Merge pull request #49 from ksinghal28/master

Adding lab news updates, people, and publications

_posts/2022-08-01-Khanfar-pathway.md

@@ -0,0 +1,16 @@
+---
+layout: page
+title:  "Mariam Khanfar accepted to Precision Medicine Pathway"
+teaser: "Mariam Khanfar has been awarded a place in the 2022 Cohort of the Precision Medicine Pathway."
+header:
+    image_fullwidth: "genvis-dna-bg_optimized_v1a.png"
+breadcrumb: true
+---
+
+Starting this fall, Mariam will join the Precision Medicine Pathway at Washington University. The overall goal of the Precision Medicine Pathway is to prepare students to be at the forefront of meeting the challenges in defining and implementing precision medicine. The Pathway will introduce students to the use of genomic and genetic information in the diagnosis and treatment of disease, from covering current concepts and practice to identifying gaps that remain to be filled. The Pathway will (a) expand students’ educational experience into the clinical realm; (b) facilitate making clinical connections related to thesis research, where relevant; (c) provide career path information, from introducing potential areas for postdoctoral research to alternatives to the traditional Principle Investigator track.
+
+<div class="row">
+    <div class="small-12 columns">
+        <img src="/assets/img/team/mariam_khanfar.png">
+    </div>
+</div>

_posts/2023-04-11-Xia_ThesisDefense.md

@@ -0,0 +1,9 @@
+---
+layout: page
+title:  "PhD Defense - Congrats Dr. Xia!"
+teaser: "PhD candidate, Huiming Xia, successfully defended her thesis"
+header:
+    image_fullwidth: "genvis-dna-bg_optimized_v1a.png"
+breadcrumb: true
+---
+Huiming Xia, a PhD candidate in the Computational & Systems Biology (CSB) program, successfully presented and defended her PhD thesis on ["Improving Neoantigen Prioritization Methods for Personalized Cancer Vaccines"](https://openscholarship.wustl.edu/cgi/viewcontent.cgi?article=4001&context=art_sci_etds).

_posts/2023-07-27-Richters_MillerDefense.md

@@ -0,0 +1,9 @@
+---
+layout: page
+title:  "PhD Defense - Congrats Dr. Richters!"
+teaser: "PhD candidate, Miller Richters, successfully defended their thesis"
+header:
+    image_fullwidth: "genvis-dna-bg_optimized_v1a.png"
+breadcrumb: true
+---
+Miller Richters, PhD candidate in the Molecular Genetics and Genomics (MGG) program, successfully presented and defended their PhD thesis on "Investigating Novel Neoantigen Sources for Personalized Cancer Vaccines".

_posts/2023-09-11-Singhal-Travel-award.md

@@ -0,0 +1,16 @@
+---
+layout: page
+title:  "ITCR Travel award - Kartik Singhal"
+teaser: "Kartik Singhal received a travel award to present at the 2023 NIH/NCI Informatics Technology for Cancer Research (ITCR) Annual Meeting!"
+header:
+    image_fullwidth: "genvis-dna-bg_optimized_v1a.png"
+breadcrumb: true
+---
+
+Kartik Singhal, a PhD Candidate in the Griffith lab won a travel award to present his poster titled, "A streamlined pipeline for the design and administration of personalized neoantigen cancer vaccines", at the 2023 ITCR annual meeting held in Chicago, Illinois. 
+
+<div class="row">
+    <div class="small-12 columns">
+        <img src="/assets/img/team/kartik_singhal.jpg">
+    </div>
+</div>

_posts/2024-01-05-Freshour_ThesisDefense.md

@@ -0,0 +1,9 @@
+---
+layout: page
+title:  "PhD Defense - Congrats Dr. Freshour!"
+teaser: "PhD candidate, Sharon Freshour, successfully defended her thesis"
+header:
+    image_fullwidth: "genvis-dna-bg_optimized_v1a.png"
+breadcrumb: true
+---
+Sharon Freshour, PhD candidate in the Human and Statistical Genetics (HSG) program, successfully presented and defended her PhD thesis on "Applications of Bioinformatics for Exploring the Genomic Landscape of Cancer and Characterizing Treatment Response for Precision Oncology". She is now working as a Bioinformatics Research Scientist for St. Jude Children’s Research Hospital.

_posts/2024-07-18-wgs_chimeric_twins_paper.md

@@ -0,0 +1,18 @@
+---
+layout: page
+title:  "Lab Publication - Human Genetics and Genomics Advances"
+teaser: "Whole-genome sequences reveal zygotic composition in chimeric twins"
+header:
+    image_fullwidth: "genvis-dna-bg_optimized_v1a.png"
+breadcrumb: true
+---
+While most dizygotic twins have a dichorionic placenta, rare cases of dizygotic twins with a monochorionic placenta have been reported. The monochorionic placenta in dizygotic twins allows in utero exchange of embryonic cells, resulting in chimerism in the twins. In practice, this chimerism is incidentally identified in mixed ABO blood types or in the presence of cells with a discordant sex chromosome. Here, we applied whole-genome sequencing to one triplet and one twin family to precisely understand their zygotic compositions, using millions of genomic variants as barcodes of zygotic origins. Peripheral blood showed asymmetrical contributions from two sister zygotes, where one of the zygotes was the major clone in both twins. Single-cell RNA sequencing of peripheral blood tissues further showed differential contributions from the two sister zygotes across blood cell types. In contrast, buccal tissues were pure in genetic composition, suggesting that in utero cellular exchanges were confined to the blood tissues. Our study illustrates the cellular history of twinning during human development, which is critical for managing the health of chimeric individuals in the era of genomic medicine.
+
+
+<div class="row">
+    <div class="small-12 columns">
+        <img src="/assets/img/news/twins_Yoon.jpeg">
+    </div>
+</div>
+
+Read the paper: [HGG Advances](https://www.cell.com/hgg-advances/fulltext/S2666-2477(24)00040-X)

pages/publications.md

@@ -28,6 +28,10 @@ header:
 <h2 data-magellan-destination="2024">2024</h2>
 <a name="2024"></a>
 
+{% include publication authors="Yoon CJ, Nam CH, Kim T, Lee JS, Kim R, Yi K, Koh JY, Kim J, Won H, Oh JW, Griffith OL, Griffith M, Sung J, Kim TY, Cho D, Choi JS, Ju YS" title="Whole-genome sequences reveal zygotic composition in chimeric twins" journal="HGG Adv. 2024 May" doi="10.1016/j.xhgg.2024.100301" pmid="38773773"%}
+
+{% include publication authors="Hoang MH, Skidmore ZL, Rindt H, Chu S, Fisk B, Foltz JA, Fronick C, Fulton R, Zhou M, Bivens NJ, Reinero CN, Fehniger TA, Griffith M, Bryan JN, Griffith OL" title="Single-cell T-cell receptor repertoire profiling in dogs" journal="Commun Biol. 2024 Apr" doi="10.1038/s42003-024-06174-w" pmid="38649520"%}
+
 {% include publication authors="Ramirez CA, Becker-Hapak M, Singhal K, Russler-Germain DA, Frenkel F, Barnell EK, McClain E, Desai S, Schappe T, Onyeador OC, Kudryashova O, Belousov V, Bagaev A, Ocheredko E, Kiwala S, Hundal J, Skidmore ZL, Watkins MP, Mooney TB, Walker J, Krysiak K, Gomez F, Fronick CC, Fulton RS, Schreiber RD, Mehta-Shah N, Cashen AF, Kahl BS, Ataullakhanov R, Bartlett NL, Griffith M, Griffith OL, Fehniger TA" title="Neoantigen Landscape Supports Feasibility of Personalized Cancer Vaccine for Follicular Lymphoma" journal="Blood Adv. 2024 May" doi="10.1182/bloodadvances.2022007792" pmid="38713894"%}
 
 {% include publication authors="Cannon M, Stevenson J, Stahl K, Basu R, Coffman A, Kiwala S, McMichael JF, Kuzma K, Morrissey D, Cotto K, Mardis ER, Griffith OL, Griffith M, Wagner AH" title="DGIdb 5.0: rebuilding the drug-gene interaction database for precision medicine and drug discovery platforms" journal="Nucleic Acids Res. 2024 Jan" doi="10.1093/nar/gkad1040" pmid="37953380"%}

pages/team.md

@@ -44,12 +44,12 @@ header:
 <h2 data-magellan-destination="Graduate_Students">Graduate Students</h2>
 <a name="Graduate_Students"></a>
 
-{% include team_member member_name="Sharon" full_name="Sharon Freshour, BSc" bio='Sharon is a graduate student in the Human and Statistical Genetics program at Washington University in St. Louis. She graduated from St. Edwards University in Austin Texas in 2016 with a degree in Mathematics.' image="/assets/img/team/sharon_freshour.jpg" role="Graduate Student" %}
-
 {% include team_member member_name="My" full_name="My Hoang, BA" bio='My is a graduate student in the Computational and Systems Biology program at Washington University in St. Louis. She graduated from Earlham College in 2020 with a degree in Biochemistry.' image="/assets/img/team/my_hoang.jpeg" role="Graduate Student" %}
 
 {% include team_member member_name="Mariam" full_name="Mariam Khanfar, MSc" bio='Mariam is a graduate student in the Human and Statistical Genetics program at Washington University in St. Louis. She graduated from Jordan University of Science and Technology in Jordan in 2016 with a B.S. in Medical Laboratory Sciences and a Masters in Diagnostic Molecular Biology and Human Genetics in 2019. ' image="/assets/img/team/mariam_khanfar.png" role="Graduate Student" %}
 
+{% include team_member member_name="Allen" full_name="Allen Li, MSc" bio='Allen is a graduate student in the Computational and Systems Biology program at Washington University in St. Louis. He graduated from Tsinghua University in 2021 with a B.S. in Biological Science and from Harvard University in 2023 with an M.Sc. in Computational Biology and Quantitative Genetics.' image="/assets/img/team/allen_li.png" role="Graduate Student" %}
+
 {% include team_member member_name="Isabel" full_name="Isabel Risch, BSc" bio='Isabel is currently an MD/PhD student in the Computational and Systems Biology program. She completed her undergraduate education at WashU, where she received degrees in Spanish and Biology. She is interested in using bioinformatics to explore the ways in which the immune system interacts with various disease processes, including cancer.' image="/assets/img/team/isabel_risch.png" role="Graduate Student" %}
 
 {% include team_member member_name="Kartik" full_name="Kartik Singhal, BSc" bio='Kartik is a graduate student in the Molecular Genetics and Genomics program at Washington University in St. Louis. He graduated from University of California, Davis in 2018 with a degree in Biotechnology. He is interested in using single cell genomic and transcriptomic techniques to better understand the immune response to tumors.' image="/assets/img/team/kartik_singhal.jpg" role="Graduate Student" %}
@@ -82,10 +82,10 @@ header:
 
 {% include team_member member_name="Luke" full_name="Luke Hendrickson" bio='Luke is a graduate student in the Computer Science program at Missouri University of Science and Technology. He received his B.S. in Computer Science and a minor in Bioinformatics from Missouri University of Science and Technology in 2024. He is working with the lab as a part of the 2024 Summer Genomics Program. He is primarily working on the pVACtools project with the lab.' image='/assets/img/team/luke_hendrickson.jpg' role='Intern' %}
 
-{% include team_member member_name="Johnny" full_name="Johnny Yang" bio='Johnny is a class of 2025 undergraduate student in Chemistry. He joined the lab as an ASPIRE summer scholar student in 2024 summer. He is currently working on a pVACtools project in the lab.' image='/assets/img/team/johnny_yang.png' role='Intern' %}
-
 {% include team_member member_name="Binghan" full_name="Binghan Yan" bio='Binghan is a class of 2027 undergraduate student in Computational Biology. He is working on comparing tools that try to predict neoantigen-TCR interactions.' image='/assets/img/team/binghan_yan.jpg' role='Intern' %}
 
+{% include team_member member_name="Johnny" full_name="Johnny Yang" bio='Johnny is a class of 2025 undergraduate student in Chemistry. He joined the lab as an ASPIRE summer scholar student in 2024 summer. He is currently working on a pVACtools project in the lab.' image='/assets/img/team/johnny_yang.png' role='Intern' %}
+
 <h2 data-magellan-destination="Alumni">Alumni</h2>
 <a name="Alumni"></a>
 
@@ -103,6 +103,8 @@ header:
 
 {% include team_member member_name="Yang" full_name="Yang-Yang Feng, BSc" bio='Yang-Yang is a medical student at Washington University in St. Louis, and conducted a year of research in the Griffith Lab. He completed his undergraduate at Yale University in 2016, where he obtained a B.S. in Molecular Biophysics and Biochemistry. Broadly speaking, he is interested in applying mathematical and computational techniques to investigating the fundamental principles of cancer immunology and translating these discoveries into novel immmunotherapies. More specifically, he was involved in a diverse set of projects in the lab, including <a href="http://civicdb.org">CIViC</a>, <a href="http://dgidb.org">DGIdb</a>, pVACtools, Regtools, and various collaborative clinical efforts.' image="/assets/img/team/yangyang_feng.png" role="Medical Student/MD5" %}
 
+{% include team_member member_name="Sharon" full_name="Sharon Freshour, PhD" bio='Sharon completed her PhD in Human and Statistical Genetics in the Griffith lab in 2024. Previously, she graduated from St. Edwards University in Austin, TX in 2016 with a degree in Mathematics.' image="/assets/img/team/sharon_freshour.jpg" role="Graduate Student" %}
+
 {% include team_member member_name="Felicia" full_name="Felicia Gomez, PhD" bio='Dr. Gomez was a postdoc and then Instructor working in collaboration with the Griffith and <a href="http://www.fehnigerlab.org/">Fehniger Laboratories</a> at the McDonnell Genome Institute and The <a href="http://oncology.wustl.edu">Department of Medicine – Division of Oncology</a>. Dr. Gomez led a deep sequencing analysis of Hodgkin lymphoma genomes with the goal of describing somatic events characteristic of this malignancy.  Dr. Gomez is now Assistant Professor of Medicine with her own lab at WashU but continues to collaborate with members of the Griffith and Fehniger laboratories, as well was the Washington University Genomics Tumor Board on projects related to the genomics of Hodgkin and Non-Hodgkin lymphomas. Dr. Gomez’s research goals include developing strategies to translate genomic data into improved patient care. She is specifically interested in working toward the inclusion of diverse human populations in translational genomic research. Dr. Gomez also has a leadership role in the Department of Medicine as the co-chair of the Trainee Inclusion and Cultural Awareness Task Force. In this role she works to identify challenges related to diversity and inclusion that Medicine trainees face and the implementation of solutions to these challenges.' image="/assets/img/team/felicia_gomez.jpg" role="Instructor in Medicine" %}
 
 {% include team_member member_name="Justin" full_name="Justin Guerra" bio='Justin Guerra is a math major at University of Texas, San Antonio. Justin joined the lab as part of the Amgen Scholars program.' image="/assets/img/team/justin_guerra.jpg" role="Lab Assistant/Staff Curator" %}
@@ -125,7 +127,7 @@ header:
 
 {% include team_member member_name="Avi" full_name="Avinash Ramu, MSc" bio='Avi was a Bioinformatician at the McDonnell Genome Institute. He made major contributions to the Genome Modeling System, regtools, and others. He is currently a PhD student at Washington University.' image='/assets/img/team/avi_ramu.jpg' role='Bioinformatician' %}
 
-{% include team_member member_name="Megan" full_name="Megan Richters" bio='Megan Richters completed a PhD in the Griffith Lab in the Molecular Genetics and Genomics program at Washington University in St. Louis. Previously, she graduated from the University of Louisiana at Monroe in 2014 with a B.S. in Biology. She is interested in assessing the impact of intratumoral heterogeneity on neoantigen prediction accuracy as well as exploring novel sources of neoantigens for personalized cancer vaccines.' image="/assets/img/team/megan_richters.png" role="Graduate Student" %}
+{% include team_member member_name="Miller" full_name="Miller Richters" bio='Miller Richters completed a PhD in the Griffith Lab in the Molecular Genetics and Genomics program at Washington University in St. Louis. Previously, they graduated from the University of Louisiana at Monroe in 2014 with a B.S. in Biology. They are interested in assessing the impact of intratumoral heterogeneity on neoantigen prediction accuracy as well as exploring novel sources of neoantigens for personalized cancer vaccines.' image="/assets/img/team/miller_richters.png" role="Graduate Student" %}
 
 {% include team_member member_name="Lana" full_name="Lana Sheta" bio='Lana originally joined the lab for a summer research project as part of the Amgen Scholars program and worked on the CIViC project. Lana completed her undergraduate degree at the University of Nevada and later transitioned to a part time staff position in the lab' image="/assets/img/team/lana_sheta.jpg" role="Staff Scientist/Editor" %}