Venue: Room 542, 5th floor, Lab Builiding B, Leninskie Gory 1, building 73.
E-mail listserv: CBsem@googlegroups.com
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| Date | Speakers | Seminar subject |
|---|---|---|
| 23 May | N.B. Gudimchuk (Physics Department, MSU) | Dynamics of microtubules and mechanisms of chromosome transport during cell division |
| 6 May | D.Kozhevnikova, N. Kosarim | Bachelor and Master theses |
| 29 Apr | A. Sharyafetdinova | JC: Effect of histone tails on binding to regulatory proteins |
| 15 Apr | G. Timokhin | Involvement of Z-DNA in the organization of chromatin architecture and epigenetic regulation |
| 8 Apr | L. Singh-Palchevskaya | JC: Structural and functional features of archaeal and viral histones |
| 1 Apr | N. Kosarim | Progress report |
| 25 March | A. Knyazeva | Progress report: Histone plasticity in MD simulations |
| 18 March | A. Gribkova | JC: Short H2A histone variants are expressed in cancer |
| 11 March | G. Timokhin G. Vykhodtsev |
Progress report: Progress report: Modeling different forms of DNA |
| 4 March | A.K. Shaytan | organizational |
| 25 Feb | N.Kosarim D.Kozhevnikova |
Progress report: Analyzing the Influence of Monovalent Cations Type on the Structure and Dynamics of Nucleosome Linker Region Prgress report: Development of methods for analyzing next-generation sequencing data in experiments on lentiviral transduction of mesenchymal stem cells |
| 18 Feb | G.A. Armeev | Voila Dashboards for quick prototyping |
| 11 Feb | A.K. Shaytan | organizational Notes, planning |
| Date | Speakers | Seminar subject |
|---|---|---|
| 26 Apr | Bachelor thesis practice talk | |
| 21 Apr | E. Bogdanova | Progress report: Expansion of the set of sequences of microbial rhodopsins by their artificial analogs |
| 31 March | L.Singh | Progress report: Classification of histone variants |
| 24 March | N.Kristovsky A. Kniazeva |
Status review: Efficiency evaluation of Forster resonance energy transfer by molecular modelling Status review: Molecular dynamics mechanisms of canonical and H2A.Z-nucleosomes |
| 17 March | G. Timokhin P. Burmistrov |
Status review: Integrative modeling of chromatin at the supranucleosomal level Status review: Modeling the 3D structure of D. melanogaste chromatin |
| 10 March | A. Greshnova R. Novikov |
Status review: Evolutionary potential of transcription factors for regulatory rewiring Status review: Design of a nucleic acid biosensor based on two dCas9 proteins |
| 3 March | A.Gribkova | PTM readers: Chromodomains |
| 24 Feb | P.Burmistrov | Topological polymorphism of nucleosome fibers and folding of chromatin |
| 17 Feb | A.K. Shaytan | organizational Notes, planning |
| Date | Speakers | Seminar subject |
|---|---|---|
| 23 Dec | Galina viryasova (A.N. Belozersky Institute Of Physico-Chemical Biology) | The role of chromatin remodeling complexes on the example of blood cell differentiation |
| 16 Dec | canceled | |
| 9 Dec | Nils Krietenstein (University of Massachusetts Medical School) | The Organization of the Genome: From Beads-on-a-String to Chromosome Folding |
| 2 | canceled | |
| 25 Nov | D. Kozhevnikova | JC: Genomic Nucleosome Organization Reconstituted with Pure Proteins |
| 18 Nov | G. Vykhodtsev | Snf2 remodeler |
| 11 Nov | P. Zaytsev | JC: Towards the construction of the artificial microbial consortia |
| 4 Nov | a national holiday in Russia | |
| 28 Oct | F. Pavlov (HSE) | Recognition of DNA Secondary Structures as Nucleosome Barriers with Deep Learning Methods |
| 21 Oct | G. Timokhin | JC: The 3D genome today |
| 14 Oct | J. Pospelova | JC: Overwiew on histone dynamics |
| 7 Oct | K. Tarasov A. Gribkova |
Science news JC: Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding |
| 30 Sep | G. Timokhin | Science news Micro-C analysis by Dovetail Genomics |
| 23 Sep | A. Osipova D. Kozhevnikova |
Sophomore summer practice: Modeling of nucleosome with SIN-mutations Sophomore summer practice: MNase-seq analysis |
| 16 Sep | A. Minakov G. Vykhodtesv |
Sophomore summer practice: Analysis oh histone mutations Sophomore summer practice: Modeling of the influence of Snf2 remodeler on nucleosome conformational mobility |
| 09 Sep | A.K. Shaytan | organizational Notes, planning |
| Date | Speakers | Seminar subject |
|---|---|---|
| 11 Mar 2020 | A.K. Shaytan | organizational notes, planning |
| 25 Mar 2020 | K. Tarasov L. Singh |
Science news Journal club: Histone variants and isoforms |
| 1 Apr 2020 | A. Neugodov E. Bogdanova |
April Fool’s Day Science news Master thesis: Protein secondary structure prediction with branched deep convolutional neural network |
| 8 Apr 2020 | G. Timokhin M. Chernykh |
Science news Master thesis: Modeling of targeted interaction of BeM9 toxin with voltage-gated sodium channels |
| 15 Apr 2020 | A. Galkevich A. Greshnova |
Science news JC: Robustness and evolvability in living systems #1 |
| 22 Apr 2020 | A. Greshnova K. Tarasov |
JC: Robustness and evolvability in living systems #2 Progress report: Computer modelling of lipodisks |
| 29 Apr 2020 | A. Kniazeva G. Timokhin |
Science news JC: DNA computing |
| 6 May 2020 | A. Gribkova R. Novikov |
JC: SWI/SNF – PRC2 Antagonism and Its Importance in Cancer Progress report: Analysis of peptide interactions with nucleosome acidic patch #1 #2 |
| 13 May 2020 | J.Pospelova A. Neugodov |
Science news Bachelor thesis: Phyletic distribution of histone variants in eukaryotic organisms |
| 20 May 2020 | R. Novikov A. Kniazeva |
Science news JC: Single-Molecule FRET Studies Using Multiparameter Fluorescence Detection #1 |
| 27 May 2020 | A. Greshnova A. Kniazeva |
Science news JC: Single-Molecule FRET Studies Using Multiparameter Fluorescence Detection #2 |
| 3 June 2020 | K. Tarasov A. Neugodov |
Science news Bachelor thesis: Phyletic distribution of histone variants in eukaryotic organisms #2 |
| 10 June 2020 | J. Pospelova G. Timokhin |
Science news JC: Hi-C data to physical distances |
| 17 June 2020 | A. Shaytan | Q&A |
| 24 June 2020 | P.Burmistrov | TBA |
| Date | Speaker(s)/Seminar subject | Notes |
|---|---|---|
| 13 Nov | A.K. Shaytan, G. Armeev | organizational notes |
| 20 Nov | G. Timokhin / A. Kniazeva | Science News: Hydrophobic stabilization of DNA helix, Prime genome editing, R-loops, histone lactylation, correlation of thermodynamic and information entropies / Journal club: review on Bowman G.D. articles about remodelers |
| 27 Nov | A.K. Shaytan, G. Armeev | Science News; R and Statistica, newton.bioeng: notes for users |
| 4 Dec | R.Novikov / G. Timokhin | Science News / New methods in 3D-genomics, Cohesin in epigenetics, loop extrusion hypothesis |
| 11 Dec | A.Galkevich / K. Tarasov | Science News / Electron paramagnetic resonance (EPR) and lipids |
| 18 Dec | K. Tarasov / G. Timokhin | Science News / Topological data analysis |
| 25 Dec | L. Singh | Journal club: Histone variants and isoforms |
| Date | Speaker(s)/Seminar subject | Notes |
|---|---|---|
| 5 Mar | A.K.Shaytan | organizational notes, planning |
| 12 Mar | A.K.Shaytan / A. Greshnova | ref letter writing / Intro to CRISPR-Cas systems |
| 19 Mar | P. Kos, Faculty of Physics | PHD thesis talk |
| 26 Mar | A. Kniga | Updates on modeling proteins with Rosetta |
| 2 Apr | A. Kniazeva | Lomonosov Universiade practice talk on modeling histone H2A-H2B plasticity |
| 16 Apr | G. Armeev | Report on Les Houches chromatin conference, program here |
| Date | Speaker(s)/Seminar subject | Notes |
|---|---|---|
| 3 Oct 2018 | A.K.Shaytan, G. Armeev | organizational notes, RACIRI presentation, maths discussion |
| 10 Oct 2018 | A. Kniga/ I. Yaroshevich | “Rosetta: making a model of apartate-N-acetyltпостроение модели аспартат-N-ацетилтрансферазы”/Quantum mechanics … |
| 17 Oct 2018 | Y. Pospelova | Force fields in MD simulations + report on Nobel Prizes 2018 |
| 24 Oct 2018 | E. Andreeva | New software for MD topology design automation: GIFTED |
| 31 Oct 2018 | G. Armeev | PHD thesis practice talk: Integrative modeling of nucleosomes |
| 7 Nov 2018 | A. Osipova + A. Neugodov | Intro into Epigenetics |
| 14 Nov 2018 | Dr. Ivan Gushchin, MIPT | X-ray crystallography |
| 21 Nov 2018 | Arthur Zalevskiy, FBB | Peptide design using molecular modeling |
| 28 Nov 2018 | iGEM discussion, A. Shaytan, A. Greshnova | |
| 5 Dec 2018 | R. Novikov | Book club |
| 12 Dec 2018 | A. Knyazeva | Free energy calculation in MD, Into to Plumed |
| 19 Dec 2018 | A. Shaytan | Writing manuscripts and theses |
| 26 Dec 2018 |
| Date | Speaker(s)/Seminar subject | Notes |
|---|---|---|
| 13 Feb 2018 | A.K.Shaytan | organizatinonal notes, plans for 2018, notes on careers in science and R&D project management. |
| 20 Feb 2018 | Jypyter notebooks | notes |
| 27 Feb 2018 | армеев | |
| 6 March 2018 | Настя Огиенко про iGEM + Армеев | |
| 13 March 2018 | Книга | |
| 20 March 2018 | Обсуждение практикума по синтетической биологии | |
| 27 March 2018 | Армеев spFRET | презентация |
| 3 April 2018 | Тарасов | |
| 10 April 2018 | ||
| 17 April 2018 | Сидоренко | Сопроводительный документ |
| 24 April 2018 | Грибкова | презентация |
| 8 May 2018 | отменен | |
| 15 May 2018 | отменен | |
| 22 May 2018 | Басс+ Новиков | |
| 29 May 2018 | отменен | |
| 5 June 2018 | Поспелова | презентация |
| 19 June 2018 | Князева | |
| 26 June 2018 | Грибкова+Андреева | |
| 3 July 2018 | ||
| 10 July 2018 |
