The following are the projects and labs that are currently searching for computational postdocs and could host a Collaboratory fellow:

Jonathan Jacobs, MD., Ph.D.
Director, Microbiome Core
UCLA Microbiome Center
Division of Digestive Diseases, Department of Medicine
CHS A3-115
10833 Le Conte Ave.
Los Angeles, CA, 90095
310-825-9333
JJacobs@mednet.ucla.edu
http://www.microbiome.ucla.edu/directory/name/jonathan-jacobs-md-phd/
http://gastro.ucla.edu/site.cfm?id=472

Next-generation sequencing technologies have revolutionized our understanding of the importance of the microbiome in human health. The Jacobs laboratory studies the interaction of gut bacteria and the intestinal immune system, in particular how dysbiosis – i.e. altered composition and function of the intestinal microbiome – contributes to the pathogenesis of inflammatory bowel disease (IBD). This postdoctoral fellowship will focus on multi’omics integration of 16S ribosomal RNA sequence data with clinical metadata, shotgun metagenomics, proteomics, and metabolomics to define microbes and their products that promote IBD and other diseases. Projects include observational cohort studies of gastrointestinal diseases, a longitudinal prospective study of families at high risk for IBD, dietary intervention studies, and animal model experiments (including the use of humanized gnotobiotic mice). This position will also entail collaboration with diverse investigators at UCLA and other Los Angeles area academic centers utilizing the recently established Microbiome Core for their microbiome projects.

Applicants should have extensive experience in bioinformatics analysis of high dimensional datasets in fields such as metagenomics, transcriptomics, proteomics, and metabolomics. The position requires prior statistical training and programming skills, at a minimum the ability to write scripts for data analysis in environments such as R. Past exposure to microbiome research is not required.


Laboratory of Luisa Iruela-Arispe
https://www.mcdb.ucla.edu/Research/Arispe/
Dept. Molecular, Cell and Dev. Biol.
Director, Molecular Biology Institute
Chair, Molecular Biology IDP
(310) 794-5763
arispe@mcdb.ucla.edu

Our laboratory has developed a series of mouse genetic models to delineate the process of endothelial regeneration in vivo. Using these models, we have compiled data sets that reveal the frequency of cell division, potential clonality information, speed of migration, and directionality. We are currently seeking a post-doctoral fellow to mine these data sets and contribute to the understanding of regeneration in blood vessels. The development of computer modeling to mimic the process and predict outcomes of pathology will also be a goal of this project. The new post-doctoral fellow is not expected to have biological background, rather to bring bioinformatics and computer modeling experience to our lab and learn the biological principles from us. Motivation, creativity, a track record of productivity and strong computational biology experience are essential, we will provide the rest.

Luisa Iruela-Arispe, Ph.D.
Professor and Vice-Chair
Dept. Molecular, Cell and Dev. Biol.
Director, Molecular Biology Institute
Chair, Molecular Biology IDP
(310) 794-5763
arispe@mcdb.ucla.edu

Tom Chou
Depts. of Biomathematics and Mathematics

tomchou@ucla.edu
www.biomath.ucla.edu/tchou

Our current research interests involve developing new theoretical and
mathematical frameworks to describe subcellular/macromolecular
biophysics and evolving cell populations in the context of evolution,
immunology, cancer, and drug resistance. While the theoretical tools
we develop are motivated by a specific system or data set, we aim to
formulate models general enough to be applicable to related systems and
future data. Current projects in my lab include:

1. Developing a geometric and statistical mechanical model for
epigenetic inheritance in the context of nucleosome positioning. We
would like to understand, thorough a biophysical model of protein-DNA
interactions, how histone binding is partially preserved through a
replication fork. The relative effects of sequence and histone
dissociation and sliding will be explored.

2. Developing stochastic models of clone lineages and analyzing drug
dose response curves. We will analyze experimental data on
dose-response curves of anti-cancer drugs on barcoded cancer cell
lines (triple negative breast cancer). The in vitro data will be used
to infer the fitness landscape in the presence of one or two drugs. By
using mathematical models that incorporate populations of cell
barcoding and cell heterogeneity, as well as plasticity and dormancy,
we aim to gain understanding into drug resistance and drug synergies.

3. Deriving stochastic models of cellular and lineage aging. We will
derive multispecies stochastic models incorporating age-dependent
birth and death rates and finite lineage ages. Quantities such as a
ordered lineage extinction times will be analyzed and computed. These
results will be cast as a mathematical inverse problem so that
statistical inference in the aging parameters can be performed.


Laboratory of Xinshu (Grace) Xiao
https://www.ibp.ucla.edu/research/xiao/Home.html
Associate Professor, Department of Integrative Biology and Physiology
2000E Terasaki Life Sciences Building
610 Charles E. Young Drive S.
Los Angeles, CA, 90095
Phone: (310) 206-6522
Email: gxxiao@ucla.edu

Our lab develops and applies novel bioinformatic methods to address biomedical questions. We previously developed a series of methodologies to tackle challenges in the analysis of high-throughput RNA-sequencing (RNA-seq) data. These methods were applied to study the function of genomic mutations in gene expression, RNA editing, extracellular RNA profiling and biomarker discovery, and small regulatory RNAs in mammalian cells. Postdoc positions are available to combine the power of bioinformatics with experimental sciences to address questions in the above aspects. We closely collaborate with experts in the biological, medical and clinical realms to investigate these topics. We are looking for highly motivated and ambitious postdocs with a strong bioinformatic background who are excited about an inter-disciplinary training to bridge computational and biomedical sciences.


The Pasarow Mass Spectrometry Laboratory

Kym Francis Faull, Ph.D.
Director, Pasarow Mass Spectrometry Laboratory
Hemel Institute of Neuroscience and Human Behavior
Professor, Department of Psychiatry and Biobehavioral Sciences
David Geffen School of Medicine at UCLA
Tel. 310.206.7881 (office)
310.206.7886 (lab)
Fax 310.206.2161
Email: faull@chem.ucla.edu

General remarks. The UCLA Pasarow Mass Spectrometry Laboratory (PMSL) serves as a research laboratory, a mass spectrometry core laboratory, and a teaching venue to provide instruction in analytical chemistry. There are two main themes researtch – metabolomics and proteomics. One focus in the next 3-5 years will be on translational research, biomarker discovery and the molecular underpinnings of disease. Computational expertise is needed to bring this research to fruition.

Metabolomics. There are three research projects that are of particular interest here. We will/are profiling lumbar (collected from living patients) and ventricular (collected at autopsy) cerebrospinal fluid (CSF) from patients with Familial Alzheimers Disease (FAD) and late onset Alzheimer’s Disease looking for early markers of disease onset. We are also profiling urine collected from patients who have undergone kidney transplants, in the search for early biomarkers of kidney rejection, and we will profile human seminal fluid in the search from early biomarkers of prostate cancer. These three projects are now in their initial stages but will be an important focus of our research program for the next 3-5 years. Computational expertise will play a vital role in each of these projects.

Proteomics: Proteomics and biomarker discovery. These two areas of research are actively pursued in the PMSL, and are under the direction of Adjunct Professor Julian Whitelegge. Biomarkers of ionizing radiation exposure are under investigation in model systems and provide opportunities for informatics expertize moving forward. This is a collaborative project with Bill McBride in Radiation Oncology and Joseph Loo in Biological Chemistry. It includes tissue and plasma proteomics and the appearance of organ-specific markers in the blood.


Professor Victoria Sork
Department of Ecology & Evolutionary Biology
4139 Teriyaki Life Science Building
610 Charles E. Young Drive East
Los Angeles, CA 90095-7239
Phone: (310)825-7755
visork@ucla.edu

UCLA Oak Genomics
We have a post-doc position opening to join an oak genomics project funded by the NSF Plant Genome Research Program to provide a complete, high-quality sequence of the valley oak genome with structural and functional annotations of genic regions and repetitive elements. The project will develop and implement innovative genome assembly tools for the valley oak genome using PacBio sequencing. The postdoc for this position will play a major role in the annotation component of the project and will also conduct gene expression experiments with the goal of improving identification, validation, and annotation of genes underlying phenotypes associated with local adaptation to climate response. In consultation with others, the post-doc will design his/her experiments with access to greenhouse, growth chambers, and two common gardens of ca.7000 trees planted at two sites maintained by the US Forest Service.

The applicant should possess a PhD or equivalent in the biological sciences, preferably with empirical, analytical or bioinformatics training in molecular or evolutionary genetics. Previous experience in molecular techniques, next-gen sequence analysis, and variant calling are preferable. A research track record with relevant publications in peer-reviewed journals is desirable.


Laboratory of S. Lawrence Zipursky
Professor of Biological Chemistry; Investigator of the Howard Hughes Medical Institute
5784 MRL
675 Charles E. Young Dr. South
Los Angeles, CA 90095
Phone: (310) 825-2834
lzipursky@mednet.ucla.edu

Opportunity to combine genetics, RNA sequencing, bioinformatics and neuroscience research.
The molecular code neurons use to match pre and postsynaptic neurons during the assembly of neural circuits remains an outstanding unsolved question in the brain sciences. We have previously characterized the role of a large family of cell recognition molecules encoded by the Dscam1 locus that allows neurons to discriminate between self and non-self. We have recently turned our attention to identifying the molecules that specify the matching of synaptic partners. In a large RNA sequencing project (Tan et al Cell (2015), in press) we have discovered that during synapse formation neurons express hundreds of cell surface and secreted proteins. These are candidates for mediating interactions between developing neurons. Indeed, by comparing our data to the protein interaction data base for Drosophila cell surface proteins we have shown that synaptic partners express many different pairs of cell surface proteins expressed on synaptic partners. Among these we have discovered a family of proteins with extensive matches between pre and postsynaptic partners, suggesting that these proteins may play a role in specifying interactions between different synaptic partners. A similar project is also underway in the mouse. We are looking for motivated, creative and ambitious postdoctoral fellows to merge bioinformatics and experimental genetics and imaging approaches to uncover the logic of the cellular recognition mechanisms underlying synaptic partner selection.


Robert Prins, Ph.D.
Associate Professor of Neurosurgery
Ph. 310-825-4207
Email:rprins@mednet.ucla.edu

Probably the most fundamentally critical barrier to developing a successful cure for glioblastoma is the problem of treatment resistance. Given the heterogeneous nature of malignant gliomas, a combination of diverse approaches will likely be needed in concert to overcome tumor treatment resistance, including immunotherapy and molecularly targeted agents. To effectively develop such combination therapeutic approaches, we need a better understanding of the varied fields of brain tumor immunology, tumor metabolism, cancer stem cells, and epigenetic targets in glioma. Our SPORE application as a whole aims to improve scientific knowledge in these various critical areas of brain cancer biology by proposing four main research projects that represent a balance and diversity of translational approaches to innovatively and rationally tackle the problem of treatment resistance and glioblastoma relapse. The UCLA SPORE in Brain Cancer has an available postdoctoral position for a researcher trained in bioinformatics. In this position, the expert in bioinformatics will analyze complex sequencing data (exome, RNA Seq, TCR Seq, CNV) from 4 distinct research projects that are part of the NIH SPORE application.
Project 1: Active immunotherapy combined with checkpoint modulation for glioblastoma
(Project Leaders: Linda M. Liau, MD, PhD and Robert M. Prins, PhD)
Project 2: Targeting metabolic vulnerabilities in glioblastoma
(Project Leaders: Timothy F. Cloughesy, MD, Steven Bensinger, VMD, PhD, & David Nathanson, PhD)
Project 3: Inhibition of radiation-induced phenotype conversion in glioblastoma (Project Leaders: P. Leia Nghiemphu, MD and Frank Pajonk, MD, PhD)
Project 4: Novel epigenetic treatment of IDH mutant gliomas
(Project Leaders: Harley I. Kornblum, MD, PhD and Albert Lai, MD, PhD)

For further information, contact Dr. Prins or Dr. David Nathanson, Ph.D.| Assistant Professor of Molecular and Medical Pharmacology | Ph. 310-825-8813 | Email: dnathanson@mednet.ucla.edu


Dr. Antoni Ribas, MD, Ph.D.
Professor of Medicine, Surgery, and Molecular and Medical Pharmacology
11-934 Factor Bldg.
UCLA Medical Center
10833 Le Conte Ave.
Los Angeles, CA, 90095
Phone: 310-206-3928
Fax: 310 825-2493
e-mail: aribas@mednet.ucla.edu

PD-1 blockade immunotherapy leads to unprecedented levels of long term responses in patients with multiple metastatic cancers. Fully understanding why some patients respond and others do not will allow defining combination therapies and provide new treatment avenues for patients. A postdoctoral position is available for a researcher trained in bioinformatics to undertake research in samples obtained from patients and mouse models to analyze the effects of immunotherapy for cancer. Some of the studies will involve analysis of T cell responses to tumor antigens, as well as studies of mechanisms of innate and acquired resistance to anti-PD-1 and adoptive cell transfer therapy. Major efforts will be devoted to deconvolute RNASeq data to capture the effects of immunotherapy in complex cellular mixtures in the tumor microenviroment. The postdoctoral fellow will have the ability to undertake experimental biology studies testing hypothesis arising from the sample analyses.


Dr. Dinesh Rao Lab  http://pathology.ucla.edu/site.cfm?id=759

1. Transcriptome analysis of non-coding RNA and RNA-binding proteins in B-cell development

2. Transcriptome analysis of B-cell tumors is p53-deficient mice

3. Single-cell transcriptome analyses in microRNA and RNA-binding protein knockout mice

4. Genomic analyses of CRISPR/Cas9-edited primary B-cells to determine novel elements that regulate B-cell development

High-throughput analyses have revealed a plethora of novel elements within the genome, including non-coding RNA and other elements that can modulate RNA homeostasis. Our lab is interested in understanding how these elements regulate normal and malignant development within a subset of immune cells known as B-lymphocytes. The developmental hierarchy of these cells is well-defined in mice and we are using high-throughput techniques to define how these novel elements superimpose on protein coding gene expression programs to facilitate development and how they go awry during malignancy. The lab has a firm basis in experimental biology, and the in silico skills of the post-doctoral collaboratory fellow would allow us to make rapid progress in our work.