Bioinf-l

bioinf-l@kam.mff.cuni.cz

63 discussions

Lecture invitation: Disease maps: building and analysing graphical models of biomedical knowledge
by Petr Danecek 20 Mar '23

20 Mar '23

Dear all, the next seminar will take place on Wednesday, please see the details below. We look forward to seeing you all! Title: Disease maps: building and analysing graphical models of biomedical knowledge Speaker: Marek Ostaszewski, Luxembourg Centre for Systems Biomedicine Date and time: Wednesday 22/3/2023 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S3 https://bioinformatika.mff.cuni.cz/seminar/ Best wishes, Petr Danecek ------------------------------- *Marek Ostaszewski* */Disease maps: building and analysing graphical models of biomedical knowledge/* Disease maps encode knowledge about molecular pathophysiology in both visual and computational format, helping interdisciplinary exchange between bench scientists, clinical researchers and bioinformaticians. In this talk I’ll introduce the concept based on the example of Parkinson’s disease map and demonstrate it as a tool for visual exploration, analytics and investigating complex data. Then, I’ll describe the evolution of the approach and how it was picked up by a broader research community leading to a large-scale effort to build the COVID-19 Disease Map.

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Lecture invitation: Building complex bioinformatics pipelines using Snakemake
by Petr Danecek 06 Mar '23

06 Mar '23

Dear all, the next seminar will take place on Wednesday, please see the details below. We look forward to seeing you all! Title: Building complex bioinformatics pipelines using Snakemake Speaker: Joern Gerchen Date and time: Wednesday 8/3/2023 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S3 https://bioinformatika.mff.cuni.cz/seminar/ Best wishes, Petr Danecek ---------------- *Joern Gerchen: /Building complex bioinformatics pipelines using Snakemake/* Polyploidy, the presence of multiple genome copies as a result of whole-genome-duplications, is often thought to cause immediate repruductive isolation between polyploids and diploid relatives, due to inviability and sterility of hybrid offspring. However, recent research showed evidence of introgression (gene-flow via hybridization and backcrossing) between diploid and polyploid lineages. In this seminar I will introduce my PostDoc project, which uses population genomic analyses to quantify the degree of introgression between multiple natural plant lineages with variable ploidy and assess to what degree it can contribute to adaptive evolution. In order to determine the degree of inter-ploidy introgression, variant calling and subsequent population genomic analyses have to be run for each non-model species in a ploidy-aware manner. These analyses require complex custom bioinformatics pipelines, which have to be run repeatedly for multiple lineages on HPC computing clusters. Implementing and running these types of workflows in an efficient and reproducible manner can be challenging. As an approach to overcome these issues I will introduce Snakemake, which allows to implement automated, scalable and reproducible bioinformatics workflows.

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Lecture invitation: Functionalizing the cancer genome base-by-base with CRISPR editing and computational tools
by Petr Danecek 02 Dec '22

02 Dec '22

Dear all, the next seminar will take place next week, please see the details below. We look forward to seeing you all! Title: Functionalizing the cancer genome base-by-base with CRISPR editing and computational tools Speaker: Victoria Offord, WSI Date and time: Wednesday 7/12/2022 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S6 http://bioinformatics.cuni.cz/seminar Best wishes, Petr Danecek ------------------------------- Victoria Offord /Functionalizing the cancer genome base-by-base with CRISPR editing and computational tools/* * Over the last decade, the reduction in costs for high throughput technologies has enabled us to sequence more human genomes than ever before. We can see this in the rapid expansion of the repositories used to store and share genetic data amongst researchers. To date, over 1.5 million variants have been submitted to ClinVar, a public database of clinically relevant variants. However, over 50% of these are variants of uncertain significance (VUS) for which we have no clear interpretation of their function. Multiplexed Assays of Variant Effect (MAVEs) can be used to generate variant effect maps, which, over time, may be used to aid clinical interpretations. Saturation genome editing (SGE) is a CRISPR-based MAVE which allows us to test all possible single- and multi-nucleotide or amino acid variations across a genomic region. We’ll discuss SGE, the community, available resources, tools being developed and how the data that we’ve been generating may go on to aid in the interpretation of VUS.

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Lecture invitation: AlphaFold DB, Increasing the structure coverage of the sequence space by a thousand times
by Petr Danecek 18 Nov '22

18 Nov '22

Dear all, the next seminar will take place next week, please see the details below. We look forward to seeing you all! Title: AlphaFold DB, Increasing the structure coverage of the sequence space by a thousand times Speaker: Mihaly Varadi, EMBL Date and time: Wednesday 23/11/2022 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S6 https://bioinformatika.mff.cuni.cz/seminar/ Best wishes, Petr Danecek ------------------------------- *Mihaly Varadi* */AlphaFold DB: Increasing the structure coverage of the sequence space by a thousand times/* I will give a brief introduction about why (predicted) protein structures can be useful, and then talk briefly about how the protein structure prediction field grew over the years. I will also talk about AlphaFold, its strengths and weaknesses, and explain the various types of output coming from the AI, in particular about the various confidence measures. Then I'll talk about the database (what types of data, what technology, how to access the data) and then briefly about the place of AlphaFold DB in the wider context of other predicted protein structure providers and initiatives such as the 3D-Beacons.

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Lecture invitation: Measures of quality of clusters in hierarchical clustering of flow cytometry data
by Petr Danecek 14 Oct '22

14 Oct '22

Dear all, the next seminar will take place next week, please see the details below. We look forward to seeing you all! Title: Measures of quality of clusters in hierarchical clustering of flow cytometry data Speaker: Tomáš Sieger Date and time: Wednesday 19/10/2022 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S6 https://bioinformatika.mff.cuni.cz/seminar/ Best wishes, Petr Danecek ---------------- *Tomáš Sieger: **/Measures of quality of clusters in hierarchical clustering of flow cytometry data/* Hierarchical clustering enables unsupervised analysis of multidimensional data, yielding a dendrogram, a hierarchical tree of clusters of data samples. However, the dendrogram does not readily specify the quality of individual clusters in it. In the lecture, we will show measures of quality of clusters in hierarchical clustering, developed in our group, that can be used to guide selection of meaningful clusters in flow cytometry data. The new unsupervised method enables automated processing of large amounts of data without a need of costly and subjective manual intervention. In future, we need to study the general applicability of our measures of cluster quality and validate them on other data sets.

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lecture invitation: Sequence space and protein functional classification
by Petr Danecek 03 May '22

03 May '22

Dear all, the next seminar will take place this Wednesday, please see the details below. We look forward to seeing you all! Best wishes, Petr Danecek Date and time: Wednesday 20/04/2022 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S6 https://bioinformatika.mff.cuni.cz/seminar/ Title: Sequence space and protein functional classification Speaker: Alessandra Carbone Affiliation: Department of Computational and Quantitative Biology, Sorbonne University Abstract: Functional classification of proteins from sequences alone has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of the evolution of living organisms and for biotechnological applications. In this talk, I will explain how rethinking the sequence space with multiple profile models leads to the functional classification of proteins. I will present ProfileView, a sequence-based computational method designed to functionally classify sets of homologous sequences. ProfileView relies on two main ideas: the use of multiple profile models whose construction explores evolutionary information in available databases, and a novel definition of a representation space in which to analyse sequences with multiple profile models combined together. ProfileView classifies protein families by enriching known functional groups with new sequences and discovering new groups and subgroups.

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lecture invitation: Novel strategies for virtual screening and drug repurposing
by Petr Danecek 28 Mar '22

28 Mar '22

Dear all, the next seminar will take place this Wednesday, the details are below. We look forward to seeing you all. Title: Novel strategies for virtual screening and drug repurposing: the lesson learned from the SARS-CoV-2 pandemy Speaker: Giulio Vistoli Date and time: Wednesday 30/03/2022 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S6 https://bioinformatika.mff.cuni.cz/seminar/ Best wishes, Petr Danecek

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REMINDER: Investigating the Genetics of Sexual Reproduction in 200,000 Humans
by Petr Danecek 21 Mar '22

21 Mar '22

Dear all, just a gentle reminder the next seminar will take place this Wednesday, the details are below. We look forward to seeing you all. Best wishes, Petr Danecek --------------------------------- Title: Investigating the Genetics of Sexual Reproduction in 200,000 Humans Speaker: Eugene Gardner Date and time: *Wednesday 23/03/2022 - 17:20 *Location: MFF UK, Malostranské nám. 25*, lecture hall S9 ** * Abstract:Why genes in the human genome are under significant constraint remains a mystery. New genetic variants arise in the germline due to mutation. While the majority are genetically neutral and have no effect on phenotype, some variants confer either an advantage and proceed towards fixation via positive selection, or a disadvantage and are removed from the gene pool by negative selection. The context of where a given variant arises in the genome strongly predicts whether it is eliminated or becomes fixed, with the function of the gene impacted among the most predictive for coding variation. Genes that are depleted of deleterious genetic variation (DGV) due to negative selection are said to be “constrained”. Depending on the method of calculation and dataset used, the human genome contains ~3,000 such genes. While genes associated with dominant diseases such as developmental disorders are among the most constrained genes in the human genome, well-characterised gene-disease pairs only comprise ~35% of all genes determined to be under significant constraint. Based on the principles of evolution, it can be assumed that natural selection shapes genic constraint by reducing an individual’s ability to pass on their genes via sexual reproduction. As part of recent work, using sequencing data for 200,000 humans from the UK Biobank Study, we have shown that genetic variants that damage these genes are associated with markedly reduced reproductive success, primarily due to increased childlessness, with a stronger effect in males than in females. We provided evidence that increased childlessness is likely mediated by genetically associated cognitive and behavioural traits, which may mean male carriers are less likely to find reproductive partners. This reduction in reproductive success may account for 20% of purifying selection against heterozygous variants that ablate protein-coding genes. While this genetic association could only account for a very minor fraction of the overall likelihood of being childless (less than 1%), especially when compared to more influential sociodemographic factors, it may influence how genes evolve over time.

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lecture invitation: Investigating the Genetics of Sexual Reproduction in 200,000 Humans
by Petr Danecek 07 Mar '22

07 Mar '22

Dear all, please be sure to mark your calendars for the next lecture in our invited speakers series. Our guest will be Eugene Gardner, a postdoctoral research associate at Trinity Hall in Cambridge, and he will present his most recent work on *Wednesday 23/03/2022 at 17:20* at Malostranské náměstí. The lecture hall will be announced later. Please see the details below. Best wishes, Petr Danecek --------------------- Speaker: Eugene Gardner Title: Investigating the Genetics of Sexual Reproduction in 200,000 Humans Abstract:Why genes in the human genome are under significant constraint remains a mystery. New genetic variants arise in the germline due to mutation. While the majority are genetically neutral and have no effect on phenotype, some variants confer either an advantage and proceed towards fixation via positive selection, or a disadvantage and are removed from the gene pool by negative selection. The context of where a given variant arises in the genome strongly predicts whether it is eliminated or becomes fixed, with the function of the gene impacted among the most predictive for coding variation. Genes that are depleted of deleterious genetic variation (DGV) due to negative selection are said to be “constrained”. Depending on the method of calculation and dataset used, the human genome contains ~3,000 such genes. While genes associated with dominant diseases such as developmental disorders are among the most constrained genes in the human genome, well-characterised gene-disease pairs only comprise ~35% of all genes determined to be under significant constraint. Based on the principles of evolution, it can be assumed that natural selection shapes genic constraint by reducing an individual’s ability to pass on their genes via sexual reproduction. As part of recent work, using sequencing data for 200,000 humans from the UK Biobank Study, we have shown that genetic variants that damage these genes are associated with markedly reduced reproductive success, primarily due to increased childlessness, with a stronger effect in males than in females. We provided evidence that increased childlessness is likely mediated by genetically associated cognitive and behavioural traits, which may mean male carriers are less likely to find reproductive partners. This reduction in reproductive success may account for 20% of purifying selection against heterozygous variants that ablate protein-coding genes. While this genetic association could only account for a very minor fraction of the overall likelihood of being childless (less than 1%), especially when compared to more influential sociodemographic factors, it may influence how genes evolve over time.

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List server upgrade
by Martin Mareš 29 Dec '21

29 Dec '21

Dear colleagues, we upgraded our list server to Mailman 3. We tried to preserve as much of the old list's configuration as possible, but there might be changes. If you encounter any problems, please let us know. The web interface of the list server (for both subscribers and administrators) lives here: https://kam.mff.cuni.cz/mailman3/ You are welcome to adjust the settings of your subscription there. Also, list archives will be available there. Happy new year KAM Computer Wizards

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