update oct24

content/posts/oct24_fishchic.md

@@ -0,0 +1,14 @@
+---
+title: "Preprint describing single cell multiomics analysis of zebrafish embryos"
+date: 2024-09-24
+draft: false
+language: en
+featured_image: ../assets/images/posts/zebrafish_umaps.png
+summary: We just released a new preprint describing our single cell multiomics analysis of histone modifications and gene expression of zebrafish embryos
+author: vivek
+authorimage: ../assets/images/global/author.png
+categories: News
+tags: News
+---
+
+We are excited to [release our new preprint](https://www.biorxiv.org/content/10.1101/2024.09.23.614335v1) describing a single-cell multiomics analysis of histone modifications and gene expression during zebrafish development. By applying our newly developed experimental protocol called TChIC, we show how histone modifications and transcription are correlated during development and how a lineage-specific activation and silencing of key developmental genes is achieved. Also, we apply an explainable machine learning model to identify active/repressive roles of transcription factors based on their chromatin signature.

content/publications/_index.md

@@ -4,6 +4,13 @@ title: 'Publications'
 archive: https://scholar.google.com/citations?view_op=list_works&hl=en&hl=en&user=gDipTycAAAAJ&sortby=pubdate
 
 paper:
+  - Title: "Single-cell multi-omic analysis reveals principles of transcription-chromatin interaction during embryogenesis"
+    Authors: Bhardwaj V, Griffa A, Viñas Gaza H, Zeller P, van Oudenaarden A
+    Year: 2024
+    Journal: biorXiv
+    Link: "https://www.biorxiv.org/content/10.1101/2024.09.23.614335v1.full"
+    Weight: 1
+
   - Title: "User-friendly exploration of epigenomic data in single cells using sincei"
     Authors: Bhardwaj V, Mourragui S
     Year: 2024
@@ -21,7 +28,7 @@ paper:
   - Title: "Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis"
     Authors: Zeller* P, Yeung* J, Gaza HV, de Barbanson BA, Bhardwaj V, Florescu M,  van der Linden R, van Oudenaarden A.
     Year: 2023
-    Journal: Nat. Genetics
+    Journal: Nature Genetics
     Link: "https://www.nature.com/articles/s41588-022-01260-3"
     Weight: 1
 
@@ -35,7 +42,7 @@ paper:
   - Title: MAPCap allows high-resolution detection and differential expression analysis of transcription start sites.
     Authors: Bhardwaj V*, Semplicio G*, Erdogdu NU, Manke T & Akhtar A
     Year: 2019
-    Journal: Nat. Commun.
+    Journal: Nature Communications
     Link: "https://www.nature.com/articles/s41467-019-11115-x"
     Weight: 1
 
@@ -49,21 +56,8 @@ paper:
   - Title: "High-resolution TADs reveal DNA sequences underlying genome organization in flies."
     Authors: "Ramírez F*, Bhardwaj V*, Arrigoni L, Lam KC, Grüning BA, Villaveces J, Habermann B, Akhtar A & Manke T"
     Year: 2018
-    Journal: "Nat. Commun."
+    Journal: Nature Communications
     Link: "https://www.nature.com/articles/s41467-017-02525-w"
     Weight: 1
 
-  - Title: "DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome."
-    Authors: "Aktaş T, Avşar Ilık İ, Maticzka D, Bhardwaj V, Pessoa Rodrigues C, Mittler G, Manke T, Backofen R & Akhtar A"
-    Year: 2017
-    Journal: Nature
-    Link: "https://www.nature.com/articles/nature21715"
-    Weight: 1
-
-  - Title: "deepTools2: a next generation web server for deep-sequencing data analysis."
-    Authors: "Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F & Manke T"
-    Year: 2016
-    Journal: "Nucleic Acids Res."
-    Link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987876/"
-    Weight: 1
 ---

content/team/_index.md

@@ -4,7 +4,7 @@ title: 'Team'
 member:
   - Name: "Vivek Bhardwaj"
     Image: ../assets/images/team/vbhardwaj_headshot.png
-    Jobtitle: "PI"
+    Jobtitle: "Group Leader"
     Linkedinurl: "https://www.linkedin.com/in/vivekbhr"
     Mail: "[email protected]"
     Weight: 1
@@ -30,6 +30,13 @@ member:
     Mail: "#"
     Weight: 1
 
+  - Name: "Caspar Bannink"
+    Image: ../assets/images/team/unknown.jpg
+    Jobtitle: "Intern"
+    Linkedinurl: "#"
+    Mail: "#"
+    Weight: 1
+
   - Name: "You"
     Image: ../assets/images/team/unknown.jpg
     Jobtitle: "Join Us"

hugo.yaml

@@ -64,7 +64,7 @@ params:
       - text: "By learning the quantitative, dose-response relationship between the epigenetic factors and the decision making process of the cells, we would be able to efficiently reprogram the stem cells into a desired cell type. We can use this understanding to build therapies towards regenerative medicine, healthy aging and cancer."
     links:
       - text: Learn more about epigenetic reprogramming
-        url: "#"
+        url: "posts/references/"
 
   p2:
     heading: "Our approach"
@@ -82,7 +82,7 @@ params:
       - text: "We apply a data-driven biology approach to our projects. Half of our work is focussed on extracting new insights from quantitative epigenomics and multi-omics data of developing cells, with the aim to learn new mechanistic models of cell identity and function. The rest half of our work is focussed on building new bioinformatic methods and tools to analyse the data from such technologies, and making them available to biologists."
     links:
       - text: Learn more about our projects
-        url: "posts/news-post-1/"
+        url: "posts/news-1_kickstart/"
     image: "images/pages/vblab_projects.png"
     logos:
       - identifier: a