February 6, 2018

4th Annual “Host-Pathogen Interactions: Circuits to Systems" Symposium.

The 4th Annual Host-Pathogen Interactions: Circuits to Systems Symposium will be held on February 6, 2018 at the Sanford Consortium for Regenerative Medicine. This year’s speaker list consists of a panel of outstanding scientists, including Drs. Harmit Malik, Kristian Andersen, Mariano Garcia-Blanco, John Young, Paul Ahlquist, Louis Picker, Brad Rosenberg, Beatriz Fontoura, Yuan Chang, Glen Barber, and Rafael Medina Silva. The symposium is organized by FluOMICS in partnership with the FluDyNeMo consortium and the ‘Innate Immune Responses and Vaccines against Tumor-associated Herpesviruses’ P01 grant.

December 15, 2017

Workshop: Integrative Genomic Analysis with GenePattern

Due to high demand, a second GenePattern workshop is offered by the Cancer Cell Map Initiative (CCMI) and FluOMICS on December 15, 2017.

December 6, 2017

CRISPR Screening Workshop

Pooled CRISPR-based screens have become an important tool for functional genomics. The goal of the workshop is to provide attendees with the tools and knowledge to design, execute and analyze screens leading to reliable, reproducible and sensitive results. This workshop is organized by Olivier Harismendy and Kristen Jepsen (UCSD) with support from FluOMICS, Agilent, Illumina, and Synthego.

November 7, 2017

Workshop: Integrative Genomic Analysis with GenePattern

GenePattern enables researchers at all levels of computational expertise to use hundreds of tools for the analysis of gene expression, sequence variation, proteomics, and more, through an intuitive interface that requires no coding. In this hands-on workshop, participants will learn how to identify analyses relevant to their scientific objectives, analyze and visualize gene expression (including RNA-seq) and other genomic data, ensure that their analyses are reproducible, and create and publish research narratives that serve as a live, executable, sharable representation of a study. This workshop is organized by the Cancer Cell Map Initiative (CCMI) with support from FluOMICS.

June 26, 2017

Two new pilot projects have been awarded through the FluOMICS program

Development of a web-based computational tool for integrating and navigating systems biology data and models.
David Jimenez-Morales, University of California, San Francisco. San Francisco, CA
Lars Pache, Sanford Burnham Prebys Medical DIscovery Institute. La Jolla, CA

The central goal of this project is the development of a tool to enable the interoperability of network models developed by the FluOMICS program with data available in the NIAID Bioinformatics Research Centers for Infectious Diseases. This new tool will facilitate data exploration and dynamically update model outputs by providing access to customizable model parameters, allowing the scientific community to access data and models in an informative fashion

Structural and functional classification of influenza virus regulated host cell lncRNAs.
Megan Shaw, Icahn School of Medicine at Mount Sinai. New York, NY.

The goal of this pilot project is a characterization of the structural landscape of influenza regulated human and mouse lncRNAs. This encompasses an assessment of their conservation across species via comparative genomics, and a validation of the function of lncRNAs in mouse and human cells.

March 16, 2017

Intellectual Property and Licensing Workshop

This workshop, taking place at the Sanford Consortium for Regenerative Medicine, brings together inventors, legal and business professionals from the local San Diego community to discuss recent updates in intellectual property law and sponsored research.

January 24, 2017

Cytoscape Workshop

Cytoscape is the most popular software for analyzing and visualizing molecular networks and biological pathways. It provides many powerful features for integrating these networks with annotations, gene expression profiles and other state data. In this hands-on clinic, organized by FluOMICS and SDCSB, workshop attendees will work through tutorials and pose questions along the way that will be directly addressed by Cytoscape tutors and developers.

January 23, 2017

3rd Annual “Host-Pathogen Interactions: Circuits to Systems" Symposium.

FluOMICS, in partnership with the FluDyNeMo consortium and the Innate Immune Responses and Vaccines against Tumor-associated Herpesviruses P01 grant, hosted a day-long symposium at the Sanford Consortium for Regenerative Medicine on January 23, 2017 to highlight recent advances and breakthroughs in the field of systems research of infectious disease. Speakers included Drs. Sara Cherry, Paul Thomas, Michael Gale, Reed Shabman, Jeff Cox, Betsy Herold, Gustavo Palacios, Jacques Banchereau, Robert Davey, Pei-Yong Shi, Charlie Rice, as well as two talks given by postdoctoral fellows in the Program, Judd Hultquist (UCSF) and Laura-Isobel McCall (UCSD). The talks were followed by a poster session and reception. Dr. Kelsey Haas (UCSF) received a travel grant to help cover travel costs to the Symposium.

October 27, 2016.

Metabolomics Conference.

This conference brought together nationally and internationally renowned scientists with those from across the San Diego Torrey Pines Mesa who are focused on the study of small molecule metabolites and metabolic biochemistry. The meeting included investigators with interest in technical mass spectrometry, analytical chemistry and the biological applications of these emerging tools. Speakers consisted of Mohit Jain, UCSD (organizer); Gary Siuzdak, Scripps; Christian Metallo, UCSD; Sophia Lunt, Michigan State University; Kumar Sharma, UCSD; Pieter Dorrestein, UCSD; Rany Salem, UCSD and Daniel Nomura, UC Berkeley. Hosted by SDCSB and FluOMICS.

October 20, 2016

CRISPR Screening Workshop.

Pooled CRISPR based screens have become an important tool for functional genomics. Multiple laboratories in La Jolla are initiating screens and developing standard operating procedures for screen design, execution and analysis. The goal of the workshop was to provide attendees with the tools and knowledge to design, execute and analyze screens leading to reliable, reproducible and sensitive results. Speakers included Olivier Harismendy (organizer), Ana Bojorquez, John Paul Shen, Philipp Spahn, Eric Van Nostrand and Kristen Jepsen of UCSD. Hosted by SDCSB in partnership with FluOMICS.

September 7, 2016.

Hands-on Cytoscape Clinic.

In this workshop, organized by SDCSB and FluOMICS, the Cytoscape development team used a completely new format to provide a hands-on tutorial in an intimate classroom setting. Attendees at the yearly spring workshop had previously requested a non-lecture format where individuals can pose problems that will be directly addressed by Cytoscape tutors and developers. The fall workshop was held as a clinic, where Cytoscape users signed up for 15 minute slots where he/she presented a problem (preferentially with actual data), and Cytoscape tutors, developers, and users were able to address it directly on the spot. Hosted by Barry Demchak, UCSD.

May 19, 2016

A Cytoscape Workshop was co-hosted by FluOMICS and SDCSB.

Cytoscape is the most popular software for visualizing molecular networks and biological pathways and for integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. In this workshop, the Cytoscape development team from Trey Ideker’s lab presented a series of lectures and hands-on demonstrations covering a range of issues for both beginning and advanced users. Speakers included Barry Demchak (organizer), Keiichiro Ono and Dexter Pratt of UCSD.

March 24, 2016

Intellectual Property and Licensing Workshop.

Organized by Dr. Kamala Janiyani of UCSD, this workshop brought together intellectual property professionals, entrepreneurs, researchers and students to discuss the recent developments in the area of intellectual property and licensing. Invited speakers included Greg Reilly, California Western School of Law; James Herkenhoff, Knobbe Martens; John Cabeca, USPTO; Matthew Brown, BD Biosciences; Tracie Carroll, SBPMDI; Victoria Cajipe, UCSD; Scott M Iyama, Orrick, Herrington and Sutcliffe LLP and Mridula Pottathil Sherin, UCSD.

March 10, 2016

We would like to announce that a new pilot project has been awarded through the FluOMICS program to:
Benjamin tenOever and Kris White, Icahn School of Medicine at Mount Sinai. New York, NY.

The goal of this project is to develop a novel tool for the study of mRNA degradation rates in the presence of an active IAV infection. We will then apply this new technique to obtain the first comprehensive view of transcriptome stability dynamics during infection. Through bioinformatic analysis of this new and existing data from the U19 consortium we will be able to determine cis-acting mRNA sequences that are targeted and the overall role degradation plays in modulation of the host environment. Specific Aims are (1) to develop novel tools to study intrinsic host mRNA stability throughout the IAV life cycle in vitro, and (2) to determine mRNA stability at a global level in IAV-infected cells.

January 4, 2016

"Host-Pathogen Interactions: Circuits to Systems" Symposium.

The NIAID-funded Systems Biology Centers, FluOMICS and FluDyNeMo Programs, in collaboration with San Diego Center for Systems Biology (SDCSB) hosted the 2nd Annual "Host-Pathogen Interactions: Circuits to Systems" Symposium. The symposium brought together scientist from diverse disciplines with presentations covering application of systems biology to study viral and bacterial infections, modeling of biological networks, and development of computational resources. Lauren Aguado, Kelsey Haas, Marie-Theres Pohl, Michael Schotseart, and Ana Veiga were selected as recipients of travel awards to attend the symposium.

New Metascape version

A new version of our Gene Annotation and Analysis tool “Metascape” has been released, now implementing best practices for multi-list meta-analyses.

November 4, 2015

The 2nd Annual “Host-Pathogen Interactions: Circuits to Systems" Symposium will be hosted by the NIAID-funded FluOMICS and FluDyNeMo Programs in collaboration with SDCSB.

Elucidating the molecular mechanisms that govern host-pathogen interactions is a subject of intense research in the field of infectious disease. National and local thought leaders will discuss current gaps in our understanding of how pathogens manage to evade host immune surveillance and establish acute and chronic infection states. Cutting edge systems biology approaches will be highlighted to describe recent advances in molecular and systems analyses of microbial-host interactions, disease pathogenesis, and immune responses. The Symposium is a day-long event on January 4, 2016 at the Sanford Consortium for Regenerative Medicine in La Jolla, California. The speaker lineup includes Drs. Eva Harris, Daniel DiMaio, Eva Friebertshäuser, Bert Semler, Victor Nizet, Yingyao Zhou, Rafick Sekaly, Sean Whelan, Ivan Marazzi and Stuart Sealfon. Participation is FREE, but registration is required for all attendees. Deadline to submit abstracts and travel grant applications is December 7th, 2015. Link

October 8, 2015

We have just launched Metascape, a new gene annotation and analysis tool. The aim of Metascape is to develop a set of reliable, productive and intuitive tools that help biomedical research community to analysis gene/protein lists and make better data-driven decisions. Although a plethora of databases and tools exist for gene annotation and gene list enrichment analysis, it remains challenging for researchers, especially those who are not trained to programming, to gather some very basic annotation data for their list of genes.

The Metascape web site and tools enable users to apply popular bioinformatics analyses to one or multiple gene/protein lists in order to make effective data-driven gene prioritization decisions. Just with a few mouse clicks, we can start from lists of gene/protein identifiers, extract rich annotations and identify statistically enriched pathways.

September 5, 2015

We would like to announce that a new pilot project has been awarded through the FluOMICS program:

Jeffrey R. Johnson, The J. David Gladstone Institutes. San Francisco, CA

The mass spectrometric analysis of complex protein mixtures is often hindered by a high degree of complexity. Abundant proteins dominate the mass spectrometer’s duty cycle producing spectra that are highly redundant and obscure the detection of less abundant proteins. This proposal aims to develop a novel technology to simplify complex protein mixtures by isolating partially digested N-terminal protein fragments. The successful implementation of such a method will increase the coverage of the proteome that may be captured and reduce the instrument time required to obtain a comprehensive snapshot of the proteome. Eliminating fractionation methods for proteome analysis will also allow for label-free quantification methods to be applied to characterize protein dynamics with high sensitivity and in biologically relevant systems with ease.

August 10, 2015

Workshop: Quantitative Proteomics Approaches to Study Host-Pathogen Relationships.

In partnership with SDCSB, a best-practices Workshops in Proteomics will be organized by Jeff Johnson of the Krogan lab on September 10th at the SCRM. This workshop will focus on the best practices in the field for applying quantitative proteomics approaches to study host-pathogen relationships. Speakers will describe the latest and most effective methods for probing protein-protein interactions, post-translational modifications, as well as advanced approaches to add quantitative value to proteomics studies. Special attention will be placed on experimental design and bioinformatics strategies for each approach that maximize the amount of biological information that can be extracted from highly complex proteomics data.

Summer Course in Quantitative Biology

In July, FluOMICS successfully co-hosted together with SDCSB and Dr. Lev Tsimring of UCSD the La Jolla Labs Quantitative Biology summer course ( The course included chalkboard lectures on mathematical modeling, an integrated computer lab for hands-on exploration and research presentations from leaders in the field, including host-pathogen interactions. Fluomics will again co-host this course in the summer of 2016. Further details of the course program will be available in early 2016.

March 24, 2015

Announcement of upcoming SDCSB/FluOMICS co-hosted workshops:

Metabolomics Workshop on March 27, 2015, organized by Mohit Jain, an Asst Prof at the UCSD School of Medicine

For registration and detailed information, visit

January 4, 2015

We would like to announce that two pilot projects have been awarded through the FluOMICS program:

Global assessment of virus-induced host protein mislocalization events

Sumit Chanda, Sanford Burnham Instititue. La Jolla, CA

The goal of this project is to develop and execute a high-throughput screen to assess alterations in host protein subcellular localization after influenza infection. To address the hypothesis that viruses retarget host protein distribution to evade immune detection, we propose to establish and optimize a high-throughput screening platform to interrogate subcellular (trans)localization events. The screen to be performed will evaluate the impact of influenza infection on the localization of ~500 host proteins that encode a variety of genes related to pattern recognition, interferon signaling and interferon-dependent target genes. To facilitate the highthroughput approach, epitope-tagged cDNAs will be transduced into cells, and after viral challenge, cells will be fixed, stained, and imaged utilizing high-content microscopy. Refined automated imaging analysis algorithms will enable us to computationally identify differential localization events. Validation and kinetic analysis of trafficking events targeted by influenza. To assess the biological relevance of candidate genes identified in SA1, we will assess the translocation events of endogenous proteins (when antibodies are available), as well as perform kinetic analyses of translocation with RFP-tagged proteins (3-5 genes).

Influenza virus-induced changes in host 3D genome architecture

The goal of this highly innovative Fluomics pilot proposal is to characterize changes in the three dimensional configuration of the host genome in response to influenza virus infection to establish how long-range chromatin interactions contribute to regulation of the virus-host transcriptional network. We hypothesize that these events contribute to viral replication and/or disease pathogenicity. For these studies we will employ Hi-C, a powerful technique that couples spatial proximity DNA ligation with massively parallel sequencing technology, and that is capable of resolving promoter-enhancer regulatory domains as well as large scale rearrangement of chromosomes.