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BIO390 - Introduction to Bioinformatics

Summary

The handling and analysis of biological data using computational methods has become an essential part in most areas of biology. In this lecture, students will be introduced to the use of bioinformatics tools and methods in different topics, such as molecular resources and databases, standards and ontologies, sequence and high performance genome analysis, biological networks, molecular dynamics, proteomics, evolutionary biology and gene regulation. Additionally, the use of low level tools (e.g. Programming and scripting languages) and specialized applications will be demonstrated. Another topic will be the visualization of quantitative and qualitative biological data and analysis results.

Practical Information

  • Autumn semesters
  • 1 x 2h / week
  • Tue 08:00-09:45
  • UZH Irchel campus, Y03-G-85
  • OLAT - but not much there...
  • KALTURA for lecture recordings
    • videos are posted with some delay due to editing etc.
  • Course language is English

Some very approximate learning goals may provide you with additional guidance - but plese be aware that those may not be particularly adjusted to a given course edition.

For entries of previous lectures please scroll down to the previous entries.

Previous

BIO390 Repeat Exam

BIO390 UZH HS22 - Introduction to Bioinformatics

The repeat exam will be on January 24, 2023:

  • time: 10:15-11:45
  • Y03-G-85 (normal lecture hall, unless noted of change)
  • multiple (single + multiple) choice w/ one or two open questions
  • no material, phones etc.
  • student ID for entrance
  • please refer to the learning goals for guidance
    • ¡topics may be edited throughout the course!
    • these just provide some non-exclusive guidance
Continue reading

BIO390 Exam

BIO390 UZH HS22 - Introduction to Bioinformatics
08:15-09:45 @ UZH Irchel Y03-G-85

The exam will be on the last day of the course on site:

  • time: 08:15-09:45
  • ¡¡¡ NEW: Room change to Y15-G-20 !!!
  • multiple (single + multiple) choice w/ one or two open questions
  • no material, phones etc.
  • student ID for entrance
  • please refer to the learning goals for guidance
    • ¡topics may be edited throughout the course!
    • these just provide some non-exclusive guidance
Continue reading

Genomic Data Risks & Opportunities

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Michael Baudis

The understanding of the impact of inherited and somatic genome variants on phenotypes and diseases requires a thorough understanding of such variants amongst populations in general and carriers of the phenotypes and diseases in particular. Such information can only be provided through the inclusion of data from a multitude of genome resources in variant evaluation efforts, including such from outside (international) jurisdictions. However, opening such resources carries the inherent risk of breaching privacy, particularly through re-identification of individuals or their relatives and potentially through the exposure of individual genome-related personal information including phenotypic and "performance" prediction and relative disease risk.

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Clinical Bioinformatics

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Valerie Barbie (Director SIB Clinical Bioinformatics)

Medical practice is undergoing a revolution around personalized health: this major change is driven by the continuous development of cost-effective high-throughput technologies that produce gigantic quantities of data in numerous areas, from imaging to genomics, and of the corresponding tools required to process these data.

Continue reading

Building a Genomics Resource

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Michael Baudis

In this lecture we will use our Progenetix resource, a website providing information about genomic copy number mutations in cancer - to present the different components needed for generating, storing, representing, visualizing and accessing a specific type of genomic data and associated classifications.

Continue reading

Components of the Semantic web

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Ahmad Aghaebrahimian (ZHAW)

Biomedical science is rich in structured and unstructured textual data including but not limited to hundreds of ontologies as well as millions of scientific publications. Semantic web and its stack of standards provide an efficient way for organizing knowledge extracted from such huge volume of data. Modeling data in knowledge graphs makes complex question answering and reasoning over abundance of information manageable and feasible. In this session we will find out how.

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Text Mining and Search Strategies

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Patrick Ruch (HES-SO/HEG Geneva)

Search engines, stemming, NGRAMs ... and much more.

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Biological Networks

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Pouria Dasmeh

This part of the course BIO390 (Introduction to Bioinformatics) will review examples of biological networks their basic properties.

Continue reading

Proteomics

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Katja Baerenfaller, Swiss Institute of Allergy and Asthma Research (SIAF) and University of Zurich

In proteomics one of the important bioinformatics tasks is to generate lists of reliably identified peptides and proteins in mass spectrometry-based experiments. For this, amino acid sequences are assigned to measured tandem mass spectra. The quality of the peptide spectrum assignments are scored and criteria are applied that allow to distinguish the good from the bad hits and to estimate the quality of the dataset.

Continue reading

Metagenomics

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Shinichi Sunagawa (ETHZ)

Abstract:

Microorganisms are numerically dominant on Earth and drive the cycling of energy, elements and matter. Thanks to advances in high-throughput DNA sequencing technologies and computational power, microbial communities can now be studied without the need to cultivate them in a laboratory setting. Essential tasks in studying microbial communities include the identification and quantification of their member taxa and the pair-wise compositional comparison of different microbial communities.

Continue reading

Regulatory Genomics and Epigenomics

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Izaskun Mallona

Continue reading

Machine Learning for Biological Use Cases

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Valentina Boeva (ETHZ)

Brief note: In this lecture V. Boeva will cover the standard machine learning methods used in the analysis of biological data: dimensionality reduction, clustering, classification and regression.

Continue reading

Statistical Bioinformatics

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Mark Robinson

Continue reading

Biological Sequence Informatics

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Christian von Mering

The analysis of biological sequences - primarily DNA, RNA and protein sequences - constitutes one of earliest and core areas of bioinformatics. This lecture introduces principles and examples of bioinformatic sequence analyses and inter-sequence comparisons. Continue reading

What is Bioinformatics? Introduction and Resources

BIO390 UZH HS22 - Introduction to Bioinformatics
08:00-09:45 @ UZH Irchel Y03-G-85

Michael Baudis

The first day of the "Introduction to Bioinformatics" lecture series starts with a general introduction into the field and a description of the lecture topics, timeline and procedures.

Topics covered in the lecture are e.g.: Continue reading

Clinical Bioinformatics

Valerie Barbie

Medical practice is undergoing a revolution around personalized health: this major change is driven by the continuous development of cost-effective high-throughput technologies that produce gigantic quantities of data in numerous areas, from imaging to genomics, and of the corresponding tools required to process these data.

Continue reading

Building a Genomics Resource

Michael Baudis

In this lecture we will use our Progenetix resource, a website providing information about genomic copy number mutations in cancer - to present the different components needed for generating, storing, representing, visualizing and accessing a specific type of genomic data and associated classifications.

Continue reading

Biomedical Text Mining

Fabio Rinaldi

What is text mining?

The ability to process text written in some human language (unstructured data), typically a large set of documents, interpret the meaning, and automatically extract concepts, as well as the relationships among those concepts, to directly answer questions of interest.

Continue reading

Biological Networks

Pouria Dasmeh

In this part of the course BIO390 (Introduction to Bioinformatics), we review examples of biological networks, and get to know their basic properties.

Continue reading

Proteomics

Katja Baerenfaller (SIAF)

In proteomics one of the important bioinformatics tasks is to generate lists of reliably identified peptides and proteins in mass spectrometry-based experiments. For this, amino acid sequences are assigned to measured tandem mass spectra. The quality of the peptide spectrum assignments are scored and criteria are applied that allow to distinguish the good from the bad hits and to estimate the quality of the dataset.

Continue reading

Metagenomics

Shinichi Sunagawa (ETHZ)

Abstract:

Microorganisms are numerically dominant on Earth and drive the cycling of energy, elements and matter. Thanks to advances in high-throughput DNA sequencing technologies and computational power, microbial communities can now be studied without the need to cultivate them in a laboratory setting. Essential tasks in studying microbial communities include the identification and quantification of their member taxa and the pair-wise compositional comparison of different microbial communities.

Continue reading

Regulatory Genomics and Epigenomics

Izaskun Mallona

Continue reading

Machine Learning for Biological Use Cases

Valentina Boeva (ETHZ)

Brief note: In this lecture V. Boeva will cover the standard machine learning methods used in the analysis of biological data: dimensionality reduction, clustering, classification and regression.

Continue reading

Statistical Bioinformatics

Mark Robinson

Continue reading

Biological Sequence Informatics

Christian von Mering

The analysis of biological sequences - primarily DNA, RNA and protein sequences - constitutes one of earliest and core areas of bioinformatics. This lecture introduces principles and examples of bioinformatic sequence analyses and inter-sequence comparisons.

Continue reading

What is Bioinformatics? Introduction and Resources

Michael Baudis

The first day of the "Introduction to Bioinformatics" lecture series starts with a general introduction into the field and a description of the lecture topics, timeline and procedures.

Continue reading

Clinical Bioinformatics

Valerie Barbie

Medical practice is undergoing a revolution around personalized health: this major change is driven by the continuous development of cost-effective high-throughput technologies that produce gigantic quantities of data in numerous areas, from imaging to genomics, and of the corresponding tools required to process these data.

Continue reading

Proteomics

Katja Baerenfaller

In proteomics one of the important bioinformatics tasks is to generate lists of reliably identified peptides and proteins in mass spectrometry-based experiments. For this, amino acid sequences are assigned to measured tandem mass spectra. The quality of the peptide spectrum assignments are scored and criteria are applied that allow to distinguish the good from the bad hits and to estimate the quality of the dataset.

Continue reading