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Inference in biological systems

01TYLPF

A.A. 2021/22

2021/22

Inference in biological systems

The course provides an introduction to molecular biology and to quantitative methods that can be used to extract information from complex biological systems, including the analysis of DNA, RNA and protein sequences, the reconstruction of phylogenetic trees, and the use of machine-learning techniques to analyze the structure of gene and protein networks.

Inference in biological systems

The course provides an introduction to quantitative methods allowing to extract meaningful information from complex biological systems. These include the analysis of DNA, RNA and protein sequences, the reconstruction of phylogenetic trees, and the study of the cell inner workings via quantitative models of gene regulation, cell compartimentalization and metabolism.

Inference in biological systems

• understanding basics notions of molecular biology; • understanding basic approaches to sequence alignment; • being familiar with structural inference and maximum entropy techniques; • being able to code simple sequence-alignment algorithms; • being able to apply basic machine-learning methods to given genetic and biological problems.

Inference in biological systems

Students will become acquainted with basic notions of molecular biology, probabilistic approaches to sequence alignment and inference of protein structures, and physical modeling of cell functions.

Inference in biological systems

Basics of probability theory, principles of statistical physics, basic programming skills (any language).

Inference in biological systems

Basics of probability theory, principles of statistical physics, basic programming skills.

Inference in biological systems

• Introduction to Molecular Biology: central dogma, DNA, RNA, proteins; gene regulation; metabolism; (20 h, C. Bosia) • Hidden Markov models: from pairwise to multiple sequence alignments; inference in protein families; phylogeny reconstruction; RNA folding; (20 h, A. Gamba) • Machine learning techniques: introduction to widely used methodologies (e.g. neural networks, random forests, convolution neural networks, Bayesian neural networks, recurrent neural networks, LSTM); application to genetic and biological studies; (20 h, E. Ficarra).

Inference in biological systems

• Elements of molecular biology: DNA, RNA, proteins. • Inference techniques: sequence alignments, structural inference, phylogeny reconstruction. • Physical biology of the cell: gene regulation, cell compartments, vesicle trafficking, metabolism.

Inference in biological systems

Inference in biological systems

Inference in biological systems

The course alternates lectures on theoretical topics (approximately 45 hours) and hands-on computer lab (approximately 15 hours), where the students will be asked to apply theoretical ideas and algorithms to selected problems.

Inference in biological systems

The course alternates lectures on theoretical topics (approximately 48 hours) and hands-on computer lab (approximately 12 hours), where the students will be invited to apply theoretical ideas and algorithms to selected problems.

Inference in biological systems

• Course handouts • B. Alberts et al., Molecular Biology of the Cell, Garland Science, 2015 • R. Durbin et al., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge Un. Press, 2002 • H.C. Nguyen, R. Zecchina and J. Berg, Inverse statistical problems: from the inverse Ising problem to data science, Adv. Phys., 66 (2017) 197-261. • S. Cocco et al., Inverse statistical physics of protein sequences: a key issues review, Rep. Progr. Phys. 81 (2018) 032601. • J. Felsenstein, Inferring phylogenies, Sinauer Associates, 2004 • C.M. Bishop, Pattern Recognition and Machine Learning, Springer, 2011 • Suggested scientific publications

Inference in biological systems

• Course handouts • R. Phillips et al, Physical Biology of the Cell, Garland Science, 2012 • P. Nelson, Biological physics, Freeman, 2004 • M. Kardar and L. Mirny, Statistical Physics in biology, MIT OpenCourseWare 8.592J / HST.452J • B. Alberts et al., Molecular Biology of the Cell, Garland Science, 2015 • R. Durbin et al., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge Un. Press, 2002 • H.C. Nguyen, R. Zecchina and J. Berg, Inverse statistical problems: from the inverse Ising problem to data science, Adv. Phys., 66 (2017) 197-261. • S. Cocco et al., Inverse statistical physics of protein sequences: a key issues review, Rep. Progr. Phys. 81 (2018) 032601. • J. Felsenstein, Inferring phylogenies, Sinauer Associates, 2004 • Suggested scientific publications

Inference in biological systems

Modalità di esame: Prova orale obbligatoria;

Inference in biological systems

The oral test will consist of 2-3 broad questions on the main topics of the lectures. The individual project will consist of the application of computational and machine-learning techniques to a given biological problem, and will be presented as ppt slides in an oral discussion. The grading of the project will contribute to 1/3 of the overall assessment.

Inference in biological systems

Exam: Compulsory oral exam;

Inference in biological systems

The oral test will consist of the in-depth presentation of a scientific work chosen by the Student among those discussed in the course and uploaded in the 'Material' section of the course site (or among other works otherwise related to the topics of the course), and of 2-3 broad questions on the main topics of the lectures. The grading of the presentation will contribute to 1/3 of the overall assessment (the maximum grade being 30L). The purpose of the exam will be to verify the Student's understanding of basic notions of molecular biology, probabilistic approaches to sequence alignment and inference of protein structures, and physical approaches to the modeling of cell functions.

Inference in biological systems

Modalità di esame: Prova orale obbligatoria;

Inference in biological systems

The oral exam will consist of 2-3 broad questions on the main topics of the lectures.

Inference in biological systems

Exam: Compulsory oral exam;

Inference in biological systems

The oral test will consist of the in-depth presentation of a scientific work chosen by the Student among those discussed in the course and uploaded in the 'Material' section of the course site (or among other works otherwise related to the topics of the course), and of 2-3 broad questions on the main topics of the lectures. The grading of the presentation will contribute to 1/3 of the overall assessment (the maximum grade being 30L). The purpose of the exam will be to verify the Student's understanding of basic notions of molecular biology, probabilistic approaches to sequence alignment and inference of protein structures, and physical approaches to the modeling of cell functions.

Inference in biological systems

Modalità di esame: Prova orale obbligatoria;

Inference in biological systems

La prova orale prevede 2 o 3 domande di carattere generale sugli argomenti del corso.

Inference in biological systems

Exam: Compulsory oral exam;

Inference in biological systems

The oral test will consist of the in-depth presentation of a scientific work chosen by the Student among those discussed in the course and uploaded in the 'Material' section of the course site (or among other works otherwise related to the topics of the course), and of 2-3 broad questions on the main topics of the lectures. The grading of the presentation will contribute to 1/3 of the overall assessment (the maximum grade being 30L). The purpose of the exam will be to verify the Student's understanding of basic notions of molecular biology, probabilistic approaches to sequence alignment and inference of protein structures, and physical approaches to the modeling of cell functions.

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