QBIO MASTER PROGRAM	Quantitative biology in practice

At the crossroads of Biology, Physics, Chemistry and Informatics, qbio is the master program destined for students interested in studying Biology with a quantitative perspective founded on transdisciplinary approaches.

Introduction to qbio

[TOC]

Organisation

1st semester - 5 ECTS - 40 hours in the class.

The majority of classes will not be "standard" lectures. Interaction will be privileged, and the attendants should prepare the class before the frontal lecture (see link column in the table below).

Timetable

The reference Timetable is the one on GoogleDoc. Below you can find more details for each lecture and the material you have to prepare before coming to the lecture.

Instructors

[EM = Emmanuel Margeat ; LC = Luca Ciandrini; LCo = Luca Costa ; MN = Marcelo Nollmann; PEM = Pierre-Emmanuel Milhiet; SC = Sandra Cortijo (BPMP / SupAgro); JN = Jérémie Naude (IGF)]

Rooms

The course will take place in the lecture room at the QuB (to be pronounced 'cube', which is the Algeco just outside the back entrance of the CBS29).

Slots are usually 1.5h long.

Imaging and chromatin biophysics

Date	Day	#hours	Time	Topic	Where	Who	Link
19/9	Thu	1.5	15:00-16:30	DNA origami by Julie Finkel.	CBS - QuB	Ext
26/9	Thu	1.5	13:15-14:45	Basics of Imaging (45'). Basics of image processing (45').	CBS - QuB	MN	Imaging + Basics of Image Processing
26/9	Thu	1.5	15:00-16:30	Introduction to Atomic Force Microscopy (Luca Costa).	CBS - QuB	Lco	constructList
03/10	Thu	1.5	13:15-14:50	Cohesin structure and dynamics by Thomas Robert (45'). Optical tweezers and flagellar motors by Francesco Pedaci (45').	CBS - QuB	Ext
10/10	Thu	1.5	13:15-14:50	Article (30'). Confocal microscopy (30'). TIRF (30').	CBS - QuB	MN	Article + Confocal + TIRF
17/10	Tue	1.5	15:00-16:30	Article (45'). SMLM (45').	CBS - QuB	MN	Article + SMLM
18/10	Fri	1.5	9:45-11:00	Article (45'). DNA supercoiling (45').	CBS - QuB (small)	MN	Article + DNA + DNA supercoiling
24/10	Thu	1.5	13:15-16:30	Introduction to fluorescence (EM).	CBS - QuB	EM
08/11	Fri	1.5	9:45-11:00	Article (30'). Nucleosomes and epigenetics (30'). Transcription Factors (30')	CBS - QuB	MN	Article + Nucleosomes + Epigenetics + TFs
14/11	Thu	1.5	15:00-16:30	Article (30'). Higher-order chromatin structure (30'). Loop Extrusion (30')	CBS - QuB	MN	Article + Chromatin structure + Loop extrusion
29/11	Fri	1.5	9:45-11:00	Article (45'). Multiplexing methods I (45')	CBS - QuB	MN	Article + Multiplexing microscopy

Gene regulation and modelling

Date	Day	#hours	Time	Topic	Where	Who	Link
17/9	Tue	1.5	10:30-12:00	Introduction and course organisation (30') - Modelling tools: ODE	CBS - QuB	LC	- D.J. Wilkinson, "Stochastic modelling for quantitative description of heterogeneous biological systems", Nature Reviews (2009) doi:10.1038/nrg2509 - Introductory construct - Modelling ODE
19/9	Thu	1.5	13:15-14:45	Modelling tools: Stochasticity and simulations 1	CBS - QuB	LC	- Revise Exponential distribution - Exponential distribution video - Modelling stoc
04/10	Fri	1.5	11:30-13:00	Modelling tools: Stochasticity and simulations 2	CBS - QuB (small)	LC	Modelling stoc
10/10	Thu	1.5	15:00-16:30	Gene expression and regulation	CBS - QuB	LC	Uri Alon, An introduction to systems biology, 2nd Ed. - Ch1 and Ch2
11/10	Fri	1.5	9:45-11:15	Gene regulation; Negative and positive autoregulation.	CBS - QuB	LC	2nd chapter from Uri Alon, An introduction to systems biology, 2nd Ed. - Associated notebook
22/10	Tue	1.5	10:00-11:30	Random Walks - 2D RW and macromolecules as Random Walks	CBS - QuB	LC	Read R.Phillips et al., Physical Biology of the cell, 2nd Ed. Pages 311 - 322; 127-129; (Ch13 is not compulsory, but a useful ref for the diffusion equation) - Associated notebook
	Thu	1.5	13:15-14:45	Introduction to neurophysics	CBS - QuB		Revise Ch1 from Strogaz' book - Associated notebook
	Thu	1.5	15:00-16:30	Random Walks - 2D RW and macromolecules as Random Walks	CBS - QuB
	Fri	1.5	11:30-13:00	Measuring Gene Expression from Cytometer and Plate Reader experiments	CBS - QuB	LC
	Tue	1.5	9:45-11:15	Geometric analysis of excitability	CBS - QuB	JN	Ch2 from Strogaz' book - Associated notebook
	Fri	1.5	11:30-13:00	Gene expression noise in plants	CBS - QuB	SC	Cortijo and Locke (2020)

Membrane Biophysics

Date	Day	#hours	Time	Topic	Where	Who	Link
		1.5	16:45-18:15	Introduction	CBS - QuB	PEM	Material given by email
		1.5	11:30-13:00	Imaging and spectroscopy of biological membranes	CBS - QuB (small)	PEM
		1.5	11:30-13:00	Experimental characterization of biological membranes	CBS - QuB (small)	PEM
		1.5	11:30-13:00	Probing membrane mechanics	CBS - QuB (smal;)	LCo

Evaluation

Evaluation by projects (compulsory 5*20%). Students will have to return 5 compulsory homework projects - assignments, no other exam is planned.

Assignments

Assignments given by LC should be sent to him by email (.ipynb file plus other needed material in case) by the deadline. Returning the homework with a delay will bring you a penalty.

When you send the assignment by email, please use the subject Assignment X - Intro qbio (where Xis the number of the assignment); name the file as AX_NameSurname.ipynb and put all the necessary files (datasets, images,...) in a directory named data. Then zip the files and send the archive. For instance, when Luca sends the assignment 3, he will name the file A3_LucaCiandrini.ipynb, put all data in the folder data, compress everything in a single file to be sent in a message with subject Assignment 3 - Intro qbio.

Bibliography (books only)

1. An introduction to Systems Biology, Uri Alon
2. Physical Biology of the cell, R. Phillips et al.
3. Cell biology by the numbers, R. Milo and R. Phillips
4. Biological Physics: Energy, Information, Life, Philip Nelson
5. Random Walks in Biology, Howard
6. A first course in Network Science, F. Menczer, S. Fortunato and C. A. Davis
7. Network Science,A.L Barabasi, available on line http://networksciencebook.com/