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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 (Venusberg-Campus 1 Building 11). You can also join online at: 

Schedule

 

Date Journal Club
27.09.2022 Alexander Hustinx progress report + next project brief
13.09.2022 Hannah Klinkhammer progress report
06.09.2022 Bone2Gene Pitch & Eurodysmorpho rehearsals
30.08.2022 Meghna progress report
22.08.2022 Sonia Landwehr
Impact of high salt diet on the mouse gut microbiome
19.07.2022

Tzung progress report

19.07.2022

Rana Aldisi

Paper presentation:  Ultra-rare disruptive and damaging mutations influence educational attainment in the general population (pubmed.ncbi.nlm.nih.gov/27694993/)

12.07.2022

Post-Doc applicant: German Demidov

More info: In 'Tuesday Meeting' mattermost channel

28.06.2022 Tzung defense rehearsal
17.05.2022 ESHG poster discussion
03.05.2022

Aswinkumar Vijayananth

An explainable deep-learning algorithm for the detection of acute intracranial hemorrhage from small datasets (https://www.nature.com/articles/s41551-018-0324-9

19.04.2022

Fabian Brand & Alexej Knaus

New results from Radar study

 05.04.2022  Nanditha Mallesh

Single-cell proteo-genomic reference maps of the hematopoietic system

https://www.nature.com/articles/s41590-021-01059-0
22.03.2022 

Fabian Brand

Topic: Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED https://www.nature.com/articles/s41587-020-0731-9


Behnam Javanmardi

Topic: Readfish enables targeted nanopore sequencing of gigabase-sized genomes https://www.nature.com/articles/s41587-020-00746-x

 08.03.2022

 Progress Report: Sebastian Rassmann & Behnam Javanmardi

 Topic: Bone2Gene


Marathon reheresal of poster/talks for 32nd Annual Meeting of the German Society for Human Genetics

01.03.2022

Guest Talk: Manueal Goldkuhle 

Topic: Natural language processing in systematic reviews

22.02.2022

Guest Talk: Jannik (Kerstin U. Ludwig Group)

Topic: Evaluation of rare variants in 55 genes in severely affected COVID-19 people (approx. 1600 cases, 5500 controls)

15.02.2022

Progress Report: Aakash Mantri 

Topic: Impact of synbiotic intake on liver metabolism in healthy participants and their potential preventive effect on non-alcoholic fatty liver disease (NAFLD)

 08.02.2022 Tzung-Chien Hsieh 
Topic: Overcoming barriers to data sharing with medical image generation: a comprehensive evaluation
25.11.2021

Guest Talk: Marie Oestreich [DZNE]

Topic: Privacy preserving collaboration in medicine

 30.11.2021

Progress Report: Miguel Ibarra & Behnam Javanmardi

Eye2DR: integrating phenotypic and genotypic data for the diagnosis of diabetic retinopathy 

AGD practise: Uni club: https://goo.gl/maps/56zrKST4griRD7eY6

 23.11.2021 Behnam Javanmardi
Topic: Deep-learning-based prediction of late age-related macular degeneration progression
https://www.nature.com/articles/s42256-020-0154-9
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
 Link: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009141
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'
Link: https://www.medrxiv.org/content/10.1101/2021.06.19.21259117v1
 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
Link: https://academic.oup.com/hmg/article/30/10/952/6166199?login=true
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
 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
 18.05.2021

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
 https://www.nature.com/articles/s41586-021-03243-6
 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
https://www.nature.com/articles/s41586-020-2308-7
 30.03.2021

Rana Aldisi
Structural variation in the 3D genome
Link: https://www.nature.com/articles/s41576-018-0007-0?proof=t

Presentation

 23.03.2021 Nanditha Mallesh
AlphaFold 
https://www.nature.com/articles/s41586-019-1923-7
 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
 16.02.2021  ESHG Abstract Discussion
Link: https://2021.eshg.org/
 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
 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
 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
 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 

 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 

& Flowcat:project update

 10.11.2020
: Expanding Next-Generation Phenotyping  X-RAY 
20.10.2020   
Ashly Sebastine

Topic: The RSNA Pediatric Bone Age Machine Learning Challenge
Link: https://pubs.rsna.org/doi/10.1148/radiol.2018180736
 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
 
 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
Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6176870/
 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/
 04.08.2020  
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
 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
 
 14.07.2020

Guest talk:  Marie Oestreich, Master Student Bioinformatics, University of Bonn
Topic: " A network-based approach for omics data integration

 

 07.07.2020  
 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
 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
 16.6.2020  
 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 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449884/)
 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
 
 21.04.2020  
14.04.2020 Max and Nanditha
CytoNorm: A Normalization Algorithm for Cytometry Data
https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.23904
 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
 03.03.2020 Ashly Sebastine:
Nitrogen bearing molecules in low-mass star-forming regions
 11.02.2020  
  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
 21.01.2020  
17.12.2019 Alexej
Teamkommunumatuon / Team-building
laufendes Ergebnisprotokoll
10.12.2019 Journal Club (Alexej Knaus)
Making new genetic diagnoses with old data
Slides
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
 08.10.2019  Varsome - Tharindu
 24.09.2019  A survey on Deep Transfer learning
https://arxiv.org/abs/1808.01974  -- Nanditha
 10.9.2019  
 27.8.2019 Introduction to facial recognition
ArcFace (https://arxiv.org/abs/1801.07698)
 11.6.2019  
 04.06.2019
  https://arxiv.org/pdf/1801.07698.pdf
  https://arxiv.org/pdf/1506.00511.pdf
 
07.05.2019  
30.04.2019  
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
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  
11.12.2018 Heiko Reutter and lab members
04.12.2018 Friederike David, RNAseq pipeline
27.11.2018  
20.11.2018 Martin Atta Mensah Photogrammetry on DONSON and FA patients.
13.11.2018  
30.10.2018 Carlo Maj (Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders)
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)
21.08.2018 PARTEK-FLOW Help Session
14.08.2018 Oleg Borisov (PheWAS)
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
10.07.2018 Alexej: Discussion on SOP of Exomes
04.07.2018  
12.06.2018 Alexej, Carlo, Tzung-Chien: ESHG poster presentation
22.05.2018 Ming and Oleg (ACMG/AMP Bayesian classification)
15.05.2018 Alexej Knaus (cDNMs in oocytes)
08.05.2018 Carlo (TWAS in schizophrenia)
24.04.2018 Dejan (Deep learning on variant data)
17.04.2018 Tzung-Chien (face-matching)
10.04.2018 Ming Wai Yeung (deep learning on GWAS data -> PDF)
03.04.2018 Fabian Brand (image-based deep learning -> PDF)
26.03.2018 Dejan Dukic (GWAS faces)
19.03.2018 Carlo and Oleg (TWAS -> PDF)
12.03.2018 Alexej Knaus (Clustered de novo in Oocytes)
05.03.2018 Tzung-Chien (DPDL for GfH)
26.02.2018 Mohammed and Lipika (Intro)
19.02.2018 Peter Krawitz (RadarSoldiers)
12.02.2018 Dejan Dukic (Introduction)
05.02.2018 Tzung-Chien Hsieh (DPDL)
29.01.2018 Julian Hecker (WES)
19.02.2018 Peter Krawitz (RadarSoldiers)
12.02.2018 Dejan Dukic (Introduction)

 

 


 

 

 

 

 

 

 

 

 

 

 

 

 

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