On-campus Research Opportunities (Undergraduate)

This page is updated annually. Some projects may already be taken, and new projects may be available. The projects below give an indication of the types of projects available in each lab, but please browse faculty web pages and contact professors directly to discuss current opportunities.

Labs with Undergraduate Projects

Vikas Bansal,

Steve Briggs,

Pieter Dorrestein,

Yoav Freund,

Kyle Gaulton,

Michael Gilson,

Christopher Glass,

Lawrence Goldstein,

Melissa Gymrek,

Jina Huh,

Amy Kiger,

Andrew McCammon,

Siavash Mirarab,

Pavel Pevzner,

Michael Rosenfeld,

Julian Schroeder,

Palmer Taylor,

Gene Yeo,

  • Gene Yeo, Cellular and Molecular Medicine
  • Gene Yeo, Cellular and Molecular Medicine

Sheng Zhong,

Vikas Bansal | Pediatrics

Vikas Bansal | Pediatrics

Email Contact: vibansal [at] ucsd.edu

Research in our lab is focused on human genetic variation and understanding its role in human disease using a combination of computational algorithms, statistical analysis and data from high-throughput DNA sequencing technologies. We have a number of projects available for rotation students that have the potential to become thesis projects. Students with an interest in developing new algorithms/methods and analyzing high-throughput DNA sequencing data are welcome to contact us.

Project: PCR duplication rate in high-throughput DNA sequencing experiments

When: Winter 2016, Spring 2016, Summer 2016, Any Quarter
Last updated: 01/13/2016

PCR amplification is an important step in the preparation of DNA sequencing libraries for high-throughput sequencers. Estimating the true PCR duplication rate is important to avoid bias in downstream analyses such as variant calling (DNA-seq), estimating gene expression levels (RNA-seq) and detection of allele specific binding (Chip-seq). In this project, the goal is to estimate and analyze the PCR duplication rate using statistical methods that utilize genetic variation present in an individual human genome. 

Vikas Bansal | Pediatrics

Email Contact: vibansal [at] ucsd.edu

Research in our lab is focused on human genetic variation and understanding its role in human disease using a combination of computational algorithms, statistical analysis and data from high-throughput DNA sequencing technologies. We have a number of projects available for rotation students that have the potential to become thesis projects. Students with an interest in developing new algorithms/methods and analyzing high-throughput DNA sequencing data are welcome to contact us.

Project: Small insertion/deletion variants in the human genome

When: Winter 2016, Spring 2016, Summer 2016, Any Quarter
Last updated: 01/13/2016

Short insertions/deletions (indels) represent the second most frequent form of variation in the human genome and are frequently the causal mutation in rare Mendelian disorders. Short indels are over-represented in low-complexity regions of the genome that are prone to errors during library preparation and sequencing and mis-alignment after sequencing. We currently lack an accurate estimate of the number of short indels in an individual human genome. The goal of this project is to develop new methods for the accurate detection of indels in an individual human genome and to build a gold standard set of indels using multiple types of DNA sequencing datasets including long read PacBio and Hi-C.

Vikas Bansal | Pediatrics

Email Contact: vibansal [at] ucsd.edu

Research in our lab is focused on human genetic variation and understanding its role in human disease using a combination of computational algorithms, statistical analysis and data from high-throughput DNA sequencing technologies. We have a number of projects available for rotation students that have the potential to become thesis projects. Students with an interest in developing new algorithms/methods and analyzing high-throughput DNA sequencing data are welcome to contact us.

Project: Variant calling in difficult regions of the genome using Hi-C data

When: Winter 2016, Spring 2016, Summer 2016, Any Quarter
Last updated: 01/13/2016

Hi-C technology, a method originally developed to study the 3-D architecture of genomes, has found many applications in the assembly and analysis of genetic variation in human genomes. We have previously published a method to generate chromosomal-scale haplotypes using whole-genome Hi-C data (Nature Biotech. 31, 1111–1118, 2013). In this project, he goal is to utilize Hi-C read pair data to identify mutations in regions of the genome that are not accessible using standard DNA sequencing approaches. This project potentially involves both computational methods development and generation of sequence data using the Hi-C method.

Steve Briggs | Biological Sciences

Steve Briggs | Biological Sciences

Email Contact: sbriggs [at] ucsd.edu

The specific state of the proteome in a given cell, tissue, or organism is known as the proteotype. The proteotype integrates constraints imposed by the genotype, the environment, and by developmental history (e.g., a leaf cell has a different proteotype than a root cell with the same genotype in the same environment). The proteotype directly determines phenotype since all molecules are made by and regulated by proteins. Thus, a complete description of the proteotype should define a phenotype at the molecular level. We are constructing an Atlas of Proteotypes that currently includes 162,777 peptides from 41,553 proteins in 65 different tissues and stages of development. In addition, we have identified and measured more than 30,000 phosphopeptides from these same samples. The 65 resultant proteotypes are revealing thousands of unanticipated regulatory relationships. The relationships between mRNA levels and protein levels are fascinating; they indicate that protein levels from some genes are regulated by transcription but that most protein levels are under post-transcriptional control. Inspection of our data explains tissue specific traits such as oil accumulation in the embryo that results from selective accumulation of proteins from common mRNAs.

Project: Stoichiometry of the cell

When: Spring 2012, Summer 2012, Fall 2012
Last updated: 04/08/2012

With the rise of quantitative proteomics it is now possible to measure the absolute number of protein molecules in a cell. We are using multiple reactions monitoring (MRM) with a triple quadrupole mass spectrometer of heavy and light isotope-labeled peptides to quantify signaling and metabolic dynamics with a focus on the post-translational modifications of phosphorylation and acetylation. By placing biology on a quantitative basis we are contributing to several fundamental advances: the ratios of different proteins to each other are being determined (i.e., the stoichiometry); results from our lab can be combined with data from other labs because they are measured in absolute units; the ratios of proteins to metabolites or RNAs can be ascertained. We are constructing pathway proteotypes for signaling and metabolism to identify proteins whose levels are incompatible with a simple role in the process. To contribute to this effort we would like a student to construct an MRM database. The database will store all the heavy peptides we have available in the lab along with information about the proteins from which they are derived. We will store MS/MS information for peptides that we have observed in our proteome surveys using linear ion trap mass spectrometers. The database will store all reaction/transition data that we have obtained for each peptide along with the signal strength for each reaction product. MS1 scans with the triple quadrupole mass spectrometer will be included to evaluate the purity/intensity of the heavy peptides. This database will be of great use to the many labs that are beginning to place biology on a quantitative foundation.

Calit2 Faculty | Calit2

Calit2 Faculty | Calit2

Project: Calit2 Summer Undergraduate Research Program

When: Summer 2012, Summer 2013
Last updated: 05/15/2012

The UCSD Calit2 Summer Undergraduate Research Scholar Program provides college students with the opportunity to perform hands-on research under the guidance of a UCSD faculty advisor over a 10-week period. The student can either assist in an ongoing research project or propose a new project. Students choose and work with a faculty advisor to develop a research proposal as part of the application process. In keeping with Calit2's multidisciplinary thrust, students from all academic majors are encouraged to apply.

Students will attend weekly seminars to learn more about applying to and preparing for graduate school, funding opportunities for research, connecting with current UCSD graduate students, career opportunities in academia and industry, and making good scientific presentations. All participants will display the results of their research efforts at a poster session at the end of the program a Certificate of Merit will be awarded.

For more information, see the program website, this article, and recent summer projects.

Application deadline has been early March each year.

Pieter Dorrestein | School of Pharmacy

Pieter Dorrestein | School of Pharmacy

Email Contact: pdorrestein [at] ucsd.edu

Project: Post-Translational Modifications Projects

When: Open
Last updated: 03/04/2009

The Dorrestein laboratory is interested in the functional aspects and biosynthesis of post-translational modifications (PTMs). Of particular interest are orphan genes (genes currently assigned to have no known function) that are responsible for the generation of bioactive natural products (e.g. antibiotics, anti-cancer agents etc.) or PTMs. This research aims to understand the functions of such genes by the use of high-resolution mass spectrometry. To achieve this goal, the lab will have the most advanced mass spectrometer on the UCSD campus. Please see the Research page on the lab website for descriptions of current research projects.

Yoav Freund | Computer Science and Engineering

Yoav Freund | Computer Science and Engineering

Email Contact: yfreund [at] ucsd.edu

Project: Digital Mouse Brain Atlas

When: Summer 2013, Any Quarter
Last updated: 08/26/2013

This Project is in collaboration with the Kleinfeld Lab (http://physics.ucsd.edu/neurophysics/) and the Mitra Lab (http://brainarchitecture.org/mouse/about).

The idea is to use a combination of machine learning and computer vision algorithms to create a digital atlas of the mouse brain.

This would require developing detectors of landmarks that exist in a majority of the brains. As the data size is large (tens of tera-bytes) the work will involve using a hadoop cluster.

Requirements: Python, computer vision, machine learning/statistics.
 

Kyle Gaulton | Pediatrics

Kyle Gaulton | Pediatrics

Email Contact: kgaulton [at] ucsd.edu

The Gaulton lab studies the effects of human genetic variation on gene regulation and diabetes risk. We use computational and statistical methods to integrate genome sequence information with epigenomic annotation and molecular QTL data.

Project: Genetic and epigenomic fine-mapping of diabetes risk loci

When: Any Quarter
Last updated: 05/27/2016

This project involves dense genetic fine-mapping of diabetes risk loci, integrating fine-mapping data with large-scale genomic and epigenomic maps using published and novel models to identify causal variants, cell types and networks, and applying these predictive models to identify additional diabetes risk loci.

Kyle Gaulton | Pediatrics

Email Contact: kgaulton [at] ucsd.edu

The Gaulton lab studies the effects of human genetic variation on gene regulation and diabetes risk. We use computational and statistical methods to integrate genome sequence information with epigenomic annotation and molecular QTL data.

Project: Predicting causal genes at diabetes risk loci

When: Any Quarter
Last updated: 05/27/2016

This project involves development of novel methods for integrating genetic association data with epigenomic annotation, expression QTLs and chromatin QTLs to predict causal genes of diabetes risk variants.

Kyle Gaulton | Pediatrics

Email Contact: kgaulton [at] ucsd.edu

The Gaulton lab studies the effects of human genetic variation on gene regulation and diabetes risk. We use computational and statistical methods to integrate genome sequence information with epigenomic annotation and molecular QTL data.

Project: Predicting genome-wide pleiotropic effects of diabetes risk variants

When: Any Quarter
Last updated: 05/27/2016

This project involves development of novel mixture model approaches to predicting and quantifying the extent of pleiotropy among diabetes risk variants genome-wide.

Michael Gilson | School of Pharmacy

Michael Gilson | School of Pharmacy

Email Contact: mgilson [at] ucsd.edu

We work on many aspects of molecular mechanism, modeling and design.  Our core interests are in the physical chemistry and algorithms underpinning computer-aided drug design methods, but we also have much wider interests, such as simple model receptors for studying molecular recognition; how molecule motors work; chemical informatics and its interface with bioinformatics; how membranes work; and synthetic catalysts and nanoparticles.

Project: Information theory studies of protein sequence and structure

When: Fall 2015, Winter 2016, Spring 2016, Summer 2016
Last updated: 06/24/2015

While working on methods of computing entropy from molecular simulation data, we stumbled on an interesting mathematical angle for studying correlations in high-dimensional spaces. The math can be applied in various realms, and we got some interesting results applying it to residue-residue (and higher-order) correlations within protein sequences.

Thus, this would be an exploratory project to see if we can learn new things about sequence-function relationships in proteins, and maybe about how to design new proteins, by studying residue-residue correlations, particularly in the context of 3D protein structures.

Christopher Glass | Cellular and Molecular Medicine

Christopher Glass | Cellular and Molecular Medicine

Email Contact: ckg [at] ucsd.edu

Dr. Glass’ primary interests are to understand transcriptional mechanisms that regulate the development and function of macrophages. Macrophages play key roles in immunity, wound repair, development and tissue homeostasis. Dysregulation of macrophage functions contribute to a broad spectrum of human diseases, including atherosclerosis, diabetes, neurodegenerative diseases, and cancer. A major effort of the Glass laboratory is to use genomics assays and associated bioinformatics approaches to understand how macrophage gene expression programs are established and how they are influenced by different tissue environments and disease. An important concept to emerge from these studies is that enhancers can be exploited to deduce the transcription factors and upstream signaling pathways that drive context-specific transcriptional outputs. Students are welcome to select projects from current areas of active investigation.

Project: Natural genetic variation and macrophage gene expression

When: Any Quarter
Last updated: 07/26/2017

Many lines of evidence, including genome-wide association studies, indicate that non-coding genetic variation plays a major role in determining phenotypic diversity. We were among the first laboratories to define the impact of natural genetic variation on enhancer selection and function (Heinz et al, Nature 2013 PMID 24121437), but at present it remains difficult to predict the impact of non-coding variation on gene expression. In a novel and ambitious effort, we systematically characterized the genome wide patterns of mature RNA (RNA-seq), nascent RNA (GRO-Seq), transcriptional initiation (5’GRO-seq), histone modifications and binding profiles of lineage-determining and signal-dependent transcription factors (ChIP-seq), DNA methylation (bisulfite sequencing), and chromatin conformation (HiC, capture HiC and PLAC-seq), in resting and activated macrophages derived from 5 different inbred strains of mice providing ~60 million single nucleotide variants, ~6 million InDels and several hundred thousand structural variants. This data set provides a unique resource for investigating the impact of non-coding variants on transcription factor binding, enhancer activation and target gene expression. We are currently developing new computational methods for analyses of these data with a goal of explaining effects of non-coding mutations and predicting patterns of gene expression in new mouse strains. Related projects are investigating the relationships of genetic variation between selected mouse strains and their different susceptibilities to metabolic and cardiovascular disease. This general project area is both challenging and open ended and there are a wide range of directions that rotation projects could take. As examples, recent rotation students have implemented machine learning approaches to investigate how sequence variants affect collaborative binding between lineage-determining transcription factors.

Christopher Glass | Cellular and Molecular Medicine

Email Contact: ckg [at] ucsd.edu

Dr. Glass’ primary interests are to understand transcriptional mechanisms that regulate the development and function of macrophages. Macrophages play key roles in immunity, wound repair, development and tissue homeostasis. Dysregulation of macrophage functions contribute to a broad spectrum of human diseases, including atherosclerosis, diabetes, neurodegenerative diseases, and cancer. A major effort of the Glass laboratory is to use genomics assays and associated bioinformatics approaches to understand how macrophage gene expression programs are established and how they are influenced by different tissue environments and disease. An important concept to emerge from these studies is that enhancers can be exploited to deduce the transcription factors and upstream signaling pathways that drive context-specific transcriptional outputs. Students are welcome to select projects from current areas of active investigation.

Project: Nature and nurture of microglia

When: Any Quarter
Last updated: 07/26/2017

Each population of tissue resident macrophages exhibits a distinct pattern of gene expression that is tuned to the developmental and homeostatic needs of that tissue. For example, brain macrophages called microglia produce factors that are trophic for neurons and monitor synapses, functions that require a brain-specific program of gene expression. A key question is how this tissue-specific program of gene expression is achieved. Through analysis of gene expression and enhancer landscapes, we obtained evidence that the microglia-specific molecular phenotype results from instructive signals in the brain that direct the activation of microglia-specific enhancers (Gosselin et al., Cell 2014 PMID 25480297). Of particular interest, delineation of the gene expression patterns and enhancer landscapes of human microglia revealed that a substantial fraction of the genes associated with non-coding GWAS risk alleles are preferentially or exclusively expressed in microglia, and many are brain environment dependent (Gosselin et al. Science 2017 PMID 28546318). These findings raise several important questions that are under active investigation, including what are the environmental factors that dictate the brain specific program of gene expression and how do human genetic variants affect the regulation of genes that are linked to neurodegenerative disease. We are taking a multi-disciplinary approach including studies of in vivo mouse models, in vitro human iPSC-derived microglia, genomic assays of microglia nuclei derived from control and Alzheimer’s disease brains, and direct analyses of the relation of genotype to gene expression in a growing of RNA-seq data base derived from purified human microglia. As an example, a recent rotation project investigated the question of whether there is any relationship between circulating monocytes (a white blood cell that can differentiate into macrophages in tissues) and microglia gene expression patterns from the same individual. 

Lawrence Goldstein | Cellular and Molecular Medicine

Lawrence Goldstein | Cellular and Molecular Medicine

Email Contact: lgoldstein [at] ucsd.edu

Project: Stem Cell GWAS in Alzheimers

When: Any Quarter
Last updated: 04/19/2012

Genome-wide association studies (GWAS) have identified polymorphic variants in many new genes linked to late-onset sporadic Alzheimer's disease (SAD). Human stem cells from patients with disease give us the opportunity to examine the connection between these variants and phenotype at the individual and cellular level. Currently we are investigating the role of the sortilin-related receptor 1 (SORL1) gene in the pathogenesis of SAD. Variants in the 5' and 3' regions of SORL1 have been linked to SAD and may lead to defective gene expression, which contributes to amyloid beta production and neuronal death in the disease. However, the variants identified by GWAS are common and not likely to be causative mutations. One important project is to use bioinformatic tools to probe the genomic region around the GWAS-associated risk variants to identify candidate rare polymorphisms, which may have an effect on phenotype. Once these variants are identified, we can genotype stem cell lines for these polymorphisms and design experiments to determine the contribution of these variants to Alzheimer's disease.

Melissa Gymrek | Computer Science and Engineering

Melissa Gymrek | Computer Science and Engineering

Email Contact: mgymrek [at] ucsd.edu

Our overall goal is to understand complex genetic variants that underlie human disease. We are particularly interested in repetitive DNA variants known as short tandem repeats (STRs) as a model for complex variation. Our work focuses on developing computational tools for analyzing and visualizing complex variation from large-scale sequencing data and applying these tools to learn about the contribution of repetitive variation to human disease.

Project: Measuring genetic constraint in the non-coding genome

When: Any Quarter
Last updated: 09/29/2016

A major result from recent genome-wide association studies (GWAS) is that the majority of genetic variants driving common human disease lie in regulatory, rather than protein-coding, regions. While it is relatively straightforward to predict the consequences of mutations in coding regions, we are far from being able to interpret and sift through the large number of non-coding variants arising from whole genome studies. Recent studies have leveraged population-wide genetics datasets to determine genes that are depleted of variation, or "constrained", and thus presumably important for human health. In this project we will develop statistical tests using large panels of human genetic variation to systematically measure constraint for a variety of regulatory annotations and evaluate the utility of these annotations for prioritizing variants from medical genetics studies.

Olivier Harismendy | Pediatrics

Olivier Harismendy | Pediatrics

Email Contact: oharismendy [at] ucsd.edu

The Oncogenomics laboratory is located in the Moores Cancer Center. Its research program is focused on the identification of genetic and epigenetic markers for cancer prevention and progression as well as drug response. The laboratory is a humid laboratory, combining both wet-lab techniques and bioinformatics analysis to study cancer samples from patients and animal models of cancer. The laboratory is also an important partner for multiple principal investigators at the Moores Cancer Center, collaborating on the design, analysis and interpretation of their genomic experiments.

Project: Development of Genomics Virtual Machines in HIPAA compliant cloud

When: Any Quarter
Last updated: 06/09/2016

Genetic information is considered protected health information (PHI) and as a consequence the highest security standards need to be applied for its storage, analysis and sharing. The oncogenomics laboratory is using state of the art iDASH compute cloud for its main computation. As a consequence, we participate in the development of optimal workflows and virtual machines for the analysis of patient-derived genomic datasets such as whole exomes, whole genomes, RNA-seq or genotyping arrays. 

In this project we will develop robust provisioning methods to establish virtual machines capable of running popular human genomic analysis workflows. We will benchmark these machines and workflows and convert some of them into standard recipes for production-grade, reproducible genomic analysis.

Olivier Harismendy | Pediatrics

Email Contact: oharismendy [at] ucsd.edu

The Oncogenomics laboratory is located in the Moores Cancer Center. Its research program is focused on the identification of genetic and epigenetic markers for cancer prevention and progression as well as drug response. The laboratory is a humid laboratory, combining both wet-lab techniques and bioinformatics analysis to study cancer samples from patients and animal models of cancer. The laboratory is also an important partner for multiple principal investigators at the Moores Cancer Center, collaborating on the design, analysis and interpretation of their genomic experiments.

Project: Genetic and epigenetic of cisplatin resistance

When: Any Quarter
Last updated: 06/09/2016

Cisplatin (cDDP) is the most commonly used chemotherapeutic drug, but most cancer eventually become resistant, leading to tumor recurrence. Several biological processes may modulate cDDP sensitivity: Drug import, export, detoxification, DNA repair, apoptosis. Drug resistance is transmitted to daughter cells, and one can build up resistant cell lines in vitro using sequential treatments. We are interested in identifying the genetic mutations that mediate this resistance. For this, we have derived resistant cell-lines from single clones of a cDDP sensitive ovarian cancer cell line. Using exome sequencing as well as target sequencing, we propose to determine mutations in genes and pathways that drive drug resistance. We will then expand the findings to the TCGA samples, using time to recurrence as an indicator of drug sensitivity.

Olivier Harismendy | Pediatrics

Email Contact: oharismendy [at] ucsd.edu

The Oncogenomics laboratory is located in the Moores Cancer Center. Its research program is focused on the identification of genetic and epigenetic markers for cancer prevention and progression as well as drug response. The laboratory is a humid laboratory, combining both wet-lab techniques and bioinformatics analysis to study cancer samples from patients and animal models of cancer. The laboratory is also an important partner for multiple principal investigators at the Moores Cancer Center, collaborating on the design, analysis and interpretation of their genomic experiments.

Project: The role of inherited variation in cancer somatic landscape

When: Any Quarter
Last updated: 06/09/2016

The role of germline or inherited variation in cancer has been studied in selected families and led to the identification of genetic variants that are dominant and responsible for cancer syndromes. Similarly, rare recessive variants with lower penetrance are responsible for the increase risk in breast and ovarian cancer (BRCA1/2). More common variants in the population have also been identified through GWAS, and have revealed multiple SNPs associated a modest increase in cancer risk. Despite these advances, multiple variants of intermediate allelic frequency in the population, or carried by patients with undocumented family history still remain variants of unknown significance (VUS) and can still play a role in tumor development. In addition, the contribution of variants located outside of the coding region has been underexplored and can now be reexamined in the light of recent maps of the regulatory landscape. The long-term goal of this research is to utilize germline genetics variation in cancer prevention and care to better stage patients or predict their response to treatment.

We propose to identify the germline variants in the UCSD Cancer center patients (targeted gene panel) as well as in the public TCGA/ICGC datasets (whole genomes). We will then test these variants, alone or in combination to identify the ones that impact cancer onset, the tumor somatic landscape or tissue specific regulatory network. The project will involve processing of high throughput sequencing data, population genetics and statistical analysis, in a HIPAA compliant cloud-computing environment.

Jina Huh | School of Medicine

Jina Huh | School of Medicine

Email Contact: jinahuh [at] ucsd.edu

My lab works in the fields of human-computer interaction, mobile health, social media, and underserved populations.

Project: InfoMediator: Weaving clinical expertise in online health comunities

When: Any Quarter
Last updated: 07/21/2017

I am looking for a student who can develop browser-based, real-time text classifiers that classify what information online forum posts need as they get posted online in the context of online health communities. The classification model in terms of features and algorithms is there; I need implementation of the model and improvement of performance. For further information, please see:
http://jinahuh.net/infomediator-weaving-clinical-expertise-in-peer-patient-conversations/

Jina Huh | School of Medicine

Email Contact: jinahuh [at] ucsd.edu

My lab works in the fields of human-computer interaction, mobile health, social media, and underserved populations.

Project: Physical activity improvement in elementary school kids through UNISEF bands

When: Fall 2017
Last updated: 07/21/2017

Protege effect refers to changing behavior better when kids are changing behavior for someone else (e.g., friend, pet, parents, etc).

UNISEF bands are designed so that when kids wear it and have physical activity, the data will be collected for funders to give needed goods for kids in developing countries, such as food, shelter, and school items.

We are introducing UNISEF bands, which is a physical activity tracker band that kids can wear on their wrists, to elementary schools. We are collecting data between baseline (not wearing UNISEF bands) and when the kids start wearing the bands to test the efficacy of wearing the bands on improved participation in their running clubs at school.

The students interested in this project will participate in collecting data, analyzing data, and publication of the research.

Jina Huh | School of Medicine

Email Contact: jinahuh [at] ucsd.edu

My lab works in the fields of human-computer interaction, mobile health, social media, and underserved populations.

Project: SHINE-L: Improving Latino families wellness through acoustic sensing

When: Any Quarter
Last updated: 07/21/2017

This project is funded by the NSF Smart and Connected Health program. We are working with Latino families to prevent child obesity through sensing and visualizing behavioral routines at home. For more information, please see:
http://jinahuh.net/fresh-improving-family-routines/
 

Terence Hwa | Physics

Terence Hwa | Physics

Email Contact: thwa [at] ucsd.edu

Terence Hwa, ​Departments of Physics and Molecular Biology

The Hwa lab (a.k.a. the Quantitative Microbiology Lab) uses a combination of experimental and theoretical approaches to elucidate the organizational principles of living systems. The goal is to quantitatively characterize the physiological behaviors and understand how they arise in terms of the underlying molecular interactions. Our lab focuses on the bacterium E. coli, because it is perhaps the best characterized in terms of molecular components and interactions. But we do also study higher organisms together with collaborating labs. Please visit our lab webpage (http://matisse.ucsd.edu) for further information.

Project: Quantitative studies of bacterial physiology

When: Any Quarter
Last updated: 08/26/2013

An outstanding challenge in making biology quantitative and predictive is how to deal with the millions or even billions of missing parameters that describe the underlying molecular interactions. In recent years, our lab pioneered a top-down approach which exploited a number of phenomenological laws to accurately predict the physiological responses of bacteria to environmental and genetic changes (e.g., nutrients, antibiotics, heterologous protein expression) [DOI: 10.1126/science.1192588]. Furthermore, insight from this quantitative physiological approach is able to pinpoint key missing molecular interactions in long-studied biological processes [DOI: 10.1038/nature12446]. The lab has a number of projects further extending this basic approach to a variety of problems in microbiology, including growth transitions, stress response, antibiotic resistance, and biofilm formation.

Lilia Iakoucheva | Psychiatry

Lilia Iakoucheva | Psychiatry

Email Contact: lilyak [at] ucsd.edu

The lab has a variety of bioinformatics projects aimed at improving understanding of the functional impact of autism mutations derived from exome and genome sequencing of the patients. We build spatio-temporal gene co-expression and protein interaction networks for psychiatric diseases and we use these networks to generate the testable hypothesis about the mechanisms of disease. We also test these hypothesis experimentally in the lab, thereby adding a translational aspect to our work. 

Project: Evaluating the effect of splicing mutations on isoform networks in autism

When: Any Quarter
Last updated: 07/21/2017

The project deals with constructing the isoform-level co-expression and protein interaction networks for predicting functional impact of the de novo splice site mutations from the patients with autism spectrum disorder (ASD). Hundreds of splice site de novo mutations are currently identified in the ASD patients, but not a single disease mechanism is established for any of these mutations. We will build and analyze isoform-level networks of brain co-expressed and physically interacting proteins; map de novo ASD mutations onto isoform-level networks to predict their functional impact; and validate the disrupted networks and pathways using CRISPR/Cas technology in neuronal and animal models. This project will discover and characterize cellular and molecular processes that are disrupted by the de novo splice site ASD mutations.

Lilia Iakoucheva | Psychiatry

Email Contact: lilyak [at] ucsd.edu

The lab has a variety of bioinformatics projects aimed at improving understanding of the functional impact of autism mutations derived from exome and genome sequencing of the patients. We build spatio-temporal gene co-expression and protein interaction networks for psychiatric diseases and we use these networks to generate the testable hypothesis about the mechanisms of disease. We also test these hypothesis experimentally in the lab, thereby adding a translational aspect to our work. 

Project: Integrative functional genomic study of pathways impacted by recurrent autism CNV

When: Any Quarter
Last updated: 07/21/2017

Copy number variants (CNVs) represent significant risk factors for Autism Spectrum Disorders (ASD). One of the most frequent CNVs involved in ASD is a deletion or duplication of the 16p11.2 CNV locus, spanning 29 protein-coding genes. Despite the progress in linking 16p11.2 genetic changes with the phenotypic (macrocephaly and microcephaly) abnormalities in the patients and model organisms, the specific molecular pathways impacted by this CNV remain unknown. To test the hypothesis that RhoA signaling is disrupted by this CNV, we will generate KCTD13 and CUL3 mouse models using CRISPR/Cas9 system and investigate dysregulated molecular pathways using RNAseq at various stages of the developing mouse fetal brain.

Amy Kiger | Biological Sciences

Amy Kiger | Biological Sciences

Email Contact: akiger [at] biomail.ucsd.edu

Cells must continuously maintain integrity and compartmentalization with demands for cellular remodeling throughout development, immunity, aging and disease. Using functional genomics, genetics and cell biological approaches in the fruit fly, Drosophila, we are studying the central roles for membrane regulation of dynamic cell structure. We have identified novel endocytosis and autophagy membrane trafficking pathways that control macrophage and muscle remodeling, with relevance to human disease. Current projects in the lab aim to discover new mechanisms of cellular remodeling through functional genomic and proteomic approaches, and to better understand the pathway networks and dynamics during cellular remodeling.

Project: Autophagy networks

When: Any Quarter
Last updated: 08/15/2012
  • Expand on our ongoing co-immunoprecipitation and mass spectrometry datasets to identify protein-protein interactions involved in autophagy.
  • In collaboration with the Ideker lab and the SDCSB Network Assembly Core, analyze coIP results and incorporate functional data into an ‘autophagy network’.
  • Test new insights predicted from network by in vivo autophagy assays.

Amy Kiger | Biological Sciences

Email Contact: akiger [at] biomail.ucsd.edu

Cells must continuously maintain integrity and compartmentalization with demands for cellular remodeling throughout development, immunity, aging and disease. Using functional genomics, genetics and cell biological approaches in the fruit fly, Drosophila, we are studying the central roles for membrane regulation of dynamic cell structure. We have identified novel endocytosis and autophagy membrane trafficking pathways that control macrophage and muscle remodeling, with relevance to human disease. Current projects in the lab aim to discover new mechanisms of cellular remodeling through functional genomic and proteomic approaches, and to better understand the pathway networks and dynamics during cellular remodeling.

Project: Computational analysis of lipid regulators and effectors in Drosophila development

When: Any Quarter
Last updated: 08/15/2012
  • Use databases and bioinformatics to identify all predicted phosphoinositide lipid regulators and effectors (binding proteins) in Drosophila.
  • Mine databases of Drosophila tissue and stage-specific gene expression, function and protein-protein interaction information for each candidate gene (above).
  • Identify potential relationships between regulators and effectors computationally and experimentally.

Amy Kiger | Biological Sciences

Email Contact: akiger [at] biomail.ucsd.edu

Cells must continuously maintain integrity and compartmentalization with demands for cellular remodeling throughout development, immunity, aging and disease. Using functional genomics, genetics and cell biological approaches in the fruit fly, Drosophila, we are studying the central roles for membrane regulation of dynamic cell structure. We have identified novel endocytosis and autophagy membrane trafficking pathways that control macrophage and muscle remodeling, with relevance to human disease. Current projects in the lab aim to discover new mechanisms of cellular remodeling through functional genomic and proteomic approaches, and to better understand the pathway networks and dynamics during cellular remodeling.

Project: High-throughput image analysis of cell morphology

When: Any Quarter
Last updated: 08/15/2012
  • In collaboration with the Tsimring lab at the BioCircuits Institute, optimize newly developed machine learning image analysis algorithms to quantify cell shape and cell shape changes.
  • Conduct new RNAi screens to test optimized image analysis algorithms, and employ established methodology to screen for new and modifying (enhancer/suppressor) gene functions in cellular remodeling.
  • Perform network analysis of large-scale RNAi screen image data.

Andrew McCammon | Chemistry and Biochemistry

Andrew McCammon | Chemistry and Biochemistry

Email Contact: jmccammon [at] ucsd.edu

The McCammon group conducts a very wide range of research activities, from the deeply biological (studies of protein and nucleic acid targets for drugs for infectious diseases, studies of protein kinase regulation, etc.) to the development of mathematical and physical methods for simulating biological processes (development of methods for solving partial differential equations, exploring the role of hydrodynamic interactions in protein-protein association, etc.). All of this work involves the use of computers; we do no experimental work in the traditional sense, but we have extensive collaborations with experimental labs at UCSD, The Scripps Research Institute, The Salk Institute, and elsewhere. A more complete perspective can best be obtained by visiting the McCammon group website (http://mccammon.ucsd.edu/). We welcome undergraduate research participants when space allows, as described in http://mccammon.ucsd.edu/UGResOp.html

Project: Computer-aided Drug Discovery

When: Any Quarter
Last updated: 04/06/2012

Physics-based computational modeling of proteins and other drug targets is developed and applied to a wide variety of diseases. Please see http://mccammon.ucsd.edu/UGResOp.html

Andrew McCammon | Chemistry and Biochemistry

Email Contact: jmccammon [at] ucsd.edu

The McCammon group conducts a very wide range of research activities, from the deeply biological (studies of protein and nucleic acid targets for drugs for infectious diseases, studies of protein kinase regulation, etc.) to the development of mathematical and physical methods for simulating biological processes (development of methods for solving partial differential equations, exploring the role of hydrodynamic interactions in protein-protein association, etc.). All of this work involves the use of computers; we do no experimental work in the traditional sense, but we have extensive collaborations with experimental labs at UCSD, The Scripps Research Institute, The Salk Institute, and elsewhere. A more complete perspective can best be obtained by visiting the McCammon group website (http://mccammon.ucsd.edu/). We welcome undergraduate research participants when space allows, as described in http://mccammon.ucsd.edu/UGResOp.html

Project: Structural Systems Biology

When: Any Quarter
Last updated: 04/06/2012

Physics-based computational modeling of biomolecules and their interactions is used to understand the emergence of cellular behavior. Please see http://mccammon.ucsd.edu/UGResOp.html

Siavash Mirarab | Electrical and Computer Engineering

Siavash Mirarab | Electrical and Computer Engineering

Email Contact: smirarabbaygi [at] ucsd.edu

Our lab specializes in reconstruction of evolutionary histories (phylogenies) from large scale datasets and applications of phylogenetic analyses to downstream analyses. Large-scale datasets include those with many genes and those with many species, and we focus on high accuracy and scalability at the same time. Many projects in this area are available, some of which are described below, but students can contact me to start on other projects as well.

Project: Multiple sequence alignment

When: Fall 2015, Winter 2016, Spring 2016, Summer 2016
Last updated: 10/08/2015

Developing methods for computing a consensus among large numbers of large multiple sequence alignments using the concept of an equivalence class.

Siavash Mirarab | Electrical and Computer Engineering

Email Contact: smirarabbaygi [at] ucsd.edu

Our lab specializes in reconstruction of evolutionary histories (phylogenies) from large scale datasets and applications of phylogenetic analyses to downstream analyses. Large-scale datasets include those with many genes and those with many species, and we focus on high accuracy and scalability at the same time. Many projects in this area are available, some of which are described below, but students can contact me to start on other projects as well.

Project: Reconstruction of species trees from gene trees

When: Fall 2015, Winter 2016, Spring 2016, Summer 2016
Last updated: 10/08/2015

Several projects are available, with different emphasis. Other projects in this general area can also be defined based on student interest.

  1. Improving ASTRAL (an algorithm for species tree reconstruction from gene trees) to handle more varied datasets, to improve scalability as the number of genes increases, and to give better theoretical analysis of the algorithm. An HPC implementation is also of interest.
     
  2. Testing ASTRAL for gene trees that include duplication and loss events in addition to incomplete lineage sorting.
     
  3. Re-analyzing a set of biological datasets using recently developed methods, and comparing their empirical performance

Pavel Pevzner | Computer Science and Engineering

Pavel Pevzner | Computer Science and Engineering

Email Contact: ppevzner [at] ucsd.edu

Project: Undergraduate Projects Available

When: Any Quarter
Last updated: 03/04/2009

See the Projects page on http://www.ubergrid.org for an extensive list of mass spec projects in the Pevzner lab and in collaborating labs. Project themes include mass spec, T-Rex Fossils, and Comparative Proteogenomics.

Michael Rosenfeld | School of Medicine

Michael Rosenfeld | School of Medicine

Email Contact: mrosenfeld [at] ucsd.edu

Lab Location: CMM-West, Rm. 345

Lab Phone: 858-534-5858

Lab Composition and Activities: Five graduate students from several programs, and a talented group of enthusiastic (also helpful) postdoctoral fellows and a full time laboratory manager. We have one general laboratory meeting, one graduate student-only meeting, and one personal meeting each week. We also have joint lab meetings with two other labs weekly.

Research Interests: Our central laboratory focus this year is to continue to utilize global genomic approaches to uncover and investigate the “enhancer code” controlled by new, previously unappreciated pathways that integrate the genome-wide response to permit proper development and homeostasis, and that also functions in disease and senescence. We have investigated these events in differentiated cells, neuronal development, stem cells, and cancer. Our biological focus is on molecular mechanisms of the “enhancer code” regulating learning and memory; aggressive prostate and breast cancer, and they underlying events of senescence/aging. Epigenomic events studied include non-histone methylation events and non-coding RNAs. We are investigating these events in development, breast and prostate cancers, and in inflammation-based disease, including degenerative CNS disease and diabetes. The emerging importance of non-coding RNAs and regulation of nuclear architecture is rapidly altering our concepts of homeostasis and disease. Our laboratory is “Seq-ing” (RIP-seq, ChIP-seq, RNA-seq, GRO-seq, CLIP-seq, ChIRP-seq), and a new “FISH-seq”, for open-ended discovery of long-distance genome interactions to uncover new “rules” of regulated gene transcriptional programs and new roles for lncRNAs in biology of normal, cancer neuro-affective disorders and aging cells. Coupling this with chemical library screens, we hope to introduce new types of therapies based on targeting specific gene enhancers, histone protein readers and writers, and lncRNAs for cancers and other diseases. Recent surprising findings have been novel roles of lncRNAs prostate and breast cancer, connection between DNA damage repair/transcription and replication, and unexpected roles of enhancer RNAs.

Current interests include:

  • The “enhancer code,” Epigenomics and transcriptional regulatory mechanisms.
  • Roles of by ncRNAs in enhancer function in signal-dependent genomic relocation and in establishing subnuclear architecture.
  • Mechanisms of signal-induced tumor chromosomal translocations events and new chemical screens for inhibitors for breast and prostate cancer.
  • The “enhancer code” or regulation of learning and memory, including Reelin-regulated enhancers.
  • Linkage of DNA damage/repair and transcription.
  • Retinoic Acid regulation of Pol III-transcribed DNA repeats in maintenance of the stem cell state, in neuronal differentiation and in senescence.
  • Molecular mechanisms of prevelant disease associated sequence variations (GWAS) in disease susceptibility loci.
  • “Epigenomics” in neuronal differentiation, cancer, diabetes and degenerative brain disease.
  • Answering the question when and how enhancers arise and became functional (stem cells to mature cell types).

Project: Bioinformatics Rotation Projects

When: Any Quarter
Last updated: 08/12/2013

Potential projects include:

  • Projects employing use of genome-wide technologies, including ChIP-seq, GRO-seq, CLIPseq-, RNA-seq, and ChIRP-seq, to elucidate molecular mechanisms of regulated enhancer lncRNA actions in cancer and stem cells;
  • Roles and mechanisms of enhancer actions in prostate and breast cancers;
  • Enhancer-based model of neurodevelopment and CNS disorders;
  • New mechanisms of long non-coding RNAs dictating physiological gene regulation in cancer transcriptional programs;
  • Understanding subnuclear structures: Roles of relocation of transcription units between subnuclear architectural structures in regulated gene expression;
  • Chemical library screens to gene signature and translocation responses as an approach toward new cancer therapeutic reagents;
  • Roles of epigenomic regulators and expression of DNA repeats in stem cells, neuronal differentiation and in senescence.

Julian Schroeder | Biological Sciences

Julian Schroeder | Biological Sciences

Email Contact: jischroeder [at] ucsd.edu

Project: Systems Biology and Engineering of Environmental and Drought Tolerance in Plants

When: Any Quarter
Last updated: 06/24/2015

Julian Schroeder's research is directed at discovering the signal transduction mechanisms and the underlying signaling networks that mediate resistance to environmental stresses in plants, in particular drought, salinity stress and CO2 responses in plants. These environmental (abiotic) stresses have substantial negative impacts on plant growth and crop yields. These environmental stresses are also relevant in reference to climate change and to maintaining available arable land to meet human needs. Research in Julian Schroeder's laboratory is using multidisciplinary approaches including genomics, bioinformatics, cell signaling, network modeling, proteomics and molecular biological towards uncovering the signal transduction network and receptors in plants that translate drought stress hormone reception, CO2 sensing and salinity stress to specific resistance responses. Some of recent research advances are being used in the biotechnology industry with the goal of enhancing stress resistance of plants and crop yields. Undergraduate research projects will include systems biology and bioinformatics and innovative analyses of large scale data sets within this research. Undergraduate research projects will be pursued to model and identify drought stress-induced and CO2-induced signaling networks based on “omic” scale data sets. Models will be directly tested by wet lab experimentation.

Julian Schroeder is Co-Director of the Center for Food and Fuel for the 21st Century. See http://www-biology.ucsd.edu/labs/schroeder for more information on the Schroeder lab.

Selected publications

  • Nishimura et al., Science (2009).
  • H.H. Hu et al., Nature Cell Biol. (2010).
  • T.H. Kim et al. Current Biol (2011).
  • Xue et al., EMBO J. (2011).
  • F. Hauser et al. Current Biol (2011).
  • B. Brandt et al., PNAS (2012).
  • R. Waadt et al., eLife (2014).
  • A.M. Jones et al., Science (2014).
  • C.B. Engineer et al., Nature (2014).
  • B. Brandt, S. Munemasa et al. eLife (2015).
  • See also: http://labs.biology.ucsd.edu/schroeder/publications.html

Palmer Taylor | School of Pharmacy

Palmer Taylor | School of Pharmacy

Email Contact: pwtaylor [at] ucsd.edu

Project: Java Web application, mobile app, and database programming for important marine collection

When: Summer 2012, Fall 2012, Winter 2013
Last updated: 08/01/2012

This project is lead by Project Scientist George Nicola. Please send inquiries to george-nicola at ucsd dot edu.

Seeking advanced undergraduate students to help with a bioinformatics project with very important therapeutic implications. The project entails creating a foundation for a digital library of the marine natural product compounds and specimens collected at the Scripps Institution of Oceanography.

Every year, UCSD investigators travel with state of the art fleet and instrumentation to remote and exotic island nations in order to collect and characterize unique and biodiverse marine species. Natural products from these marine species are sought after for their inherent diversity, and remarkable bioactivity. The specimens from this library have been used extensively in a wide range of applications, including microbiology, molecular genetics, evolution, microbial ecology, agriculture, anti-cancer, antibacterial, and biofuels. Importantly, pharmaceutical companies are increasingly searching for more molecular diversity in the collections of specimens that they screen for activity. However, the marine specimens are difficult to access by external entities because there has never been a systematic cataloguing or organizing of this vast collection. Thus, the primary objective of this project is to build a comprehensive database and web deposition/retrieval portal so that investigators can bring this vast collection of marine specimens and natural products into a suitable format that other researchers can access. A secondary objective is to build a mobile app for researchers to enter specimen data while traveling in the field, which will then synchronize with the main database.

This endeavor will be of special interest to biofuel companies looking for bacterial products for the purposes of alternative energy, and algal species that can be employed in Clean-technology, two rapidly growing areas that are creating jobs in the state of California. There is a much broader impact to creating a central database focal point: many discoveries in the laboratories of the army of researchers at UCSD has led to technologies that have been subsequently patented and commercialized. If a compound from the licensed collection turns out to be a useful drug, a considerable amount of revenue will be realized in the form of milestones and royalties.

Interested students with experience in Java web programming or Android app development should apply. Students will be able to receive course credit for this independent study.

Gene Yeo | Cellular and Molecular Medicine

Gene Yeo | Cellular and Molecular Medicine

Email Contact: geneyeo [at] ucsd.edu

We have a wide scope of projects ranging from developing novel algorithms for studying RNA processing in diseases, development and personalized medicine, and for analyzing single-cell RNA-seq data.

Project: ENCODE RNA binding proteins

When: Any Quarter
Last updated: 08/12/2012

The Yeo lab is responsible for the identification of the RNA sequence elements bound by 250 RNA binding proteins (RBPs) as part of the newest ENCODE (https://www.genome.gov/10005107) efforts. Various computational projects that pertain to integrating RNA binding sites with functional alternative splicing, RNA stability and translational changes to generate global, genome-wide predictions of what each RBP can do are available for enterprising, hard-working graduate/undergraduate students.

Gene Yeo | Cellular and Molecular Medicine

Email Contact: geneyeo [at] ucsd.edu

We have a wide scope of projects ranging from developing novel algorithms for studying RNA processing in diseases, development and personalized medicine, and for analyzing single-cell RNA-seq data.

Project: Single-cell Analysis

When: Any Quarter
Last updated: 08/12/2012

Recent studies of single cells demonstrate that the assumption that all cells of the same "type" are identical is simply inaccurate. Single, individual cells from the same population of cells differ by a lot and these differences underlie phenotypic responses to environmental stimuli. The Yeo lab is using microfluidics-based platforms to study whole transcriptome differences in single cells from a variety of biological systems, ranging from embryonic stem cells to diseased motor neurons. One of our projects is to develop new bioinformatic analytics to study cellular heterogeneity during environmental influences.

Sheng Zhong | Bioengineering

Sheng Zhong | Bioengineering

Email Contact: szhong [at] ucsd.edu

We study causal relationships between gene regulation and cellular behaviors, by developing computational and experimental methods on network modeling, stem cell engineering, epigenomic and single-cell analyses.

Project: Continued development of Comparative Epigenome Browser (Undergraduate Research Project)

When: Any Quarter
Last updated: 08/21/2013

The Comparative Epigenome Browser (CEpBrowser, http://www.cepbrowser.org) is an online data management, visualization, and analysis tool that allows the public to perform multi-species epigenomic analysis (Cell, 2012, 149: 1381-1391) (Bioinformatics, 2013, 29 (9): 1223-1225). In collaboration with the ENCODE project, this undergraduate research project will extend CEpBrowser to incorporate new ENCODE and mouse ENCODE data, implement interactive data management features, and implement new data analysis features.