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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: 



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
19.10.2021  Behnam Javanmardi
 Topic: Research Data Management: A summary of a workshop organised by the Research Data Service Center of Uni. Bonn
12.10.2021  Leonie
 Topic: SLim software intro
05.10.2021   Jennifer Daniel Onwuchekwa
Topic: Polygenic risk score analysis for the diagnosis of epilepsy
28.09.2021  Hannah Klinkhammer
Topic: Advanced modelling of polygenic risk scores
21.09.2021  Simon Dieck: Master thesis
 Topic: Smoothed Analysis of local search problems
14.09.2021  Rana Aldisi
 Topic: 'Systematic single-variant and gene-based association testing of 3,700 phenotypes in 281,850 UK Biobank exomes'
 07.09.2021 Hellen Lesmann
Topic: GMDB: Labeled Medical Imaging data for deep learning on monogenic phenotypes
10.08.2021  Guest Talk: Kevin Thurley (Biomathematics - Systems Biology of Inflammation, Bonn University)
 Topic: Data-driven modeling of immune cell interaction networks
03.08.2021  Sugi Sivalingan 
Topic: Detection of SARS-CoV-2 variants in a local outbreak of the Heinsberg district
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
15.06.2021  Miguel Ibarra
Paper Presentation: Genome-wide polygenic risk score for retinopathy of type 2 diabetes
8.06.2021  Behnam Javanmardi
Paper Presentation: Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator
 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

Fabian Brand & Alexej Knaus
Bioinformatics: Lessons to learn from Berlin CUBI:
1. Digestiflow: "From BCL to FASTQ with Ease" + "Reproducible Demultiplexing for the Single Cell Era"

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

 04.05.2021 Tzung-Chien Hsieh
ESHG talk rehersal: "Removing confounders from facial representations trained on the biased patient images"
 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
 20.04.2021  Carlo Maj
 Improving reporting standards for polygenic scores in risk prediction studies
 13.04.2021  Guest Lecture: Mohammad Taheri, M.Sc
 PhD Candidate
  06.04.2021 Alexej Knaus
LOEF Score: The mutational constraint spectrum quantified from variation in 141,456 humans

Rana Aldisi
Structural variation in the 3D genome


 23.03.2021 Nanditha Mallesh
 16.03.2021 Corona breaktime  
 02.03.2021  Sonia Munjal , Konrad Gerischer
 Associations of autozygosity with a broad range of human phenotypes
 16.02.2021  ESHG Abstract Discussion
 9.2.2021  The Lockdown Debate  
 2.01.2021  Alexander Hustinx
 Title: Localization confidence to address occlusions in face detection
 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
 12.01.2021 Guest Talk: Dr. Maria Asif (Cologne Center for Genomics (CCG))  
Title: Intellectual disability-craniodigital syndrome: From gene hunting to pathway revelation
 05.01.2021 Sonia Munjal 
Title: Search for repeating bursts for known FRBs observed at the 100m Effelsberg radio telescope
 22.12.2020   Emadeldin Hassanin: Genetic risk assessment based on both common and rare variants
 15.12.2020    Aakash Mantri: Gut Microbiome

 Rana Aldisi: Gene associations based on the burden of rare deleterious variants

Link to slides:

 17.11.2020 Nanditha Mallesh
Human-level recognition of blast cells in acute myeloid leukaemia with convolutional neural networks 
Nanditha Mallesh
flowcat: project update 
 10.11.2020    Ashly Sebastine 
: Expanding Next-Generation Phenotyping  X-RAY 
Ashly Sebastine

Topic: The RSNA Pediatric Bone Age Machine Learning Challenge
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
 29.09.2020 Guest Talk: Fr. Behnam Javanmardi (Observatoire de Paris)
Topic: Measuring the expansion rate of the Universe.
 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
 08.09.2020 Guest Talk: Randa Elshawadfy
Topic: Characterization and interpretation of machine learning and pharmacophore models for the identification of ABCC1 ligands
 18.08.2020 Carlo Maj
Topic: Genomic Risk Prediction of Coronary Artery Disease in 480,000 Adults
 11.08.2020  Oleg Borisov
 Topic: Whole genome sequencing of patients with rare diseases in a national health system

Guest talk: Yuri Tolkach, Pathology University of Köln
Topic: DeepLearining for prostate cancer pathology using NASNet
 28.07.2020  Guest talk: Muhammad Shoaib Malik
Topic: Siamase neural network to recognize disease causing genes based on clinical features
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
 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
 30.6.2020 Ashly Sebastine
Deep learning algorithm predicts diabetic retinopathy progression in individual patients
 23.6.2020 Emadeldin Hassanin
 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.  
 12.05.2020  Chengyao Peng
Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO (
 05.05.2020  Rana Aldisi
GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data (
 21.04.2020    Tharindu: ClinVar Submission form Clinical Reports
14.04.2020 Max and Nanditha
CytoNorm: A Normalization Algorithm for Cytometry Data
 07.04.2020 Tzung:
Turning a Blind Eye: Explicit Removal of Biases and Variation from Deep Neural Network Embeddings (
 03.03.2020 Ashly Sebastine:
Nitrogen bearing molecules in low-mass star-forming regions
 11.02.2020   Anatomical difference in fundus images for the delineation of sex
(Miguel Ibarra, Simon Dieck)
  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
Delineation of sex on fundus images - Presentation
10.12.2019 Journal Club (Alexej Knaus)
Making new genetic diagnoses with old data
12.11.2019 Progress report (Oleg Borisov)  
05.11.2019   Next-generation phenotyping using computer vision algorithms in rare genomic neurodevelopmental disorders ( Tzung-Chien  
 22.10.2019 Heritability in UK Biobank with LDSR ( Carlo
 08.10.2019  Varsome - Tharindu  
 24.09.2019  A survey on Deep Transfer learning  -- Nanditha
 10.9.2019    FlowCat Progress report - Nanditha
 27.8.2019 Introduction to facial recognition
ArcFace (
GestaltMatch project
 11.6.2019   rehearsal for ESHG
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 (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
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)





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