CBsem

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

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

Date Speakers Seminar subject
09 Sep 2020 A.K. Shaytan organizational Notes, planning
16 Sep 2020 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
23 Sep 2020 A. Osipova
D. Kozhevnikova
Sophomore summer practice: Modeling of nucleosome with SIN-mutations
Sophomore summer practice: MNase-seq analysis
30 Sep 2020 G. Timokhin Science news
Micro-C analysis by Dovetail Genomics
7 Oct 2020 K. Tarasov
A. Gribkova
Science news
JC: Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding
14 Oct 2020 J. Pospelova JC: Overwiew on histone dynamics
21 Oct 2020 G. Timokhin JC: The 3D genome today
28 Oct 2020 F. Pavlov (HSE) Recognition of DNA Secondary Structures as Nucleosome Barriers with Deep Learning Methods
4 Nov 2020 a national holiday in Russia  
11 Nov 2020 P. Zaytsev Microalgae
18 Nov 2020 TBA TBA
25 Nov 2020 A.Gribkova JC: Prediction of liquid-liquid phase separation proteins using machine learning
2 Dec 2020 TBA TBA
9 Dec 2020 TBA TBA
16 Dec 2020 TBA TBA
23 Dec 2020 TBA TBA

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 2019 A.K. Shaytan, G. Armeev organizational notes
20 Nov 2019 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 2019 A.K. Shaytan, G. Armeev Science News; R and Statistica, newton.bioeng: notes for users
4 Dec 2019 R.Novikov / G. Timokhin Science News / New methods in 3D-genomics, Cohesin in epigenetics, loop extrusion hypothesis
11 Dec 2019 A.Galkevich / K. Tarasov Science News / Electron paramagnetic resonance (EPR) and lipids
18 Dec 2019 K. Tarasov / G. Timokhin Science News / Topological data analysis
25 Dec 2019 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 2019 A.K.Shaytan organizational notes, planning
12 Mar 2019 A.K.Shaytan / A. Greshnova ref letter writing / Intro to CRISPR-Cas systems
19 Mar 2019 P. Kos, Faculty of Physics PHD thesis talk
26 Mar 2019 A. Kniga Updates on modeling proteins with Rosetta
2 Apr 2019 A. Kniazeva Lomonosov Universiade practice talk on modeling histone H2A-H2B plasticity
16 Apr 2019 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