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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.

Schedule

Date Journal Club Progress Report
 04.08.2020  
Guest talk: Yuri Tolkach, Pathology University of Köln
DeepLearining for prostate cancer pathology using NASNet
 
 
 28.07.2020  
Guest talk: Randa Elshawadfy, M.Sc. Life Sciences Informatics
Characterization and interpretation of machine learning and pharmacophore models for the identification of ABCC1 ligands
 
 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
 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
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    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 (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    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
 
 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   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
Simon
Delineation of sex on fundus images - Presentation
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    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  
  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
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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