Conferences & Workshops

Fourth Annual “Host-Pathogen Interactions: Circuits to Systems” Symposium
Tuesday, February 6, 2018
8:30 am – 7:00 pm
Roth Auditorium at the Sanford Consortium for Regenerative Medicine
2880 Torrey Pines Science Drive, La Jolla, CA
Register for the event here

Ensembl Tutorial
Thursday, January 11, 2018
8:30 am – 4:30 pm
UC San Diego, MET Bldg, Room 141
Hosted by Ben Moore – Ensembl Outreach Officer
European Bioinformatics Institute (EMBL-EBI)
Register for the event here

SDCSB’s Quarterly Systems-to-Synthesis Meeting (Spring 2018)
Thursday, May 17, 2018
2:00 – 5:00 pm
UC San Diego, Medical Education Telemedicine Bldg, 141-143
Registration begins spring 2018


Weekly Events

Genetics, Bioinformatics and Systems Biology Colloquium (2016-17)

qBio Seminar Series (2017-18)

Systems Biology Career Development Seminars (Spring 2017)

Monthly Events

San Diego Bioinformatics Users Series (SDBUS)

Systems Biology Club


Database for RNA pol II termination sites can be downloaded from here. Based on GRO-seq analysis, this data shows the maximum extent of the last exons in pre-mRNAs.
Davis-Turak JC … Hoffmann A. Nucleic Acids Res. 43: 699-707 (2015).

Transcriptomes (RNA-Seq) of wild type primary B cells stimulated with anti-IgM alone, BAFF alone or co-stimulated with both anti-IgM and BAFF. This data is in the GEO repository (GSE54588).
Almaden JV … Hoffmann A. Cell Rep. 9: 2098-111 (2014).

Transcriptomes (RNA-Seq) and enhancer landscapes (H3K4me2 and H3K27ac) of brain microglia and resident macrophages from the peritoneal cavity. Also PU.1 binding profiles (ChIP-Seq ) in various macrophages from NOD/ShiLtJ,  SPRET/EiJ and C57BL/6J mice. This data is in the GEO repository (GSE62826).
Gosselin D … Glass CK. Cell 159:1327-1340 (2014).

Chromatin interactions looping to the active promoters in IMR90 cells. One data set lists the locations of 11,313 anchors covering all active promoters in IMR90 cells. A second lists the locations of all target peaks interacting with these anchors. This data is in the GEO repository (GSE43070).
Jin F … Ren B. Nature 503: 290-294 (2013).

ChIP-Seq-defined binding intensities for PU.1 and C/EBPα in resting macrophages derived from C57BL/6J and BALB/cJ mice. This data is in the GEO repository (GSE46494).
Heinz S … Glass C. Nature 503: 487-492 (2013).

A structure-function study of the interaction between the NF-kB subunit RelA and the coactivator CBP/p300. The dataset consists of transcriptome profiles from RelA-deficient mouse embryonic fibroblasts (MEFs) reconstituted with wild type or mutants of RelA and then stimulated (or not) with TNFa. This data is in the GEO repository (GSE46213). This paper also reports the NMR structure of RelA bound to CBP/p300 (PDB ID: 2LWW).
Mukherjee SP … Ghosh G. PLoS Biol. 11: e1001647 (2013).

Transcriptome analysis (RNA-Seq) of 4 heterozygous diploid yeast strains (yal067c, yal031c, yal022c and yal008w) and diploid wild-type. This data is in the GEO repository (GSE42554).
Chen M … Ideker T. Cell Rep. 3: 128-137 (2013).

Genome-wide DNA methylation profiles of whole blood from 656 individuals were obtained using Illumina’s Infinium 450k human DNA methylation beadchips. This data is in the GEO repository (GSE40279).
Hannum G … Zhang K. Mol Cell. 49: 359-367 (2013).

Transcriptome analysis (Illumina MouseRef-8 v2.0 expression beadchip) of bone marrow derived dendritic cells (BMDCs) from wild-type mice, RelB single knock-out mice or cRel/RelB double knock-out mice stimulated with either CpG or Pam3CSK4. This data is in the GEO repository (GSE34990).
Shih VF … Hoffmann A. Nat Immunol. 13: 1162-1170 (2012).

Transcriptome analysis (NimbleGen genome tiling array) of mid-log cultures of wild-type Thermotoga maritima in different minimal sugar media. This data is in the GEO repository (GSE28822).
Lerman JA … Palsson BO. Nat Commun. 3: 929 (2012).

Transcriptome analysis (Illumina MouseRef-8 v1.1 and v.20 expression beadchip) of bone marrow derived macrophages (BMDMs) or mouse embryonic fibroblasts (MEFs) from wild type of NF-kB p50 knock-out mice stimulated with LPS, CpG or IFNb. This data is in the GEO repository (GSE27112).
Cheng CS … Hoffmann A. Sci Signal. 4: ra11 (2011).