Tuesday Meeting
Journal Clubs and Progress Reports
If not differently stated the Tuesday meetings are held at 9 am in the seminar room on the 2nd floor. You can also join online at:
Schedule
| Date | Journal Club | Progress Report |
|---|---|---|
| 02.11.2021 | Julia Frank Topic: Evaluation of new treatments using an ordinal scale for diseases with moderate to high short-term mortality |
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| 19.10.2021 | Behnam Javanmardi
Topic: Research Data Management: A summary of a workshop organised by the Research Data Service Center of Uni. Bonn
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| 12.10.2021 | Leonie Topic: SLim software intro |
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| 05.10.2021 | Jennifer Daniel Onwuchekwa Topic: Polygenic risk score analysis for the diagnosis of epilepsy |
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| 28.09.2021 | Hannah Klinkhammer Topic: Advanced modelling of polygenic risk scores Link: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009141 |
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| 21.09.2021 | Simon Dieck: Master thesis Topic: Smoothed Analysis of local search problems |
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| 14.09.2021 | Rana Aldisi Topic: 'Systematic single-variant and gene-based association testing of 3,700 phenotypes in 281,850 UK Biobank exomes' Link: https://www.medrxiv.org/content/10.1101/2021.06.19.21259117v1 |
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| 07.09.2021 | Hellen Lesmann Topic: GMDB: Labeled Medical Imaging data for deep learning on monogenic phenotypes |
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| 10.08.2021 | Guest Talk: Kevin Thurley (Biomathematics - Systems Biology of Inflammation, Bonn University) Topic: Data-driven modeling of immune cell interaction networks |
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| 03.08.2021 | Sugi Sivalingan Topic: Detection of SARS-CoV-2 variants in a local outbreak of the Heinsberg district |
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| 27.07.2021 | Dataset Presentation/Discussion (Preparation for the IGSB retreat) | |
| 22.06.2021 | Guest Talk: Sander Groen in 't Woud (The Radboud University Medical Center) Topic: Genetics of Solitary functioning kidney |
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| 15.06.2021 | Miguel Ibarra Paper Presentation: Genome-wide polygenic risk score for retinopathy of type 2 diabetes Link: https://academic.oup.com/hmg/article/30/10/952/6166199?login=true |
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| 8.06.2021 | Behnam Javanmardi Paper Presentation: Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator Link: https://www.nature.com/articles/s41586-021-03208-9 |
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| 1.06.2021 | ESHG Discussion round | |
| 25.05.2021 | Emadeldin Hassanin ESHG 2021 rehearsal: Breast and prostate cancer risk: the interplay of polygenic risk, high-impact monogenic variants, and family history Link: https://drive.google.com/file/d/1nfMfx8MQy1MXuMnZN8tXbCFMMDJOpcuC/view?usp=sharing |
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| 18.05.2021 |
Fabian Brand & Alexej Knaus 2. SODAR Core: a Django-based framework for scientific data management and analysis web apps 3. VarFish: comprehensive DNA variant analysis for diagnostics and research |
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| 04.05.2021 | Tzung-Chien Hsieh ESHG talk rehersal: "Removing confounders from facial representations trained on the biased patient images" |
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| 27.04.2021 | Emadeldin Hassanin
Polygenic risk score as a risk modifier on the penetrance of monogenic variants in familial forms of breast and prostate cancer
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| 20.04.2021 | Carlo Maj Improving reporting standards for polygenic scores in risk prediction studies https://www.nature.com/articles/s41586-021-03243-6 |
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| 13.04.2021 | Guest Lecture: Mohammad Taheri, M.Sc PhD Candidate |
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| 06.04.2021 | Alexej Knaus LOEF Score: The mutational constraint spectrum quantified from variation in 141,456 humans https://www.nature.com/articles/s41586-020-2308-7 |
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| 30.03.2021 |
Rana Aldisi |
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| 23.03.2021 | Nanditha Mallesh AlphaFold https://www.nature.com/articles/s41586-019-1923-7 |
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| 16.03.2021 | Corona breaktime | |
| 02.03.2021 | Sonia Munjal , Konrad Gerischer Associations of autozygosity with a broad range of human phenotypes Link: https://www.nature.com/articles/s41467-019-12283-6 |
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| 16.02.2021 | ESHG Abstract Discussion Link: https://2021.eshg.org/ |
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| 9.2.2021 | The Lockdown Debate | |
| 2.01.2021 | Alexander Hustinx Title: Localization confidence to address occlusions in face detection Link: https://scripties.uba.uva.nl/search?id=710679;setlang=en |
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| 26.1.2021 | Nanditha Mallesh: Transfer learning for deep learning based B-cell neoplasm classification | |
| 19.1.2021 | Fabian Paper Discussion: Differences between germline genomes of monozygotic twins https://www.nature.com/articles/s41588-020-00755-1 |
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| 12.01.2021 | Guest Talk: Dr. Maria Asif (Cologne Center for Genomics (CCG)) Title: Intellectual disability-craniodigital syndrome: From gene hunting to pathway revelation |
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| 05.01.2021 | Sonia Munjal Title: Search for repeating bursts for known FRBs observed at the 100m Effelsberg radio telescope |
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| 22.12.2020 | Emadeldin Hassanin: Genetic risk assessment based on both common and rare variants | |
| 15.12.2020 | Aakash Mantri: Gut Microbiome | |
| 01.12.2020 |
Rana Aldisi: Gene associations based on the burden of rare deleterious variants Link to slides: docs.google.com/presentation/d/1bvLsnwsF_M0jDvM19IbWO9EKCmu8hemKdu176a8hV6s/edit |
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| 17.11.2020 | Nanditha Mallesh Human-level recognition of blast cells in acute myeloid leukaemia with convolutional neural networks https://www.nature.com/articles/s42256-019-0101-9 |
Nanditha Mallesh flowcat: project update |
| 10.11.2020 | Ashly Sebastine : Expanding Next-Generation Phenotyping X-RAY |
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| 20.10.2020 | Ashly Sebastine Topic: The RSNA Pediatric Bone Age Machine Learning Challenge Link: https://pubs.rsna.org/doi/10.1148/radiol.2018180736 |
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| 13.10.2020 |
Guest Talk: Dr. med. Alexander Semaan [Klinik und Poliklinik für Allgemein-, Viszeral-, Thorax- und Gefäßchirurgie] Topic: Bedeutung der molekularen Diagnostik in der Grundlagenforschung und der translationen Forschung im duktalen Adenokarzinom des Pankreas |
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| 29.09.2020 | Guest Talk: Fr. Behnam Javanmardi (Observatoire de Paris) Topic: Measuring the expansion rate of the Universe. |
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| 22.09.2020 | Friederike David: Genetic contributions to transdiagnostic factor dimensions of psychopathological symptoms in patients with major psychoses | |
| 15.09.2020 | Guest Talk: Dr. med. Jonas Henn Topic: Modernizing surgial indication - Bioinformatic techniques for analysis of perioperative data |
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| 08.09.2020 | Guest Talk: Randa Elshawadfy Topic: Characterization and interpretation of machine learning and pharmacophore models for the identification of ABCC1 ligands |
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| 18.08.2020 | Carlo Maj Topic: Genomic Risk Prediction of Coronary Artery Disease in 480,000 Adults Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6176870/ |
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| 11.08.2020 | Oleg Borisov Topic: Whole genome sequencing of patients with rare diseases in a national health system Links: https://pubmed.ncbi.nlm.nih.gov/32581362/ https://pubmed.ncbi.nlm.nih.gov/28669401/ |
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| 04.08.2020 | Guest talk: Yuri Tolkach, Pathology University of Köln Topic: DeepLearining for prostate cancer pathology using NASNet |
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| 28.07.2020 | Guest talk: Muhammad Shoaib Malik Topic: Siamase neural network to recognize disease causing genes based on clinical features |
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| 21.07.2020 | Guest talk: Thomas Lordick, Master Student, University of Bonn Topic: Data Science Approaches for Identification of Genetic Impact on Cholesterol Levels in Parkinson's disease |
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| 14.07.2020 | Guest talk: Marie Oestreich, Master Student Bioinformatics, University of Bonn Topic: " A network-based approach for omics data integration |
Sanat Mishra: Introducing multisample input for PEDIA (Project update) |
| 07.07.2020 | Miguel Ibarra: Micro-aneurysm detection |
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| 30.6.2020 | Ashly Sebastine Deep learning algorithm predicts diabetic retinopathy progression in individual patients https://www.nature.com/articles/s41746-019-0172-3.pdf |
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| 23.6.2020 | Emadeldin Hassanin Paper: https://www.medrxiv.org/content/10.1101/2020.04.17.20069229v1 Slides: https://drive.google.com/file/d/1_fxtdgmQll6nIeHWZu2c946PPJeiFH6D/view?usp=sharing |
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| 16.6.2020 | Aakash Mantri: Gut-microbiome project update | |
| 19.5.2020 | Miguel Rodríguez de los Santos Rehearsal ESHG 2020: A CRISPR/Cas9-engineered mouse model for GPI anchor deficiency mirrors human phenotype and shows hippocampal synaptic dysfunctions. |
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| 12.05.2020 | Chengyao Peng Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449884/) |
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| 05.05.2020 | Rana Aldisi GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2877-3) Slides: https://docs.google.com/presentation/d/1Of3pojjRou7NAO1p765s5lAL18jslktYMq7FLD5Tehw/edit?usp=sharing |
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| 21.04.2020 | Tharindu: ClinVar Submission form Clinical Reports | |
| 14.04.2020 | Max and Nanditha CytoNorm: A Normalization Algorithm for Cytometry Data https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.23904 |
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| 07.04.2020 | Tzung: Turning a Blind Eye: Explicit Removal of Biases and Variation from Deep Neural Network Embeddings (https://arxiv.org/abs/1809.02169) https://docs.google.com/presentation/d/1uvfLg-jqn1ZWS-_ZHT7Oq50n5cj8AjOJ1hvL5ynYCSc/edit?usp=sharing |
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| 03.03.2020 | Ashly Sebastine: Nitrogen bearing molecules in low-mass star-forming regions |
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| 11.02.2020 | Anatomical difference in fundus images for the delineation of sex (Miguel Ibarra, Simon Dieck) |
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| 04.02.2020 | Integrating healthcare and research genetic data empowers the discovery of 49 novel developmental disorders Kaplanis, et al. 2020 (preprint) (Prezi: Alexej) | |
| 28.01.2020 | Characteristics of induced mutations in offspring derived from irradiated mouse spermatogonia and mature oocytes Satoh, Yasunari, et al. 2019 (Fabian Brand): PDF | APPIS-2020 conference summary (Oleg Borisov) |
| 21.01.2020 | Nanditha - BIGS progress report 1 | |
| 17.12.2019 | Alexej Teamkommunumatuon / Team-building laufendes Ergebnisprotokoll |
Simon Delineation of sex on fundus images - Presentation |
| 10.12.2019 | Journal Club (Alexej Knaus) Making new genetic diagnoses with old data Slides |
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| 12.11.2019 | Progress report (Oleg Borisov) | |
| 05.11.2019 | Next-generation phenotyping using computer vision algorithms in rare genomic neurodevelopmental disorders (https://www.nature.com/articles/s41436-018-0404-y) Tzung-Chien | |
| 22.10.2019 | Heritability in UK Biobank https://nealelab.github.io/UKBB_ldsc/ with LDSR (https://www.nature.com/articles/ng.3211) Carlo |
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| 08.10.2019 | Varsome - Tharindu | |
| 24.09.2019 | A survey on Deep Transfer learning https://arxiv.org/abs/1808.01974 -- Nanditha |
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| 10.9.2019 | FlowCat Progress report - Nanditha | |
| 27.8.2019 | Introduction to facial recognition ArcFace (https://arxiv.org/abs/1801.07698) |
GestaltMatch project |
| 11.6.2019 | rehearsal for ESHG | |
| 04.06.2019 |
Nanditha and Julian( https://www.nature.com/articles/nature25978 )
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| https://arxiv.org/pdf/1801.07698.pdf | ||
| https://arxiv.org/pdf/1506.00511.pdf | ||
| 07.05.2019 | Tzung Gestalt-Match project | |
| 30.04.2019 | 5 minute rounds | |
| 23.04.2019 | Steffen Künzel | |
| 26.03.2019 | Ming (Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank ->PDF) | |
| 12.03.2019 | Arezoo Bozorgmehr. Machine learning on general medicine issues | |
| 26.02.2019 | https://www.ncbi.nlm.nih.gov/pubmed/29590070 (Peter) | |
| 19.02.2019 | Tzung and Ming rehearsal for GfH | Rajarshi Biswas | |
| 12.02.2019 | Fabian and Oleg rehearsal for GfH | |
| 05.02.2019 | Besuch Julia Frank | Exome Pipeline (Alexej Knaus) |
| 29.01.2019 | our GPS with discussion (Oleg, Carlo, Ming, Julian) | |
| 22.01.2019 | hands on with AWS and Docker (Fabian Brand) | |
| 15.01.2019 | Miguel Ibrarra 1) Topological Charactersistics in regulatory models in bacteria 2) Generation of automatic pipelines for metabolomic analysis in Galaxy |
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| 11.12.2018 | Heiko Reutter and lab members | |
| 04.12.2018 | Friederike David, RNAseq pipeline | |
| 27.11.2018 | Fabian Brand (git repositories) | |
| 20.11.2018 | Martin Atta Mensah Photogrammetry on DONSON and FA patients. | |
| 13.11.2018 | Ming (master thesis: capturing epistasis using deep learning) | |
| 30.10.2018 | Carlo Maj (Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders) | Matthias Becker (Accelerating genomic data processing with Memory Driven Computing) |
| 25.09.2018 | Oleg Borisov (Investigation of genetic factors and polygenic modeling for the human muscle fibers composition) | |
| 18.09.2018 | Miguel Rodriguez de los Santos (Characterisation of Pathogenic Mutations in Genes involved in GPI Anchor Synthesis and –Maturation) | |
| 28.08.2018 | Nijmegen Sommer School WrapUp (Nanditha, Jonas, Alexej) | Ming(Deep learning on OCT scans)(Presentation) |
| 21.08.2018 | PARTEK-FLOW Help Session | |
| 14.08.2018 | Oleg Borisov (PheWAS) | Carlo Maj (PheWAS PRS) (Presentation) |
| 07.08.2018 | Thomas Welchowsky (KernDeepStackNet: An R package for fitting kernel deep stacking network) | |
| 24.07.2018 | Julian Hecker (Nonparametric Regression using Deep Neural Networks) | |
| 17.07.2018 | Tzung-Chien: DPDL ProgressReport | Nanditha: F2G & DPDL integration |
| 10.07.2018 | Alexej: Discussion on SOP of Exomes | |
| 04.07.2018 | Farhad (MS/MS proteomics) | |
| 12.06.2018 | Alexej, Carlo, Tzung-Chien: ESHG poster presentation | |
| 22.05.2018 | Ming and Oleg (ACMG/AMP Bayesian classification) | Oleg and Carlo (Polygenic risk scoring for Barrett esophagus and esophageal adenocarcinoma) |
| 15.05.2018 | Alexej Knaus (cDNMs in oocytes) | |
| 08.05.2018 | Carlo (TWAS in schizophrenia) | Fabian (Cardiovasc and DL) + PartekFlow |
| 24.04.2018 | Dejan (Deep learning on variant data) | |
| 17.04.2018 | Tzung-Chien (face-matching) | Dejan & Alexej (PIGU faces) |
| 10.04.2018 | Ming Wai Yeung (deep learning on GWAS data -> PDF) | |
| 03.04.2018 | Fabian Brand (image-based deep learning -> PDF) | Alexej Knaus (Review on DLS) |
| 26.03.2018 | Dejan Dukic (GWAS faces) | Sugi Sivalingan (NGS Pipeline) |
| 19.03.2018 | Carlo and Oleg (TWAS -> PDF) | |
| 12.03.2018 | Alexej Knaus (Clustered de novo in Oocytes) | Student presentation (Ming Wai) |
| 05.03.2018 | Tzung-Chien (DPDL for GfH) | |
| 26.02.2018 | Mohammed and Lipika (Intro) | Fabian Brand (Master Thesis) |
| 19.02.2018 | Peter Krawitz (RadarSoldiers) | Fabian Brand (DeepVariant) |
| 12.02.2018 | Dejan Dukic (Introduction) | Carlo Maj (Polygenic Risk Score -> PDF) |
| 05.02.2018 | Tzung-Chien Hsieh (DPDL) | Oleg Borisov (Biostatistics) |
| 29.01.2018 | Julian Hecker (WES) | Alexej Knaus (GPIBDs) |
| 19.02.2018 | Peter Krawitz (RadarSoldiers) | Fabian Brand (DeepVariant) |
| 12.02.2018 | Dejan Dukic (Introduction) | Carlo Maj (Polygenic Risk Score -> PDF) |
