seminar

Lab seminar on computational and integrative biology (V.N. Novoseletsky, A.K. Shaytan)

Organisational details

Venue: Room 542, 5th floor, Lab Builiding B, Leninskie Gory 1, building 73.
E-mail listserv: CBsem@googlegroups.com
To be added to the mailing list send request via the link https://groups.google.com/forum/#!forum/CBsem/join

Spring 2021 plan (Wednesday, 4:00 PM Online)

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

Fall 2020 plan (Wednesday, 4:00 PM Online)

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. Vykhodtesv 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

Spring 2020 plan (Wednesday, 4:00 PM room 543, Lab building B)

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

Fall 2019 plan (Wednesday, 4:00 PM room 542, Lab building B)

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

Spring 2019 plan (Tuesday, 6:00 PM room 542, Lab building B) (tentative schedule)

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

Fall 2018 plan (Wednesday, 4:30 PM room 542, Lab building B)

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    

Spring 2018 plan (Tuesdays 6PM room 542, Lab building B)

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