Simaryadav patch 1

_config.yml

@@ -1,19 +1,17 @@
 # Site settings
-title: Translational lymphoma research in the Morin laboratory at Simon Fraser University
-lab_name: Morin Laboratory
+title: Systems immunology lab at the University of Pittsburgh
+lab_name: Jishnu Lab
 author: >
-  Bruno Grande, Ryan Morin and the Morin laboratory
-institution: SFU
-email: [email protected]
-description: >
-  The Morin Laboratory performs cutting-edge lymphoma research using
-  a combination of dry lab and wet lab experiments.
+  Simar, Swapnil and the Jishnu laboratory
+institution: UPitt
+email: [email protected]
+description: "Machine Learning, Networks, Immunology, Coffee and Music"
 baseurl: ""
-url: "https://morinlab.github.io"
-twitter_username: morinryan
-github_username:  morinlab
+url: "https://simaryadav.github.io"
+twitter_username: simaryadav
+github_username:  simaryadav
 images_dir: "/images/"
-
+theme: jekyll-theme-merlot
 # Build settings
 markdown: kramdown
 include: ["_pages"]

_pages/pi/index.md

@@ -1,54 +1,23 @@
 ---
 layout: page
-title: GAMBL
-permalink: /pi/
+title: Contact Us
+permalink: /Contact Us/
 toggle: on
 rank: 6
 ---
 
-# Genomic Analysis of Mature B-cell Lymphomas
-Welcome to the project landing page for GAMBL!
+# Contact Us
 
-```
-  /$$$$$$     /$$$$$$    /$$      /$$   /$$$$$$$    /$$. 
- /$$__  $$   /$$__  $$  | $$$    /$$$  | $$__  $$  | $$. 
-| $$  \__/  | $$  \ $$  | $$$$  /$$$$  | $$  \ $$  | $$. 
-| $$ /$$$$  | $$$$$$$$  | $$ $$/$$ $$  | $$$$$$$   | $$. 
-| $$|_  $$  | $$__  $$  | $$  $$$| $$  | $$__  $$  | $$. 
-| $$  \ $$  | $$  | $$  | $$\  $ | $$  | $$  \ $$  | $$. 
-|  $$$$$$/  | $$  | $$  | $$ \/  | $$  | $$$$$$$/  | $$$$$$$$. 
- \______/   |__/  |__/  |__/     |__/  |_______/   |________/. 
-~~GENOMIC~~~~~~~~~~~~~OF~~~~~~~~~~~~~~~~~B-CELL~~~~~~~~~~~~~~~. 
-~~~~~~~~~~~~~ANALYSIS~~~~~~MATURE~~~~~~~~~~~~~~~~~~~LYMPHOMAS~. 
-```
+Thank you for your interest in our research.
 
-## Overview
+Get in touch with us for any questions or comments regarding our work and publications.
 
-The Morin laboratory is performing a meta-analysis of whole genome sequencing (WGS) and gene expression (RNA-seq) data from B-cell lymphomas using in-house and published data sets. Our analysis will explore copy number (CNV), simple somatic mutation (SSM) and structural variation (SV) patterns within and across common mature B-cell neoplasms spanning Burkitt lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, mantle cell lymphoma and chronic lymphocytic leukaemia. We will compare the prevalence of coding and non-coding driver mutations, recurrent CNVs and SVs (including gene fusions) across this spectrum of cancers. We will specifically focus on SVs involving oncogenes and both immunoglobulin and non-IG partners as well as the relationship between class switch recombination and each malignancy. Our analysis will include the comparison of SSM patterns in non-coding regions affected by aberrant somatic hypermutation (aSHM). We will use mutational signatures to infer mutational processes that contribute to SSMs in each cancer type. We will search for associations between these variables and age, EBV status and molecular subgroups. We will also analyze the available (matched) RNA-seq data for cis-regulatory alterations such as examples of allelic imbalance and mutations that affect splicing. 
+Currently, we have open positions at all levels (e.g., post-docs, graduate students, and undergrads).
 
-## GAMBL presentations
-[Novel Genetic Subgroups Inform on Shared Pathobiology within Adult and Pediatric Burkitt Lymphoma](https://ashpublications.org/blood/article/138/Supplement%201/806/480062/Novel-Genetic-Subgroups-Inform-on-Shared?searchresult=1)
+4011 The Assembly 
+5051 Centre Avenue, Pittsburgh PA 15213
 
-[Constrained FL: A Genetically Distinct Subgroup of Follicular Lymphoma with Low Rates of Somatic Hypermutation and a Reduced Propensity for Histologic Transformation](https://ashpublications.org/blood/article/138/Supplement%201/807/480061/Constrained-FL-A-Genetically-Distinct-Subgroup-of)
+[email protected]
 
-[An Open-Source Toolkit That Powers the Genome-Wide Analysis of Mature B-Cell Lymphomas (GAMBL) Project](https://ash.confex.com/ash/2021/webprogram/Session21061.html)
+412-624-5530
 
-[Complex Structural Variation Associated with Enhancer Hijacking and Loss of Tumor Suppressors in Mantle Cell Lymphoma](https://ashpublications.org/blood/article/138/Supplement%201/675/479519/Complex-Structural-Variation-Associated-with?searchresult=1)
-
-## Summary of genomes by pathology
-
-<div style="margin-bottom: 50px;">
-    <img src="{{ 'projects/pathology_gambl.svg' | prepend: site.images_dir | prepend: site.baseurl }}" />
-</div>
-
-## Simple Somatic Mutation (SSM) Load 
-
-<div style="margin-bottom: 50px;">
-    <img src="{{ 'projects/mutations-1.svg' | prepend: site.images_dir | prepend: site.baseurl }}" />
-</div>
-
-## Structural Variant (SV) Breakpoint Load
-
-<div style="margin-bottom: 50px;">
-    <img src="{{ 'projects/sv-1.svg' | prepend: site.images_dir | prepend: site.baseurl }}" />
-</div>

_pages/projects/index.md

@@ -1,32 +1,20 @@
 ---
 layout: page
-title: Projects
-permalink: /projects/
+title: Publications
+permalink: /Publications/
 toggle: on
 rank: 1
 ---
 
 <div class="lab-wrapper">
     <ul class="lab-list">
     {% for project in site.data.projects %}
-    {% if project.name and project.description %}
         <li>
             <h2>{{ project.name }}</h2>
-            {% if project.photo %}
-                <img class="float-right projects-photo" src="{{ project.photo | prepend: site.images_dir | prepend: site.baseurl }}">
-            {% endif %}
-            {% if project.funding %}
-                <p><b>Funding: </b>{{ project.funding }}</p>
-            {% endif %}
             {% if project.collaborators %}
                 <p><b>Collaborators: </b>{{ project.collaborators }}</p>
             {% endif %}
-            {% if project.assignees %}
-                <p><b>Assignees: </b>{{ project.assignees }}</p>
-            {% endif %}
-            <p>{{ project.description }}</p>
         </li>
-    {% endif %}
     {% endfor %}
     </ul>
 </div>