Epigenetics and System Biology of Stem cells and Reprogramming

Livrables

2nd Annual meeting report

Summary of 2nd annual meting

Single cell & MS technologies workshop summary

Preparation an conclusion of the Single cell & MS Technologies Workshop

final meeting report

Final EpiSyStem meeting report

3rd Annual meeting report

Summary of 3rd annual meeting

ES/iPS cells workshop summary

Preparation and conclusion of ESiPS Cell Workshop

The Jerusalem Summer School summary

Preparation and conclusion of The Jerusalem Life Science Summer School

Supervisory Board of the network

Nomination of supervisory board members

Chromatin dynamics and epigenetics course report

Preparation and conclusion of Chromatin Dynamics and Epigenetics Course

Progress report

Progress in the first year of the project.

Reprogramming and disease modelling workshop summary

Preparation and conclusion of the Reprogramming and Disease Modelling Workshop

Histone variants and genome regulation workshop summary

Preparation and conclusion of the Reprogramming and Disease Modelling Workshop

Research plan summaries

Research plan preparation and approval

Bioinformatics workshop summary

Preparation and conclusion of the Bioinformatics Workshop

Epigenetics workshop summary

Preparation and conclusion of Epigenetics Workshop

Publication in scientific journals

List of the networks publications in peerreviewed scientific journals

Outreach-activities summary

Summary of outreach activities efforts

Grant of PhD degrees

Monitoring of the PhD degrees awarded to the ESRs

1st Annual meeting report

Summary of first annual meeting

New Media activities report

Summary of the new Media disseminations activities Facebook Tweeter Instagram

Kickoff Meeting

Kickoff meeting report

Public engagement efforts

Summary of the public engagement efforts

Spetses Summer School

Co-Organisation of the Spetses Summer School with another ITN Network, ChroMe, focused on metabolism and chromatin, managed by Andreas Ladurner and Markus Buschbeck. As a part of our collaboration, we agreed to contribute at least three faculty members to participate in the Spetses summer school, and we will be sending all our ESRs there. EpiSyStem will contribute around 1K Euros for each ESR and the participating PIs will cover their own travel and accommodation expenses using the EpiSyStem budget.

International conference

Preparation and conclusion of the international conference

Project's website establishment

Setting up the Network's website

Publications

CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones

Auteurs: Danny Bavli, Xue Sun, Chen Kozulin, Dena Ennis, Alex Motzik, Alva Biran, Shlomi Brielle, Adi Alajem, Eran Meshorer, Amnon Buxboim, Oren Ram
Publié dans: Developmental Cell, Numéro 56, 2021, Page(s) 1804–1817, ISSN 1534-5807
Éditeur: Cell Press
DOI: 10.1016/j.devcel.2021.04.026

Embryonic Stem Cell Differentiation Is Regulated by SET through Interactions with p53 and β-Catenin

Auteurs: Arigela Harikumar, Patrick S.L. Lim, Malka Nissim-Rafinia, Jung Eun Park, Siu Kwan Sze, Eran Meshorer
Publié dans: Stem Cell Reports, Numéro 15/6, 2020, Page(s) 1260-1274, ISSN 2213-6711
Éditeur: Cell Press
DOI: 10.1016/j.stemcr.2020.11.004

Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins.

Auteurs: Tamar Tayri-Wilk; Moriya Slavin; Joanna Zamel; Ayelet Blass; Shon Cohen; Alex Motzik; Xue Sun; Deborah E. Shalev; Oren Ram; Nir Kalisman
Publié dans: Nature Communications, Numéro 1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-16935-w

Dppa2 and Dppa4 safeguard bivalent chromatin in order to establish a pluripotent epigenome

Auteurs: Patrick S L Lim and Eran Meshorer
Publié dans: Nature Structural & Molecular Biology, Numéro 15459993, 2020, Page(s) 685-686, ISSN 1545-9993
Éditeur: Nature Publishing Group
DOI: 10.1038/s41594-020-0453-1

The molecular and cellular features of 2-cell-like cells: a reference guide

Auteurs: Marion Genet, Maria-Elena Torres-Padilla
Publié dans: Development, Numéro 09501991, 2020, Page(s) dev189688., ISSN 0950-1991
Éditeur: The Company of Biologists Ltd.
DOI: 10.1242/dev.189688

Seizure activity and brain damage in a model of focal non‐convulsive status epilepticus

Auteurs: Diogo Vila Verde; Till S. Zimmer; Alessandro Cattalini; Marlene F Pereira; Marlene F Pereira; Erwin A. van Vliet; Giuseppe Testa; Giuseppe Testa; Vadym Gnatkovsky; Eleonora Aronica; Marco de Curtis
Publié dans: Neuropathology and applied neurobiology, Numéro 03051846, 2021, Page(s) 679-693, ISSN 0305-1846
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/nan.12693

Identifying Readers for (hydroxy)methylated DNA Using Quantitative Interaction Proteomics: Advances and Challenges Ahead.

Auteurs: Velin Marita Sequeira; Michiel Vermeulen
Publié dans: Journal of Molecular Biology, Numéro 00222836, 2020, Page(s) 1792-1800, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2019.12.014

Dosage analysis of the 7q11.23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication

Auteurs: Matteo Zanella, Alessandro Vitriolo, Alejandro Andirko, Pedro Tiago Martins, Stefanie Sturm, Thomas O’Rourke, Magdalena Laugsch, Natascia Malerba, Adrianos Skaros, Sebastiano Trattaro, Pierre-Luc Germain, Marija Mihailovic, Giuseppe Merla, Alvaro Rada-Iglesias, Cedric Boeckx, Giuseppe Testa
Publié dans: Science Advances, Numéro 5/12, 2019, Page(s) eaaw7908, ISSN 2375-2548
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/sciadv.aaw7908

Organization of the Pluripotent Genom

Auteurs: Patrick S.L. Lim and Eran Meshorer
Publié dans: Cold Spring Harbor Perspectives in Biology, Numéro 19430264, 2021, Page(s) a040204, ISSN 1943-0264
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1101/cshperspect.a040204

Esrrb is a cell-cycle-dependent associated factor balancing pluripotency and XEN differentiation

Auteurs: Sapir Herchcovici Levy, Sharon Feldman Cohen, Lee Arnon, Shlomtzion Lahav, Muhammad Awawdy, Adi Alajem, Danny Bavli, Xue Sun, Yosef Buganim, and Oren Ram
Publié dans: Stem Cell Reports, Numéro 22136711, 2022, Page(s) 1334–1350, ISSN 2213-6711
Éditeur: Cell Press
DOI: 10.1016/j.stemcr.2022.04.016

CloneSeq - Single-cell clonal 3D culture and analysis protocol

Auteurs: Xue Sun, Danny Bavli, Chen Kozulin, Alex Motzik, Amnon Buxboim, Oren Ram
Publié dans: STAR Protocols, Numéro 26661667, 2021, Page(s) 100794, ISSN 2666-1667
Éditeur: Elsvier
DOI: 10.1016/j.xpro.2021.100794

High-throughput total RNA sequencing in single cells using VASA-seq

Auteurs: Fredrik Salmen , Joachim De Jonghe , Tomasz S Kaminski, Anna Alemany, Guillermo E Parada, Joe Verity-Legg, Ayaka Yanagida, Timo N Kohler, Nicholas Battich, Floris van den Brekel, Anna L Ellermann, Alfonso Martinez Arias, Jennifer Nichols, Martin Hemberg, Florian Hollfelder, Alexander van Oudenaarden
Publié dans: Nature Biotechnology, Numéro 10870156, 2022, ISSN 1087-0156
Éditeur: Nature Publishing Group
DOI: 10.1038/s41587-022-01361-8

Delineating the heterogeneity of matrix-directed differentiation toward soft and stiff tissue lineages via single-cell profiling

Auteurs: Shlomi Brielle, Danny Bavli, Alex Motzik, Yoav Kan-Tor, Xue Sun, Chen Kozulin, Batia Avni, Oren Ram, and Amnon Buxboim
Publié dans: PNAS, Numéro 00278424, 2021, Page(s) 118 (19) e2016322118, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2016322118

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