News

News

 Congratulations to Mathematics PhD student Chris Rackauckas!

 

 Rackauckas TsukubaAward 09201710/09/17 - Chris Rackauckas, a Mathematics Department graduate student researcher in the laboratory of Dr. Qing Nie, won the Best Speaker Award for his student talk at the Tsukuba Global Science Week conference, September 24-27, 2017. Chris is also the recipient of a Ford Foundation fellowship and an NSF GRFP fellow.

The title of Chris’ talk was “The Hidden Information in Biological Randomness.”  This talk discussed how randomness (noise/stochasticity) in biological experiments can be used to distinguish between models which are the same in their average behavior, how noise in biological systems can be controlled, and displayed how hindbrain segmentation in the developing zebrafish hindbrain requires a specific amount of noise in order to produce proper development. 

 

  Congratulations to MCSB PhD student Lara Clemens!

 

Clemens Lara Edinburgh 073117

 

07/31/17 - Lara won an award for best poster in the session "Why Disorder Matters" at the 19th IUPAB (International Union of Pure and Applied Biophysics) Congress and 11th EBSA (European Biophysical Societies' Association) Congress, which took place from July 16-20th, 2017 at the Edinburgh International Conference Centre, Edinburgh, UK. Her poster was entitled,  "Intrinsically disordered signaling proteins can exhibit emergent cooperativity, sequential binding." The conference had over 1100 posters and she is one of 35 winners!  

http://www.iupab2017.org/awards

 

 

 

2017 Opportunity Awards

7/18/17

Congratulations to the winners of this year's CCBS Opportunity Awards competition based on the theme of Crossing Scales with Cell-Level Data! Each winning proposal will receive $10,000 to be shared between the faculty for lab project expenses; and a $1,000 award for research supplies to be shared between student and/or postdoctoral participants. We look forward to hearing about the projects at next year's annual CCBS retreat scheduled for Spring quarter 2018, due to be held in the Los Angeles area!

 

Title
Participants                       
Departments          

Investigating gene regulatory networks in metastasis

Kerrigan Blake, Ryan Davis, PI - Devon Lawson

Dustin Maurer, PI - Eric Mjolsness

Physiology & Biophysics

 

Computer Science

Doublet Cell Sequencing to Elucidate Stem Cell Niche in Mouse Epithelium

Dennis Ma, Nick Pervolarakis, PI - Kai Kessenbrock

Camden Jansen, PI - Ali Mortazavi  

Biological Chemistry

 

Developmental & Cell Biology

Deciphering system-level transcriptional dynamics during development of the mouse epidermis using single-cell RNA-seq

Ziguang Lin, PI - Bogi Andersen

 

Suoqin Jin, PI - Qing Nie 

Biological Chemistry & Department of Medicine 

 

Mathematics 

Characterizing Metastatic Potential by Integrated Analysis of Bulk and Single Cell DNA Sequencing

Kerrigan Blake, PI - Devon Lawson

Scott Vang, PI - Xiaohui Xie 

Physiology & Biophysics

 

Computer Science  

Perform single cell RNA-seq on the fat body of immune stimulated Drosophila melanogaster in order to characterize the heterogeneity of immune response in the fat body

Lorrayne Serra, Christina Wilcox, PI - Ali Mortazavi

 

Bryan Ramirez-Corona, PI - Zeba Wunderlich 

Developmental & Cell Biology

 

Developmental & Cell Biology 

Microscale biogeography of phage-infection and antibiotic resistance in biofilms

Kumar Perinbam, PI - Albert Siryaporn

Tara Gallagher, PI - Katrine Whiteson

Physics and Astronomy

 

Molecular Biology & Biochemistry

Indentification of tumor initiation mechanisms in human skin driven by dynamic interactions between stem cells and their niche

Mike Drummond, PI - Scott Atwood

Adam MacLean, Shuxiong Wang, PI - Qing Nie 

Developmental & Cell Biology

Mathematics 

Dissecting myofibroblast heterogeneity during cutaneous wound healing and regeneration

Adam MacLean, Yangyang Wang, PI - Qing Nie

Christian Guerrero-Juarez, PI - Maksim Plikus

Mathematics 

 

Developmental & Cell Biology

News

 

New publication from Qing Nie and Maksim Plikus on Rapid Spatiotemporal Hair Growth Patterning

July 11, 2017: Read more about their research in UCI News.
                      Full text of the article may be read on eLife.

 

Ali Mortazavi to share $10 million in NIH funding for critical genome mapping

With new NIH funding, Ali Mortazavi, UCI assistant professor of developmental & cell biology, will study the structure of all expressed genes using state-of-the-art, long-read sequencing technologies. Steve Zylius / UCI

 

                                                                                                                                                                                                                                     

February 3rd, 2017 - The National Institutes of Health is expanding its effort to create a fundamental genomics resource for scientific use in studying human health and disease. And through its Encyclopedia of DNA Elements Project, UCI assistant professor of developmental & cell biology Ali Mortazavi will share $10 million in grant funding over four years with the California Institute of Technology to establish one of eight mapping centers across the nation to pinpoint where genes and the regulatory elements that control them lie within the genome. With this award, the UCI-Caltech Precision Transcriptome Center will be able to explore the structure of all expressed genes using state-of-the-art, long-read sequencing technologies across a broader diversity of biological samples – including those from individuals with various diseases, as well as highly specialized cells – to expand the catalog of candidate functional elements in the human and mouse genomes.

 

Mathematician Qing Nie awarded foundation grant to study cancer drug resistance

Qing Nie and fellow researchers received funding from the Jayne Koskinas Ted Giovanis Foundation for Health & Policy and the Breast Cancer Research Foundation.

January 30th, 2017 - UCI mathematics professor Qing Nie and his collaborators have been awarded $455,000 to study cancer drug resistance by the Jayne Koskinas Ted Giovanis Foundation for Health & Policy and the Breast Cancer Research Foundation. Along with an interdisciplinary team of experimental cancer biologists, engineers and mathematicians, Nie hopes to identify novel and more effective treatments for patients with breast cancer. Drug resistance is a key impediment to breast cancer therapy. While genetic mechanisms of drug resistance have been a focus of many studies, the ability of a cell to dynamically evade drugs through nongenetic means ­– such as plasticity, an organism’s capacity to adapt to environmental changes – is an often overlooked mechanism for lack of drug efficacy. “Cellular plasticity gives rise to dynamic tumor difference through the generation of distinct subpopulations with diverse properties, including susceptibility to therapy,” Nie said. “We hypothesize that cell state plasticity contributes to drug resistance and that an integrated experimental and modeling approach can be used to identify rational approaches to overcome plasticity-induced resistance.”

CCBS Opportunity Award Competition

Crossing Scales with Cell-Level Data

This means research that leverages data gathered at the level of single cells to integrate understanding at higher and lower levels. For example, the successful project might use such data to better relate the properties of tissues and organs to the interactions among molecules and genes.

• Step I: Before 12:30 PM on Sunday, hand in (or email to Karen Martin) a one paragraph abstract (can even be handwritten) briefly describing the nature of the project

• Step II: Send a more complete description (up to three pages) by email by Monday April 10th, to ccbs@uci.edu.

       Currently, a review committee is being established and we anticipate awards to be announced by June 15, 2017.         

 

2016 Opportunity Awards

Congratulations to the winners of this year's CCBS Opportunity Awards competition based on the theme of Mechanisms of Disease! Each winning proposal will receive $10,000 to be shared between the faculty for lab project expenses; and a $1,000 award for research supplies to be shared between student and/or postdoctoral participants. We look forward to hearing about the projects at next year's annual CCBS retreat scheduled for March 31 - April 2nd, 2017, due to be held in Pasadena, CA! 

Title
Participants
Departments

Single Cell Heterogeneity in Wnt and Metabolism in Xenograft Colon Tumors Xenografts

 

George Chen, Marian Waterman / TBD, Kai Kessenbrock & Devon Lawson
Microbiology & Molecular Genetics / Biological Chemistry & Physiology & Biophysics 

Understanding the systems-level changes during breast tumorigenesis using single cell RNA-seq

 

Quy Nguyen, Kai Kessenbrock / Tao Peng, Qing Nie 
Biological Chemistry / Mathematics 

Metabolic profiling of bacterial persister cell formation and virulence activation 

 

Jenu Chacko, Michelle Digman / Anerudh Kannan, Albert Siryaporn 
Biomedical Engineering & Laboratory for Fluorescence Dynamics / Physics & Astronomy 

Nuclear blebbing and lamin-mediated defets in cardiomyopathies

 

Kathryn Manakova, Jun Allard / Mehrsa Mehrabi, Anya Grosberg & Michael Zaragoza 
Mathematics / Biomedical Engineering & Pediatrics 

Dynamics of IncRNAs in the X inactivation center in mouse ES and human breast cancer cells 

 

Heather Karner, Sha Sun / Lily Li, Zeba Wunderlich / Praveer Sharma, Tom Schilling 
Developmental & Cell Biology / Developmental & Cell Biology / Developmental & Cell Biology 

Spatial dynamics of mutation accrual in melanocytic nevi

 

Rolando Ruiz, Anand Ganesan / Pete Taylor, Olivier Cinquin / Sebastien de Feraudy
Biological Chemistry & Dermatology / Developmental & Cell Biology / Dermatopathology 

Gli Phospohrylation and Sufu involvement in Drug Resistant Basal Cell Carcinoma

 

Kerrigan Blake, Scott Atwood / Leo Lagunes, Lee Bardwell & German Enciso 
Developmental & Cell Biology / Developmental & Cell Biology & Mathematics 

Investigating mechanisms of epileptic seizure onset 

 

Logan Harriger, Beth Lopour / Sean Horan, John Lowengrub 
Biomedical Engineering / Mathematics 
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