 · RNA technologies
  12. Automatic detection of genomic regions with informative epigenetic patterns
    Florencio Pazos, Adrián García-Moreno, Juan Carlos Oliveros · 2018 · BMC Genomics
  13. Precision Medicine of Autoimmune Diseases
    Ayodeji Folorunsho Ajayi, Oluwadunsin Iyanuoluwa Adebayo, Emmanuel Tayo Adebayo · 2020 · IntechOpen eBooks
  14. A multi-organ map of the human immune system across age, sex and ethnicity
    Stefano Mangiola, Michael Milton, N Ranathunga, CSN Li-Wai-Suen, Alexandru Odainic, E Yang, W Hutchison, A Garnham, J Iskander, B Pal et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  15. Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis
    Kanako O. Koyanagi · 2023 · BMC Research Notes
  16. Epigenetic profiles of tissue informative CpGs inform ALS disease status and progression
    Christa Caggiano, Marco Morselli, Xiaoyu Qian, Barbara Celona, M. Thompson, Shivangi Wani, Anela Tosevska, Kodi Taraszka, G. Heuer, Shyuan Thieu Ngo et al. · 2025 · Genome Medicine
  17. Main Existing Datasets for Open Brain Research on Humans
    Baptiste Couvy‐Duchesne, Simona Bottani, Etienne Camenen, Fang Fang, Mulusew Fikere, Juliana Gonzalez-Astudillo, Joshua Harvey, Ravi Hassanaly, Irfahan Kassam, Penelope A. Lind et al. · 2023 · Neuromethods
  18. Estimation of Tumor Immune Signatures from Transcriptomics Data
    Xiaoqing Yu · 2022 · Springer handbooks of computational statistics
  19. A cell-free DNA metagenomic sequencing assay that integrates the damage response to infection
    Alexandre Pellan Cheng, Philip Burnham, John R. Lee, Matthew Pellan Cheng, Manikkam Suthanthiran, Darshana M. Dadhania, Iwijn De Vlaminck · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  20. Over-accessible chromatin links myeloma initiating genetic events to oncogenic transcriptomes and aberrant transcription factor regulatory networks
    Jaime Alvarez-Benayas, Alexia Katsarou, Nikolaos Trasanidis, Aristeidis Chaidos, Philippa C. May, Kanagaraju Ponnusamy, Xiaolin Xiao, Marco Bua, Maria Luiza B. Sousa Atta, Irene A.G. Roberts et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  21. 3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk
    Ning Liu, Timothy J. Sadlon, Ying Y. Wong, Stephen Pederson, James Breen, Simon Charles Barry · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  22. Multi-population genome-wide association study implicates both immune and non-immune factors in the etiology of pediatric steroid sensitive nephrotic syndrome
    Alexandra Barry, Michelle T. McNulty, Xiaoyuan Jia, Yask Gupta, Hanna Dêbiec, Yang Luo, China Nagano, Tomoko Horinouchi, Seulgi Jung, Manuela Colucci et al. · 2022 · medRxiv
  23. Decoding the variant-to-function relationship for LIPA , a risk locus for coronary artery disease
    Fang Li, Elise D. Flynn, Philip Ha, Mazal N. Zebak, Haoxiang M. Cheng, Chenyi Xue, Jianting Shi, Xun Wu, Ziyi Wang, Yujiao Meng et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  24. How do we measure the epigenome(s)?
    Hans‐Ulrich Klein, Philip L. De Jager · 2018 · Multiple Sclerosis Journal
  25. Mod Squad: Altered Histone Modifications in Cancer
    Matthew J. Murtha, Manel Esteller · 2018 · Elsevier eBooks
  26. Application of High-Throughput Technologies in Personal Genomics: How Is the Progress in Personal Genome Service?
    Kaoru Mogushi, Yasuhiro Murakawa, Hideya Kawaji · 2018 · Respiratory disease series
  27. Advances in epigenetic techniques to study development and diseases
    Kevin Dzobo · 2020 · Elsevier eBooks
  28. MAFB surrogates the glucocorticoid receptor ability to induce tolerogenesis in dendritic cells
    Octavio Morante-Palacios, Laura Ciudad, Raphael Micheroli, Carlos de la Calle‐Fabregat, Tianlu Li, Gisela Barbisan, Miranda Houtman, Sam G. Edalat, Mojca Frank‐Bertoncelj, Caroline Ospelt et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  29. 3DFAACTS-SNP: Using Regulatory T Cell-specific Epigenomics Data to Uncover Candidate Mechanisms of Type-1 Diabetes (T1D) risk
    Ning Liu, Timothy J. Sadlon, Ying Y. Wong, Stephen Pederson, James Breen, Simon Charles Barry · 2021 · Research Square
  30. Faculty Opinions recommendation of Resolving mechanisms of immune-mediated disease in primary CD4 T cells.
    Salvatore Spicuglia · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  31. Publicly available resources in COVID-19 research and their applications
    Katarina Baralić, Katarina Živančević, Dragica Božić, Danijela Đukić-Ćosić · 2023 · Elsevier eBooks
  32. Long noncoding RNAs and miRNAs
    Asim K. Duttaroy, Rahul Mallick · 2024 · Elsevier eBooks
  33. Genome Wide Association Analysis of Neutrophil Granularity Identifies Cdk6 as a Regulator of Neutrophil Development
    Kathryn Fleming, Kate Burley, Fernando M. Ponce-Garcia, Parsa Akbari, Claire A. Naveh, Chris Rice, Przemyslav Zakrzewski, Willem Gibbs, Sarah Groves, Christopher J. Harbort et al. · 2024 · SSRN Electronic Journal
  34. Advances in epigenetic techniques to study development and diseases
    Kevin Dzobo · 2025 · Elsevier eBooks
  35. Additional file 3 of The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability
    Jennifer Derrien, Catherine Guérin‐Charbonnel, Victor Gaborit, L. Campion, Magali Devic, Elise Douillard, Nathalie Roi, Hervé Avet‐Loiseau, Olivier Decaux, Thierry T.F. Facon et al. · 2021 · Figshare
  36. Additional file 5 of sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden
    Sonia N. Acharya, Ruth V. Nichols, Lauren E. Rylaarsdam, Brendan L. O’Connell, Theodore P. Braun, Andrew Adey · 2024 · Figshare
  37. Additional file 2 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Carmen A. Buttler, Ramirez, Daniel, Robin D. Dowell, Edward B. Chuong · 2024 · Figshare
  38. Additional file 5 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Carmen A. Buttler, Ramirez, Daniel, Robin D. Dowell, Edward B. Chuong · 2024 · Figshare
  39. Additional file 2 of sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden
    Sonia N. Acharya, Ruth V. Nichols, Lauren E. Rylaarsdam, Brendan L. O’Connell, Theodore P. Braun, Andrew Adey · 2024 · Figshare
  40. Additional file 4 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Carmen A. Buttler, Ramirez, Daniel, Robin D. Dowell, Edward B. Chuong · 2024 · Figshare
  41. Additional file 7 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Carmen A. Buttler, Ramirez, Daniel, Robin D. Dowell, Edward B. Chuong · 2024 · Figshare
  42. Additional file 9 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Carmen A. Buttler, Ramirez, Daniel, Robin D. Dowell, Edward B. Chuong · 2024 · Figshare
  43. Additional file 8 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Carmen A. Buttler, Ramirez, Daniel, Robin D. Dowell, Edward B. Chuong · 2024 · Figshare
  44. Additional file 5 of Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis
    Kanako O. Koyanagi · 2023 · Figshare
  45. Additional file 3 of Severe COVID-19-associated variants linked to chemokine receptor gene control in monocytes and macrophages
    Bernard Stikker, Grégoire Stik, Antoinette F. van Ouwerkerk, Lianne Trap, Salvatore Spicuglia, Hendriks, Rudi W., Ralph Stadhouders · 2022 · Figshare
  46. Additional file 1 of Epigenome-wide association study detects a novel loci associated with central obesity in healthy subjects
    Ting Xie, Vesna Gorenjak, Maria G. Stathopoulou, Sébastien Dadé, Eirini Marouli, Christine Masson, Helena A. Murray, Lamont, John, Fitzgerald, Peter, Panos Deloukas et al. · 2021 · Figshare
  47. Additional file 2 of Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis
    Kanako O. Koyanagi · 2023 · Figshare
  48. Additional file 1 of sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden
    Sonia N. Acharya, Ruth V. Nichols, Lauren E. Rylaarsdam, Brendan L. O’Connell, Theodore P. Braun, Andrew Adey · 2024 · Figshare
  49. Additional file 6 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Carmen A. Buttler, Ramirez, Daniel, Robin D. Dowell, Edward B. Chuong · 2024 · Figshare
  50. Additional file 4 of Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis
    Kanako O. Koyanagi · 2023 · Figshare
  51. Additional file 1 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Carmen A. Buttler, Ramirez, Daniel, Robin D. Dowell, Edward B. Chuong · 2023 · Figshare
  52. Additional file 1 of Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis
    Kanako O. Koyanagi · 2023 · Figshare
  53. Additional file 3 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
    Carmen A. Buttler, Ramirez, Daniel, Robin D. Dowell, Edward B. Chuong · 2024 · Figshare
  54. Additional file 3 of Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis
    Kanako O. Koyanagi · 2023 · Figshare
  55. Additional file 1 of Severe COVID-19-associated variants linked to chemokine receptor gene control in monocytes and macrophages
    Bernard Stikker, Grégoire Stik, Antoinette F. van Ouwerkerk, Lianne Trap, Salvatore Spicuglia, Hendriks, Rudi W., Ralph Stadhouders · 2022 · Figshare
  56. Additional file 3 of sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden
    Sonia N. Acharya, Ruth V. Nichols, Lauren E. Rylaarsdam, Brendan L. O’Connell, Theodore P. Braun, Andrew Adey · 2024 · Figshare
  57. Additional file 4 of sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden
    Sonia N. Acharya, Ruth V. Nichols, Lauren E. Rylaarsdam, Brendan L. O’Connell, Theodore P. Braun, Andrew Adey · 2024 · Figshare
  58. Pan‐Epigenetic Age Prediction in Mammals
    Zane Koch, Adam Li, Trey Ideker · 2026 · Aging Cell
  59. Altered immune and treatment response gene expression signatures among poverty-exposed children with B-ALL
    Amy Guillaumet-Adkins, Noori Sotudeh, Sayalee V. Potdar, Tushara Vijaykumar, Monica S. Nair, Valeriya Dimitrova, Julia Frede, Yana Pikman, Marian H. Harris, Andrew E. Place et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  60. Elaboration d'une procédure standardisée d'harmonisation des données de cytométrie en flux dans le cadre d'études multicentriques
    Lucas Le Lann · 2019
  61. IRF5 and the metabolic adaptations of adipose tissue macrophages upon metabolic stress
    Lucie Orliaguet · 2022 · theses.fr (ABES)
  62. An enhancer-centric approach applied to human immune system epigenomes revealed the association of macrophage enhancers with cardiovascular disease
    Juliana Estefania Arcila-Galvis, Felipe Were, David Juan, Jose Del-Rio, Christopher Andrew Lamb, Sophie Hambleton, Antonio Castrillo, Salvatore Spicuglia, Alfonso Valencia, Inès Pineda‐Torra et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  63. The epigenetic mechanisms mediating the long-term impacts of toxicants on brain functions and health
    JANE J. PAPPAS, Rita Khoueiry, Lode Godderis, ZDENKO HERCEG · 2026 · Handbook of clinical neurology
  64. FAIRsharing record for: FAANG metadata sample specification standard
    FAIRsharing Team, Peter Harrison · 2018 · FAIRsharing.org