Genome Architecture and Function agenda

July, 8th 2025

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Registration / Light breakfast

Royal Hall 1

  • 08:00 - 08:15

    Registration

  • 08:15 - 08:40

    Light breakfast

08:40 - 08:45

Welcome , Opening remarks / getting organized

Royal Hall 3

08:45 - 09:05

Historical Overview of Chromatin

Royal Hall 3

Krastan Blagoev

09:05 - 10:35

The World of HiC

Royal Hall 3

Erez Aiden

10:35 - 10:45

Working Coffee Break

Royal Hall 1

Microscopy methodology

Royal Hall 3

  • 10:45 - 11:15

    SARS-CoV-2 Dynamics through the lens of SPARTACUSS

    Alexander Atemin

  • 11:15 - 11:45

    Pyfix3d: a software for fast manual correction of segmentation data

    Rumen Stamatov

  • 11:45 - 12:15

    Modelling Cell-Cell Communication using Single-cell and Spatial Transcriptomics Data

    Daniel Dimitrov

12:15 - 13:15

Lunch break

Royal Hall 1

13:15 - 14:45

Basics of Histones and Nucleosome Structure

Royal Hall 3

Jeffrey Hayes

14:45 - 15:00

Working Coffee Break

Royal Hall 1

15:00 - 16:30

Introduction to histone biology, function

Royal Hall 3

Iva Simeonova

July, 9th 2025

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08:00 - 08:30

Light Breakfast

Royal Hall 1

08:30 - 10:00

Polymer Physics Basics

Royal Hall 3

Samuele Lipani

10:00 - 10:30

Working Coffee Break

Royal Hall 1

10:30 - 12:00

From Polymers to Chromatin

Royal Hall 3

Sumitabha Brahmachari

12:00 - 13:00

Lunch break

Royal Hall 1

13:00 - 14:30

Chromatin Modeling

Royal Hall 3

Michele Di Pierro

14:30 - 14:45

Working Coffee Break

Royal Hall 1

14:45 - 16:15

Histone modifications and transcrption: A new modeling frontier

Royal Hall 3

Herbert Levine

18:00 - 20:00

Welcome Reception/Poster Session

Royal Hall 2

July, 10th 2025

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08:00 - 08:30

Light breakfast

Royal Hall 1

08:30 - 09:00

Registration

Royal Hall 1

Welcome address

Royal Hall 3

  • 09:00 - 09:05

    Welcome Address - Deputy Minister of Education and Science, Academician Nikolay Vitanov (D.Sc.)

  • 09:05 - 09:10

    Welcome Address - Vice Presient of the Bulgarian Academy of Sciences, Corresponding Member Evdokia Pasheva (D.Sc.)

09:10 - 09:35

Opening remarks

Royal Hall 3

José Onuchic, Erez Aiden

Small scale structure/function - part I

Royal Hall 3

Chair: Herbert Levine

  • 09:35 - 10:25

    Biophysical principles of genome organization across multiple scales

    Taekjip “TJ” Ha

    Talk: 40 min, QA: 10 min
  • 10:25 - 11:05

    Transcription factor dynamics in gene expression: the long and short of it

    Arpita Upadhyaya

    Talk: 30 min, QA: 10 min
11:05 - 11:25

Coffee break

Royal Hall 1

Small scale structure/function - part II

Royal Hall 3

  • 11:25 - 12:05

    Mechanochemical coupling of DNA supercoiling and transcription

    Sumitabha Brahmachari

    Talk: 30 min, QA: 10 min
  • 12:05 - 12:45

    Gene syntax defines supercoiling-mediated transcriptional feedback

    Katie Galloway

    Talk: 30 min, QA: 10 min
12:45 - 13:40

Lunch

Royal Hall 1

13:30 - 18:00

Mountain Outing

By bus

July, 11th 2025

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08:00 - 08:30

Light breakfast

Royal Hall 1

Large scale Genome Structure - part I

Royal Hall 3

Chair: Vittore Scolari

  • 08:30 - 09:10

    3D genome dynamics reveal specific patterns of phage genome dynamics and host interactions during lytic infection of Pseudomonas aeruginosa

    Martial Marbouty

    Talk: 30 min, QA: 10 min
  • 09:10 - 09:50

    Genome folding by SMC complexes: from chromatin loops to organismal phenotypes. How genome folding impacts nematode's life

    Peter Meister

    Talk: 30 min, QA: 10 min
  • 09:50 - 10:30

    Modeling Structural Ensembles of Genomes

    Vinicius Contessoto

    Talk: 30 min, QA: 10 min
10:30 - 10:50

Working coffee break

Royal Hall 1

Large scale Genome Structure - part II

Royal Hall 3

Chair: Vittore Scolari

  • 10:50 - 11:30

    The Histone H1 CTD - A Nexus for Chromatin Regulation?

    Jeffrey Hayes

    Talk: 30 min, QA: 10 min
  • 11:30 - 12:10

    Independent roles of the H3.3 chaperone HIRA in 3D genome organisation and early replication initiation

    Tina Karagyozova

    Talk: 30 min, QA: 10 min
12:10 - 13:30

Lunch Break

Royal Hall 1

Computational methods and modeling of genome architecture - part I

Royal Hall 3

Chair: José Onuchic

  • 13:30 - 14:10

    Replicating the genome in 3D: fountains, factories and more.

    Daniel Jost

    Talk: 30 min, QA: 10 min
  • 14:10 - 14:50

    For tango it takes one: polymer model reveals monomeric cohesin as the primary loop extruder

    Kirill Polovnikov

    Talk: 30 min, QA: 10 min
  • 14:50 - 15:30

    Elucidating chromatin dynamics in health and disease via in silico approaches

    Seyit Kale

    Talk: 30 min, QA: 10 min
15:30 - 16:00

Working Coffee Break

Royal Hall 1

Computational methods and modeling of genome architecture - part II

Royal Hall 3

Chair: José Onuchic

  • 16:00 - 16:40

    The roles of RNA in gene regulation and nuclear condensation

    Krishna Shrinivas

    Talk: 30 min, QA: 10 min
  • 16:40 - 17:20

    Diploid analysis using Hi-C

    Olga Dudchenko

    Talk: 30 min, QA: 10 min
19:00 - 21:00

Conference Dinner

Shtastliveca restaurant

July, 12th 2025

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08:00 - 08:30

Light breakfast

Royal Hall 1

Emerging Applications

Royal Hall 3

Chair: Krastan Blagoev

  • 08:40 - 09:20

    3D organization of the nucleus in lymphomas

    Yegor Vassetzky

    Talk: 30 min, QA: 10 min
  • 09:20 - 10:00

    Chromatin dynamic changes during eukaryote cell cycle

    Martin Rey-Millet

    Talk: 30 min, QA: 10 min
  • 10:00 - 10:40

    Nanoscale Structure of a Transcriptional Condensate

    Kalon Overholt

    Talk: 30 min, QA: 10 min
10:40 - 11:00

Working Coffee Break

Royal Hall 1

DNA Repair - part I

Royal Hall 3

  • 11:00 - 11:40

    Probing native mitotic chromosome structure with optical tweezers and AFM

    Christian Nielsen

    Talk: 30 min, QA: 10 min
  • 11:40 - 12:20

    Pairing time-lapse super-resolution microscopy with deep learning to track chromosome dynamics

    Rumen Stamatov

    Talk: 30 min, QA: 10 min
  • 12:20 - 13:00

    Cohesin Complex Oligomerization Maintains End-Tethering at DNA Double-Strand Breaks

    Karine Dubrana

    Talk: 30 min, QA: 10 min
13:00 - 14:10

Lunch break

Royal Hall 1

DNA Repair - part II

Royal Hall 3

Chair: Stoyno Stoynov

  • 14:10 - 14:50

    Modelling disease in the mouse: H3 histone variants and cellular programs during development

    Iva Simeonova

    Talk: 30 min, QA: 10 min
  • 14:50 - 15:30

    Nucleophagy removes cytotoxic DNA lesions to prevent genomic instability: Implications for cancer therapy

    Kristijan Ramadan

    Talk: 30 min, QA: 10 min