|
|
Please note that meetings are held on **every Wednesday** between **10:45** AM - **12:00** PM. **Location is changed to** `P-00-112` (building across the bridge). <br>
|
|
|
|
|
|
*In case the room is **locked**, you can collect the key at:* **P-01-044**<br>
|
|
|
|
|
|
> The timetable for previous years can be found here: [**2017**](timetable-2017) | [**2018**](timetable-2018).
|
|
|
|
|
|
#### **FORMAT** `NEW`
|
|
|
* One **20-minute scheduled presentation**, randomly **assigned in advance!** If you wish, you can make arrangements to switch dates with someone else from the list. Please provide a title of your talk one week prior to the meeting.
|
|
|
* Two **short 10-minute presentations (XS)**, scheduled freely by yourself (expected frequency of >1 per three months)
|
|
|
* **Guest / PI** speakers can use two short time slots for their presentation. Use the first cell for name and the second for the title of their talks. Please feel free to invite guest speakers and if there is a conflict between preferred date and an already scheduled PI talk, please let us know and we’ll try to reschedule the PI lecture to accommodate for the guest speaker.
|
|
|
|
|
|
#### **TOPICS**
|
|
|
* `10-min` time slots
|
|
|
* **New Projects:** share what your new project entails and your plan of action.
|
|
|
* **Troubleshooting:** discuss problems you have been facing / ask for feedback.
|
|
|
* **Updates:** give an update on your progress and new findings / brainstorm.
|
|
|
* **New Ideas:** propose / discuss a new (mini)project.
|
|
|
* **News / Hot Topics:** give a short review of an article or news story. Use GIT to share!
|
|
|
* `20-min` time slots
|
|
|
* **Ongoing / Finished Projects:** share results of your recent project. Please **make sure to** introduce 1) your research question; 2) data type you are working with; and 3) your strategy and main findings. End with a few points for 10-minute of open discussion. **Provide your talk title ahead of time**.
|
|
|
|
|
|
<br>
|
|
|
|
|
|
|
|
|
## **2019** Timetable
|
|
|
**Date** |**Location** |**Scheduled Speaker** 20-min |**Title** |**Guest** / XS **Talk 1** 10-min |**Title of Guest Lecture** / XS **Talk 2** 10-min
|
|
|
:------------|:-------------:|:---------|:---------|:---------|:----------
|
|
|
`02 Jan` |T-00-006 | `no` | `meeting` | |
|
|
|
`09 Jan` |T-00-006 | Sander B. | BWA versus minimap2 | Yahya | 2018 Evaluation
|
|
|
`16 Jan` |T-00-006 | Bpexa Students | Bpexa Students | Ioannis Moustakas | attempt to remove batch effects in single cell analysis
|
|
|
`23 Jan` |T-00-006 | Liana Grieken (HUID) | 10x longranger pipeline |Igno Maggio (CCB/KJC) | CRISPR-CAS9 introduction and study on on-target efficiency
|
|
|
`30 Jan` |T-00-006 | Sander Tuit | Identification of tumor-associated genes for targeted T-cell therapy | Szymon M. Kiełbasa | Single Cell Sample Matcher |
|
|
|
`06 Feb` |P-00-112 | Ivo Fokkema | Population-based MAF and variant prioritization | David | Ruben Vorderman, simple testing of workflows
|
|
|
`13 Feb` |P-00-112 | Davy Cats | KeyGenes (classifying sample tissues from RNAseq counts) | Dani |
|
|
|
`20 Feb` |P-00-112 | Mario Cangiano | Network analysis of prostate cancer xenografts | Peter Taschner | Monitoring of training effects using gene expression profiles
|
|
|
`27 Feb` |P-00-112 | Dina Ruano | Neoantigen detection in low mutation rate tumors | Jihed Chouaref | Introduction|
|
|
|
`06 Mar` |P-00-112 | Brian Piepenbroek | Metagenomic analysis of cutaneous T- and B-cell lymphomas using Centrifuge | Leon/Cedrick | SV calling, merging, with test case from Project MinE
|
|
|
`13 Mar` |P-00-112 | Dani Borras | New ATACseq results for Acla homologs | Johan den Dunnen | *title*
|
|
|
`20 Mar` |P-00-112 | Ioannis Moustakas | Batch effect correction in single cell RNAseq experiments | Ellen Carbo | The rediscovery of MERS and SARS
|
|
|
`27 Mar` |P-00-112 | | *title* | Floyd Wittink (HL) | Nanopore sequencing in the LCAB
|
|
|
`03 Apr` |P-00-112 | [**BioSB 2019 Conference**](https://www.aanmelder.nl/biosb2019) | - - - - - | - - - - - | - - - - -
|
|
|
`10 Apr` |P-00-112 | Roberta Menafra | An update on the RNGS19 VIB conference | David |
|
|
|
`17 Apr` |P-00-112 | Ioannis Moustakas | Dimensionality reduction as a means of noise reduction in sc RNA-seq datasets | Leon Mei | Update on (1) running CRISPResso for CRISPR-CAS9 analysis and (2) HLA typing tools
|
|
|
`24 Apr` |P-00-112 | Bastian Hornung | Contamination everywhere | Ellen Carbo | The rediscovery of MERS and SARS
|
|
|
`01 May` |P-00-112 | Stef Janson | *title* | |
|
|
|
`08 May` |P-00-112 | [**SMRTLeiden 2019 Conference**](https://www.lgtc.nl/SMRTLeiden/) | - - - - - | - - - - - | - - - - -
|
|
|
`15 May` |P-00-112 | David San Leon Granado | FHSD and methylation | |
|
|
|
`22 May` |P-00-112 | Julieta Sepulveda Yanez | Germline variants in Diffuse large B-cell lymphoma (DLBCL) | Arjen Speksnijder (Naturalis) | Moleculair identification of plant pollen in air samples
|
|
|
`29 May` |P-00-112 | Amrish Mahes | *title* | Jorrit van Uhm (Derm internship) | Using WES data to discover CNVs, SNVs and indels in cutaneous anaplastic large cell lymphoma
|
|
|
`05 Jun` |P-00-112 | Ruben Vorderman | Singularity | |
|
|
|
`12 Jun` |P-00-112 | Bas Verbruggen | *title* | | |
|
|
|
`19 Jun` |P-00-112 | Jihed Chouaref | Morc3 single cell ATAC-seq | Sander Bollen | Index hopping on the Illumina NovaSeq |
|
|
|
`26 Jun` |P-00-112 | Ruben | smallRNA pipeline in biowdl | Jan Oosting | Pathway directed transcription analysis |
|
|
|
`03 Jul` |P-00-112 | Leon | CRISPR efficiency analysis using CRISPResso & Discussion about /exports/genomes/species/H.sapiens/ on SHARK | David San Leon | FSHD2 classifications |
|
|
|
`10 Jul` |P-00-112 | Ioannis | methylation analysis | Sander Bollen | Fast fastq archiving with fastqube |
|
|
|
`17 Jul` |P-00-112 | | | |
|
|
|
`24 Jul` |P-00-112 | | | |
|
|
|
`31 Jul` |P-00-112 | | | |
|
|
|
`07 Aug` |P-00-112 | | | |
|
|
|
`14 Aug` |P-00-112 | | | |
|
|
|
`21 Aug` |P-00-112 | | | |
|
|
|
`28 Aug` |P-00-112 | | | |
|
|
|
`04 Sep` |P-00-112 | Jasper Boom | Long read pipeline Talon | Leon Mei | SASC update and future plans
|
|
|
`11 Sep` |P-00-112 | Tom Metz (HG) | scRNA experiment and data analysis update | Ruben Vorderman | use of xWiki
|
|
|
`18 Sep` |P-00-112 | | | |
|
|
|
`25 Sep` |P-00-112 | Mark (& Jonathan) | Variant Frequency Database | |
|
|
|
`02 Oct` |P-00-112 | | | |
|
|
|
`09 Oct` |P-00-112 | | | |
|
|
|
`16 Oct` |P-00-112 | | | |
|
|
|
`23 Oct` |P-00-112 |Tooba | | |
|
|
|
`30 Oct` |P-00-112 | | | |
|
|
|
`06 Nov` |P-00-112 | | | |
|
|
|
`13 Nov` |P-00-112 | | | |
|
|
|
`20 Nov` |P-00-112 | | | |
|
|
|
`27 Nov` |P-00-112 | | | |
|
|
|
`04 Dec` |P-00-112 |Johan | Story of sequencing his personal genome | |
|
|
|
`11 Dec` |P-00-112 | | | |
|
|
|
`18 Dec` |P-00-112 | | | | |
|
|
\ No newline at end of file |