updated ribo-itp page, pubmed link and alumni

Author: cancenik

README.md

@@ -91,7 +91,7 @@ order: -1
 title: Pubmed 
 
 # Optionally, if you want the tab to link to an external site, add a link property
-link: https://pubmed.ncbi.nlm.nih.gov/?term=cenik+c&sort=date
+link: https://pubmed.ncbi.nlm.nih.gov/?term=cenik+c+NOT+thiebault&sort=date
 ---
 ```
 

_alumni/4100_ian_hoskins.md

@@ -1,6 +1,6 @@
 ---
 name: Ian Hoskins
-title: Postdoctoral Fellow
+title: PhD Student
 interests: Computational & Wet Lab
 image: /img/team/ian_hoskins_new.jpg
 im_width: 160

_alumni/4102_yue_liu.md

@@ -1,18 +1,18 @@
 ---
 name: Yue Liu
-title: Postdoctoral Fellow
+title: PhD Student
 interests: Computational & Wet Lab
 image: /img/team/yue_liu.jpg
 im_width: 160
 im_height: 160
 description:
 ---
-Yue is interested in cancer and computational biology. She used to work on how DNA damage response
-affects cancer metabolism with targeted CRISPR-screen. With both wet and dry lab experience,
-she is interested in developing bioinformatics applications that benefit bench work. 
+Yue is interested in cancer and computational biology.  
 She loves to go hiking and play the violin when she is not working.
-* 2011-2014, Shanghai Jiao Tong University,  
+* 2024, University of Texas at Austin,
+Ph.D
+* 2014, Shanghai Jiao Tong University,  
 M.S. Bioinformatics
-* 2007-2011 Shanghai Ocean University,  
+* 2011 Shanghai Ocean University,  
 B.S. Biotechnology
 

_research/RiboITP.md

@@ -17,17 +17,17 @@ permalink: /lab_research-riboitp
 
 
 <p>
-We are thrilled to share a new ribosome profiling approach that leverages the principles of microfluidics and isotachophoresis: <a href="https://www.nature.com/articles/s41586-023-06228-9">Ribo-ITP</a>. Our ongoing work is using Ribo-ITP to characterize translation control in biological contexts that remained beyond reach due to limited availability of biological material. Our studies encompass a broad range of areas, often involving collaborations with domain experts. This work is the culmination of six years of development by many talented scientists. 
+We are thrilled to share a new ribosome profiling approach that leverages the principles of microfluidics and isotachophoresis: <a href="https://www.nature.com/articles/s41586-023-06228-9">Ribo-ITP</a> (Ozadam et al., Nature):
 </p>
 
 <p>
 <i> 
-Translation regulation is critical for early mammalian embryonic development1. However, previous studies had been restricted to bulk measurements2 precluding precise determination of translation regulation including allele-specific analyses. To address this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high coverage measurements enabled the first analysis of allele-specific ribosome engagement in early development and led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allelic-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle stage oocytes is the predominant determinant of protein abundance in the zygote. The novel Ribo-ITP approach will enable numerous applications by providing high coverage and high resolution ribosome occupancy measurements from ultra-low input samples including single cells.
+Translation regulation is critical for early mammalian embryonic development. However, previous studies had been restricted to bulk measurements precluding precise determination of translation regulation including allele-specific analyses. To address this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high coverage measurements enabled the first analysis of allele-specific ribosome engagement in early development and led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allelic-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle stage oocytes is the predominant determinant of protein abundance in the zygote. The novel Ribo-ITP approach will enable numerous applications by providing high coverage and high resolution ribosome occupancy measurements from ultra-low input samples including single cells.
 </i>
 </p>
 
 <p>
 Our lab uses ribosome profiling and Ribo-ITP to study diverse biological questions, often in close collaboration with experts in specific fields. In partnership with Dr. Sarinay-Cenik (UT Austin), we identified naturally occurring human mutations that affect ribosome expression. Collaborating with Dr. Palazzo (University of Toronto), we investigated how the metabolic enzyme PKM influences translation by interacting with ribosomes (<a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10325899/">Kejiou et al., NAR</a>). In work with Dr. Buszczak (UT Southwestern), we used Ribo-ITP to characterize novel allelic variants in the ribosome biogenesis factor AIRIM in human cerebral organoids (<a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10802443/">Ni et al., Nature Cell Biology, in press</a>).
 
-We have also extended Ribo-ITP to other model organisms. In <i>C. elegans</i>, we mapped dynamic changes in translation of maternal mRNAs during the first four cell cycles of embryogenesis (<a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11741243/">Shukla et al.</a>). In yeast, using selective ribosome profiling, we found that Reh1-bound ribosomes accumulate near start codons. Our data suggest that Reh1 is displaced by the elongating nascent peptide and is the final assembly factor released from the 60S ribosomal subunit during its first round of translation (<a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11791190/">Musalgaonkar et al., Nature Communications</a>).
+We have also extended Ribo-ITP to other model organisms. In <i>C. elegans</i>, we mapped dynamic changes in translation of maternal mRNAs during the first four cell cycles of embryogenesis (<a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11741243/">Shukla et al., bioRxiv</a>). In yeast, using selective ribosome profiling, we found that Reh1-bound ribosomes accumulate near start codons. Our data suggest that Reh1 is displaced by the elongating nascent peptide and is the final assembly factor released from the 60S ribosomal subunit during its first round of translation (<a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11791190/">Musalgaonkar et al., Nature Communications</a>).
 </p>

_tabs/pubmed.md

@@ -2,5 +2,5 @@
 order: -1
 hidden: true
 title: Pubmed
-link: https://pubmed.ncbi.nlm.nih.gov/?term=cenik+c&sort=date
+link: https://pubmed.ncbi.nlm.nih.gov/?term=cenik+c+NOT+thiebault&sort=date
 ---

_team/1000_can_cenik.md

@@ -1,6 +1,6 @@
 ---
 name: Can Cenik
-title: Principal Investigator
+title: Associate Professor
 interests: everything
 image: /img/team/can_cenik.jpeg
 im_width: 160