Seminars

Feel free to join theta online seminars.
The meeting time is Thursday at 11:30 – 12:30. Stay tuned and follow the schedule below or request to be added to mailing list.
Contact person: Marek Sztuka.

Winter semester 2024/2025

Seminar schedule:

  • 11.12.24 – Dawid Słomian – mix99 course pt.2
  • 05.12.24 – Patryk Mierzejewski – “Investigation of the temporal changes in brain activity based on functional Magnetic Resonance Imaging data” Jakub Piśkiewicz  – “Measurement of structures on US images using convolutional neural networks”
  • 27.11.24 – Joanna Szyda – “Longitudinal data analysis”
  • 21.11.24 – Dawid Słomian – Mix99 course
  • 14.11.24 – Jakub Liu – Self Organizing Maps
  • 07.11.24 – Joanna Szyda – Attention is all you need by Ashish Vaswani et. al.
  • 24.10.24 – Julia Siecińska – Gaussian Mixture Models for DL feature selection
  • 16.10.24 – Magda Mielczarek – Epigenomic Approaches for the Diagnosis of Rare Diseases by Beatriz Martinez-Delgado and Maria J. Barrero
  • 09.10.24 – Maja Dębicka – Confirmatory Factor Analysis based on WHOQOL-BREF
  • 02.10.24 – Marek Sztuka – non parametric for longitudinal data, R package and methods implemented by Frank Konietschke
  • 25.09.24 – Dawid Słomian – Genome-wide association study for stature for Holstein cattle based on whole genome sequence, using a mixed linear model

Summer semester 2023/2024

  • 23.07.24 –  THETA on 7’th International Conference on Quantitive Genetics
  • 16.07.24 – Joanna Szyda, Krzysztof Kotlarz = “Approaches to feature selection, Journal club”
  • 09.07.24 – Joanna Szyda – Variable feature selecion by Frank Konietschke
  • 02.07.24 – Joanna Szyda – “GLM” + “Variable Selection Methods” by Frank Konietschke
  • 25.06.24 – Joanna Szyda – “Advanced Methods in Biometry: Linear Regression Analysis, Generalized Linear Models” by Frank Konietschke
  • 18.06.24 – Introduction to mixture models Video pt.2 
  • 12.06.24 – Prof. Dr. Frank Konietschke – “Longitudinal Data and Advanced Methods in Biometry”
  • 11.06.24 – Prof. Dr. Frank Konietschke – “The Max-t and Wilcoxon-Mann-Whitney test for high-dimensional Repeated Measures and multivariate Designs”
  • 10.06.24 – THETA members presentations about research:  M. Sztuka, M. Frąszczak, M. Mielczarek, M. Jakimowicz, T.Suchocki, K.Kotlarz
  • 28.05.24 – Jakub Liu – soft clustering with Gaussian Mixture Models (EM algorithm).
  • 21.05.24  – Krzysztof Kotlarz – Unveiling the Mystery: An Introduction to Metatranscriptome Analysis.
  • 14.05.24 – Dawid Słomian – Differential handling of missing parents in genetic evaluation of dairy cattle using single step test day SNP-BLUP model.
  • 07.05.24 – Introduction to mixture models Video
  • 30.04.24 – Joanna Szyda – Rank Aggregation
  • 23.04.24 – Michalina Jakimowicz – Genome wide association study for health traits.
  • 16.04.24- Marek Sztuka – Further mining into NN Fish Classifier.
  • 09.04.24 – Magdalena Frąszczak – Magdalena Frąszczak- Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing.
  • 02.04.24 – Holidays
  • 26.03.24 – Tomasz Suchocki – Estimation of the genetic parameters for female fertility traits in dairy cattle
  • 19.03.24 –  Magda Mielczarek – Best practices for variant calling in clinical sequencing by Daniel C. Koboldt
  • 12.03.24 – Anomaly detection course pt. 3
  • 5.03.24 – Anomaly detection course  pt. 2

Winter semester 2023/2024

  • 26.02.24 – Jakub Liu – Newton and Gauss-Newton algorithms for obtaining a maximum likelihood estimate.
  • 19.02.24 – Jakub Liu – Markov chain, Monte-Carlo, Metropolis algorithm.
  • 12.02.24 – Marek Sztuka – Neural network classifier for fish microbiome.
  •  05.02.24 – Michalina Jakimowicz – “First results of differential analysis of KEGG pathways for samples collected from the carp intestine”
  • 29.01.24 – Dawid Słomian – How does it work ? Comparison of two solvers, MiX99 and MiXBLUP.
  • 22.01.24 – Krzysztof Kotlarz – Sequencing error profiles of Illumina sequencing instruments by. Nicholas Stoler and Anton Nekrutenko
  • 15.01.24 – Anomaly Detection by. Hadi Fanaee
  • 08.01.24 – Laura Jarosz – Microbiome-wide association studies link dynamic microbial consortia to disease by Jack A. Gilbert et. al.
  • 18.12.23 – Krzysztof Kotlarz – The application of SCCS model on Infections in Multiple Myeloma Patients Treated with Anti-BCMA Bispecific Antibodies
  • 11.12.23 – Jakub Liu – Linear optimalization
  • 4.12.23 – Numerical Algorithms course pt. 3
  • 27.11.23 – Piotr Hajduk – Dietary Lipid:Protein Ratio and n-3 Long-Chain Polyunsaturated Fatty Acids Alters the Gut Microbiome of Atlantic Salmon Under Hypoxic and Normoxic Conditions by D. Huyben et. al
  • 20.11.23 – Numerical Algorithms course pt. 2
  • 13.11.23 – Numerical Algorithms course pt. 1
  • 6.11.23 – Deep Learning course pt. 2
  • 30.10.23 – Deep Learning course pt. 1
  • 23.10.23 – Daniel S. Gianola – Inferring breeding value or genetic score from incomplete pedigree, genomic and phenotypic information
  • 16.10.23 – Tomasz Suchocki -A second-level diagonal preconditioner for single-step SNPBLUP
  • 9.10.23 – Tomasz Suchocki – Computational strategies for the preconditioned conjugate gradient method applied to ssSNPBLUP, with an application to a multivariate maternal model
  • 02.10.23 – Magda Mielczarek – The effect of transcriptomic annotations in breast cancer differential gene expression study
  • 25.09.23 – Marek Sztuka – Predicting sow postures from video images: Comparison of convolutional neural networks and segmentation combined with support vector machines under various training and testing setups
  • 18.09.23 – Joanna Szyda – Supervised Rank aggregation (SRA): A novel rank aggregation approach for ensemble-based feature selection (paper, presentation)
  • 11.09.23 – Yangqing Den – A Bayesian Approach for Two-Stage Multivariate Mendelian Randomization with Mixed Outcomes

Summer semester 2🌞22/2🌞23

Seminar schedule:

  • 26.06.23:
    • Bartosz Czech – The final PhD results of the analysis of multi-omics data of Holstein cattle under heat stress condition.
    • Marek Sztuka – Hybrid genome de novo assembly of the nanopore and the Illumina data
    • Jakub Liu – Comparing execution times of common interpreted and compiled programming languages
  • 19.06.23 – Joanna Szyda – Sharma et al. (2020) TaxoNN: ensemble of neural networks on stratified microbiome data for disease prediction
  • 12.06.23 – Kristaps Kļaviņš – From sample preparation to LC-MS to data in metabolomics: the devil is in the details
  • 05.06.23 – Dawid Słomian – Methylome and metagenome sequencing
  • 29.05.23 – Michalina Jakimowicz – Comparison of MIXBLUP and BLUPF90
  • 22.05.23 – Marek Sztuka – Final next flow runs comparison results
  • 15.05.23 – Piotr Hajduk – Final analysis of covariances between expression in normal and heat-stressed rats
  • 08.05.23 – Joanna Szyda – Parallelisation with MPI – a monkey perspective
  • 24.04.23 – Dawid Słomian – Choose your model wisely – the comparison of genomically enhanced breeding values predicted by different single-step models
  • 17.04.23 – Jakub Liu – BGData – an R package for the analysis of big genomic data
  • 10.04.23 – Easter!
  • 03.04.23 – Piotr Hajduk – Convolutional neural networks in medical image understanding: a survey
  • 27.03.23 – Bartosz Czech – Heat stress and immune response phenotype affect DNA methylation in blood mononuclear cells from Holstein dairy cows
  • 20.03.23 – Bartosz Czech – Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages
  • 13.03.23 – Jakub Liu – SNP distribution amongst exons and introns in humans
  • 06.03.2023 – Piotr Hajduk – Worldwide Genetic Analysis of the CFTR Region

You can check out what we talked about in the last semester here.