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Systems Biology meetings
Presentations are scheduled Wednesdays, 1:30 - 3:00 pm.
Location: LBNL, 717 Potter Street, Berkeley, room 248; broadcast via MCI/WebEx Audio and Net Conferencing.
Unless indicated otherwise.
For information, contact Lori Salles, 510-486-7637.
Date |
Presenter(s) |
Topic |
Presentation/ |
5/8 |
ICBP Aims Planning Meeting (Closed) |
|
|
5/6 |
ICBP Aims Planning Meeting (Closed) |
|
|
4/16 |
ICBP Planning Meeting (Closed) |
Survey of protein signaling in mutiple cell lines |
|
4/15 |
Bahram Parvin |
Progress on quantitative integrative biology |
|
4/10 |
Soheil Shams |
Nexus Biodiscovery presentation/training |
|
3/24-24 |
Joint Workshop |
ICBP/CISNET programs, Bethesda, MD |
|
3/20 |
ICBP Steering Committee |
Internal renewal planning meeting |
|
3/18 |
Jian Jin/Rafael Gomez-Sjoberg |
Automated tools for high-throughput cell biology |
|
3/4 |
Igor Ulitsky |
ID of bio and clinically relevant functional modules by network & expression data |
|
1/21 |
Mark LaBarge |
The current status of Bissell Lab proposed work for the ICBP renewal |
|
2008 |
|
|
|
12/10 |
Ken Buetow/Sol Efroni, NCI/NIH |
Pathway analyses of breast cancer data |
|
10/22 |
Bahram Parvin/Valerie Weaver, UCSF |
Forcing transformation |
|
10/15 |
Joe Gray, Discussion Lead |
Discussion regarding ICBP grant renewal submission |
|
10/1 |
Bill Gibb |
Using consensus clustering to select gene sets for robust pattern classification |
|
910 |
Doris Siwak (MD Anderson Cancer Center) |
Reverse phase protein array: procedures & data highlights |
|
8/20 |
Daojing Wang |
Proteomics technologies and applications |
|
8/6 |
Samira Guccione |
Image-based approaches for genomics and proteomics in personalized medicine |
|
7/9 |
Lakshmi Jakkula |
The cancer genome atlas project (TCGA): Exon array process and experience |
|
6/11 |
Martha Stampfer/Sanchita Bhattacharya |
Normal multi-lineage HMEC: Long-term growth and characterization |
|
5/7 |
Joe Gray/Wen-Lin Kuo |
Presenting the data from the 25 drug screen |
|
4/30* |
Anna Lapuk |
Alternative splicing in GBMs: detecting cell specific isoforms, potential novel biomarkers and therapeutic targets |
|
4/23* |
Rina Gendelman |
MBayesian network inference model predictions and experimental validation |
|
4/2* |
Michael Korn/Olga Mirzoeva |
Molecular circuits mediating therapeutic synergism of MEK and PI3K inhibition |
|
3/26* |
Philippe Gascard |
Predicted signaling pathways and transcriptional networks involved in microenvironment-dependent baseline gene expression and response to the MAPK inhibitor U0126 in MDA-MB231 and T47D breast cancer cells |
|
3/19* |
Laura Heiser |
Using Pathway Logic to model cellular pathways associated with breast cancer |
|
3/12* |
Debopriya Das/Nicolas Wang |
Desatinib Study |
|
3/5 |
Shuying Sun |
Are genes methylated in breast cancer lines?-- Preprocessing and analyzing Agilent 244K CpG island methylation microarray data |
|
2/20 |
Bill Gibb |
Structural inference of protein interactions using Bayesian networks |
|
2/6 |
Paper preparation discussion |
|
|
1/30 |
Paul Spellman/Debo Das |
High throughput sequencing discussion/ |
|
1/9 |
Andy Poggio |
From colored spots to interesting hypotheses: Bayesian network analysis applied to microarray data |
|
2007 |
|
|
|
12/19 |
Mark van der Laan |
Targeted maximum likelihood for biomarker discovery, and super learning for prediction |
|
12/5 |
Xiaolin Nan |
ERK1/2 dynamics in living cells: observations, implications, and directions |
|
11/28 |
Rina Gendelman |
Interrogation of microarray data using Bayesian network inference modeling |
|
11/21 |
Mark La Barge |
An overview of recent reviews of the Raf-Mek-Erk pathway |
|
11/7 |
Mara Jeffress |
MAPK signaling: an overview |
|
10/10 |
Alain Belivieu |
MAPK-Mediated MMP-9 activity as a central signaling node for acinar-morphogenesis of human mammary epithelial cells in laminin-rich extracelluar matrix |
|
9/26* |
Heidi Feiler/Nick Wang |
Proliferation and apoptosis data generated on ACCS |
|
9/19* |
Bahram Parvin |
Multivariate characterization of cell-based assays |
|
9/12 |
Paul Yaswen |
ARNAi-mediated delineation of Raf-Mek-Erk signaling specificity in human breast cells |
|
9/5 |
Rich Neve |
AKT paper |
|
8/22 |
Judith Campisi |
The senescent secretome: Modified low density protein array analyses provide biological insights into mechanisms of aging and cancer |
|
8/1 |
Sanchita Bhattacharya; intro by Andy Wyrobek |
Microarray Bioinformatics; HMEC cells exposed in vitro to ionizing radiation |
|
7/18 |
Paul Spellman |
Presents on MDAMB231 |
See private data page |
5/30 |
Sorger Systems Biology group(Harvard) |
Introduction of their work |
|
5/23 |
Gray ICBP group (Korn, Neve et al.) |
Introduction of their work |
|
5/16* |
Dr. Doris Siwak (MD Anderson Cancer Center) |
Antibody Validation Procedures and Considerations for RPPA Assays |
|
5/9 |
Dr. Steven Wiley (Director Biomolecular Systems Initiative, Pacific Northwest National Laboratory) |
Autocrine Circuits and Feedback Control in EGF Receptor Signaling |
|
4/25* |
Debopriya Das |
Latest predictive marker data |
|
4/11 |
Prahlad Ram (MDACC) |
Modeling the MAPK1,2 signaling network |
|
2/21 |
Patrick Flaherty (Arkin Lab) |
A Kinetic Model for G protein-coupled Signal Transduction |
|
2/14 |
Rich Neve/Sach Mukherjee |
ERK-Pathway connectivity depends on tumor subtype context |
|
2/7 |
No meeting (Steering Committee meets) |
|
|
1/31 |
No meeting (Steering Committee meets) |
|
|
1/24* |
No meeting |
|
|
1/17 |
Paul Spellman |
Luminex plans |
|
1/10 |
Laura Heiser/Rina Gendelman |
Dynamic Models and the way forward |
|
1/3 |
No meeting |
|
|
2006 |
|
|
|
12/27* |
No meeting (Holiday) |
|
|
12/20* |
No meeting |
|
|
12/13* |
Susan Fisher |
Clinical Proteomics Technology Assessment in Cancer |
|
12/6* |
No Meeting (Consortium Meeting) |
|
|
11/29* |
No Meeting (Director's Review LSD) |
|
|
11/22* |
No Meeting (Thanksgiving) |
|
|
11/15 |
Rich Neve et al. |
RPPA Proteomics discussion (rescheduled from 11/1) |
|
11/8 |
Guest Speakers |
Philip Lee, Ph.D. (Director, R&D CellASIC Corporation) on new technologies for the analysis of cellular phenotypes such as invasion using microfluidic devices. These represent a major advance on the classic Boyden chamber assay Peter Van der Horn, Erik Gentalen and Kevin Hacker from Cell Biosciences will give a much more detailed view of their FireFly system including some recent data on MEK and EGFR as well as other collaborations they have to show the utility of the system for analysing the proteome. |
|
11/1* |
Rich Neve |
Proteomics |
|
10/25* |
Laura Heiser/Philippe Gascard |
PL models with 2D and 3D data superimposed. |
|
10/18 |
All, led by Joe Gray and Mary Helen Barcellos-Hoff |
3D discussion continued |
|
10/11 |
All, led by Joe Gray |
Project design discussion and debrief NCI site visit |
|
10/4 |
All |
Preparation for NCI site visit of 10/6 |
|
9/27 |
Joe Gray |
EAB debrief and discussion (Gray); Preparation NCI site visit (Gray); Discussion moving forward with Xenograft work (All) |
|
9/20 |
Div. |
RPPA Data (Heiser, Neve, Korn, Mills); Discussion/preparation EAB mtg of 9/26 (All) |
|
9/13 |
Paul Spellman |
Berkeley Cancer Genome Center |
|
9/6 |
No meeting |
|
|
8/30* |
Michael Korn/Nick Wang/Heidi Feiler |
Detailed Experiment Design Planning Discussion; Cellomics vs Flow Assays |
|
8/23* |
Philippe Gascard |
Continuation 2D and 3D Biology Discussion |
|
8/16 |
All; led by Joe Gray |
Brainstorming Session: Next Experiment Design |
|
8/9 |
Viktor Raskin (ICBP Summer '06 Fellow) Philippe Gascard |
Automated analysis of reverse phase protein expression samples (Raskin) Screening for genes responding differently to U0126 treatment in MDA-MD-231 cells cultured in 2D versus 3D (Gascard) |
|
8/2 |
Nick Wang/Rich Neve |
Cytometry |
|
7/26 |
Wen-Lin Kuo/Rich Neve/Debo Das |
How data is generated (Kuo/Neve) |
|
7/19* |
No meeting |
|
|
7/12 |
Paul Jasper (MIT) |
Altered Signaling and Sensitivity in EGFR Mutant Cell Lines |
|
7/5* |
No meeting |
|
|
6/28* |
No meeting |
|
|
6/21 |
Sach Mukherjee (UCB, Statistics, Speed Lab) |
Characterizing connectivity using Bayesian networks |
|
6/14 |
Andre Goga (UCSF)/Mara Jeffres (Yaswen Lab) |
Experiments using miRNA and siRNA (Goga); Plans for using a cDNA library to screen for genes conferring resistance to Mek inhibitors (Jeffres) |
|
6/7 |
John Dueber (QB3) |
Synthetic Biology |
|
5/31* |
John Conboy |
Programmed alternative splicing pathways in normal development and in human disease |
|
5/24 |
Sue Celniker |
Progress towards modeling epithelial cancers in flies |
|
5/17 |
No meeting |
|
|
5/10* |
Nick Wang/Damir Sudar/Bahram Parvin |
Discussion of Cellomics endpoints |
|
5/3 |
No meeting; MSRI Workshop |
|
|
4/26 |
Joe Gray |
Experimental Planning |
|
4/19 |
Bill Muller, |
"Oncogene mediated signal transduction in transgenic mouse mouse models of human breast cancer" |
|
4/12 |
Philippe Gascard/Debo Das |
Distinct response of MDA-MB-231 and T47D cells grown in 2D or 3D to U0126+EGF treatment |
|
4/5 |
No meeting (AACR mtg) |
|
|
3/29* |
Michael Korn |
Experimental planning |
|
3/22 |
Joe Gray/Wen-Lin Kuo/Paul Spellman |
Planning next round experiments. Also, discussion ICBP and Data Analysis Pathway workshop, MSRI, May 3-5, and (re)presentation at next ICBP consortium meeting, Wash DC, April 30-May 2. |
|
3/17, 2pm (instead of 3/15) |
Bud Mishra, |
Inheritance of Loss: Human Cancer Genome Project; Genetics of Loss and Gain in Copy Numbers |
|
3/8* |
Jian Jin/Heidi Feiler/Rich Neve |
Jian: basic update cell core | |
3/1, 1 pm |
Joe Gray |
Current status; follow up exp. design discussions |
|
2/22 |
Rene Bernards, NKI, The Netherlands/Paul Yaswen |
An shRNA barcode screen identifying novel molecular pathways involved in Iressa resistance in non-small cell lung cancer (NSCLC) |
|
2/15* |
No meeting |
|
|
2/8 |
Michael Korn |
Proposed Experimental Approach and Core Usage |
|
2/1 |
All |
Experimental Design Discussion |
|
1/25 |
No meeting (UCSF BOP Retreat in SF) |
|
|
1/18 |
Laura Heiser/Paul Spellman |
PL Analysis of time course data |
|
1/11 |
Strategy session on modeling, etc. |
First hour: SRI will comment on current microarray results and experimental design to help with further planning. |
|
1/4 |
No meeting |
|
|
2005 |
|
|
|
12/28 |
No meeting |
|
|
12/21 |
Genee Lee |
2D/3D experiment design |
|
12/14 |
Bernie Lesieutre, MSD, LBNL |
Identification of Severe Multiple Contingencies in Electric Power Networks |
|
12/7 |
No meeting |
|
|
11/30 |
Paul Spellman, SRI, et al. |
Comments on data |
|
11/23 |
Michael Korn, Rich Neve |
Update EGF Pathwayperturbation Experiment |
|
11/16 |
No meeting |
|
|
11/9 |
No meeting |
|
|
11/2* |
Paul Spellman |
Prediction of Signaling System Activity in a Genetically Diverse Model of Breast Cancer |
|
10/26 |
Chris Barker, Gladstone Institute |
Validation of an Automated System for RNA Isolation from Solid Tissues |
|
10/19 |
All, lead by Joe Gray |
Brainstorming Session |
|
10/12 |
Mary Helen Barcellos-Hoff, Mina Bissell |
Update on 3D Experiments (U54 ICBP) |
|
10/5 |
Rich Neve |
Update Cell Culture |
|
9/28* |
Heidi Feiler, Jeremy Semeiks |
Update HTA |
|
9/21* |
Debo Das |
Inferring transcription subnetworks from limited expression data |
|
9/14* |
No meeting |
|
|
9/7 |
Bahram Parvin |
Update on Core 2 (U54 ICBP) |
|
8/31 |
Heidi Feiler, Nick Wang, Rich Neve |
Update on Core 1 (U54 ICBP): Cell Culture core and CGH |
|
8/24 |
Frank Chen |
Quantum Dots |
|
8/17 |
Discussion lead by Joe Gray |
Future plans research U54 ICBP: focus on experiments |
|
8/10* |
No meeting |
|
|
8/3 |
Mina Bissell, M.H. Barcellos-Hoff |
Project 3 |
|
7/27 |
Discussion lead by J. Gray/ F. McCormick |
Future plans research ICBP U54 |
|
7/20* |
No meeting |
|
|
7/13* |
No meeting |
|
|
7/6 |
Bahram Parvin |
Core 2 |
|
6/29* |
Frank McCormick |
Interrogating the MAP-K pathway |
|
6/22* |
No meeting |
|
|
6/15 |
Gianfranco de Feo, Quantum Dot |
Mosaic gene expression assay system |
|
6/8 |
Barry Bunin |
Archive mine and selectively share collaborative drug discovery data |
|
6/1* |
No meeting |
|
|
5/27, Fri |
Frank McCormick |
Pathway curration |
|
5/10 |
Lead by Joe Gray |
Design and scheduling of experiments probing the biology of the MEK pathway (focus ICBP U54) |
|
4/27 |
Ting Ting Zhang, PBD, LBNL |
|
|
4/20 |
No meeting |
|
|
4/13 |
Martha Stampfer |
Core 3 |
|
4/6* |
Heidi Feiler, Frank Chen |
High Throughput Analysis system |
|
3/30 |
Michael Korn, Paul Yaswen |
Update siRNA working group |
|
3/22, Tue |
Frank McCormick |
Pathways |
|
3/16 |
Paul Spellman |
Project 1 |
|
3/9* |
Open Discussion lead by Rich Neve |
Core 1 |
|
2/16 |
Michael Korn |
CCT |