(Hershey In-House Seminar and Discussion Group)
Coordinated by Michael Q. Zhang (mzhang@cshl.edu). Contact Lincoln Stein (lstein@cshl.edu) in case Michael is not in.
The duration will be about one hour. The format is flexible with lunch
provided. Formally, all regular participants are listed alphabetically. You can
choose to present anything that may be "cool" or useful to the field.
For example, you could give a talk on a research project or new results,
introduce a review article, new paper or an algorithm, present a tutorial on
special topics in biology, computer science, statistics, book publication or
software licensing, etc. From time to time, we will also have talks from
visitors or other CSHL personnel who want to speak to us. You could also give a
presentation followed by open discussion. Participants are welcome to make
other suggestions on format or topics. Anyone who is not able to speak or who
would like to speak on another date should try to switch with another person.
If you need more than one session or if we insert a guest speaker, the speaker
list will automatically be shifted down. Let Paloma
Please email Paloma Anderson (anderson@cshl.edu) with a topic title as early as you can. If you wish to include a reference for a current paper or background review, you can send it later. Speaker is responsible for making sure the equipment required is in place and is working properly. (Please check the projector before the meeting. If there is a problem, call AV at x8365).
(See below for previous seminars given in this series, suggested topic links and other resources.)
| Date |
Presenter |
Topic/Paper |
| 05/14 |
Wang, Haibin |
Evolution of song culture in zebra finch |
| 05/21 |
Lin, John |
Text Mining and Literature Curation for Human Brain Connectivity Architecture |
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SEMINAR SERIES END - WILL BEGIN AGAIN IN THE FALL |
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PREVIOUS SEMINARS IN THIS SERIES |
|
| Date |
Presenter |
Topic/Paper |
| 09/12 |
Eisen, Michael - Visiting Scientist, Lawrence |
Function and Evolution of Regions Bound by Drosophila Transcription Factors |
| 09/19 |
Feng, Xin |
Incorporate Geneways into Naive Bayes Classifier for Functional Interaction Predication |
| 09/26 |
Xuan, Zhenyu |
Hybrid Selection with Solexa Sequencing |
| 10/03 |
Gessler,
Damian - Visiting Scientist, |
SSWAP: Simple Semantic Web Architecture and Protocol |
| 10/10 |
Wong, Wing Hung - Visiting
Scientist, |
A gene regulatory network in mouse embryonic stem cells |
| 10/10-13 |
CSHL Meeting - Functional Genomics and Systems Biology |
|
| 10/11-13 |
RECOMB Regulatory Genomics 2007 - Boston/MIT |
|
| 10/17 |
Taylor, James - Visiting Member/Instructor, Courant Institute, NYU - McClintock Conference Room |
Extracting signals from multi-genome alignments for identification of functional elements |
| 10/17-30 |
CSHL Course - Programming for Biologists |
|
| 10/24 |
Heywood, Todd - McClintock Conference Room |
BlueHelix (HPCC): Architecture and Applications |
| 10/31 |
Kluger, Yuval - Visiting Scientist, Skirball Institute of Biomolecular Medicine, NYU - McClintock Conference Room |
State Dependent Gene Regulatory Networks |
| 11/1-5 |
CSHL Meeting - Genome Informatics |
|
| 11/07 |
Duan,
Shenghua -
Visiting Postdoc, Mello Lab, |
Bioinformatics in RNA Interference |
| 11/7-13 |
CSHL Course - Computational & Comparative Genomics |
|
| 11/14 |
Sumazin,
Pavel - Visiting Assoc. Research Scientist, Joint Centers for
Systems Biology, |
Sequence-Centric Analysis of the Affect of BCL6 and Myc on Burkitt's Lymphoma |
| 11/18-19 |
CSHL Course - The Genome Access Course |
|
| 11/21 |
Thanksgiving |
|
| 11/28 |
|
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| 12/05 |
Stark, Alexander - Computational Biology and Bioinformatics, The Broad Institute, MIT |
|
| 12/12 |
Zhao,
Hongyu - Visiting Scientist, |
|
| 12/19 |
Schones, Dustin - Visiting Postdoc, LMI/NHLBI/NIH |
A nucleosome landscape for the human genome |
| 12/26 |
Christmas |
|
| 01/02 |
New Year |
|
| 01/09 |
McCombie, Dick |
|
| 01/14-17 |
The
Sixth Asia Pacific Bioinformatics Conference |
|
| 01/16 |
|
Defining splicing regulatory networks of the tissue-specific splicing factors Fox-1/2 by phylogenetic analysis |
| 01/23 |
|
ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes |
| 01/30 |
Rosenfeld, Jeffrey - McClintock Conference Room |
Determination of Enriched Histone Modifications in Non-genic Parts of the Human Genome |
| 02/06 |
|
Computational Mapping and Statistical Analysis of Transcriptional Factor Binding Site in ChIP-PET and Chip-seq Experiments |
| 02/13 |
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Finding functional motifs in eukaryotic promoters using sequence characteristics and positional preferences |
| 02/20 |
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Copy Number Data Analysis and Visualization |
| 02/27 |
Wang, Xiaowo |
Computational analysis of microRNA promoters |
| 03/05 |
|
Trajectory measures describing the locomotor behavior of Drosophila melanogaster in a circular arena |
| 03/12 |
|
Computational modelling of development of neural curcuitry |
| 03/19 |
|
Part
1: Generating and analyzing metabolic profiles to study CNS disease |
| 03/26 |
|
A
simple way to detect significant local DNA copy number aberrations Array CGH data is noisy.
In addition to the technical measurement noise, many tumors have a
large number of different aberrations (DNA amplifications or deletions).
An aberration is more likely to have biological significance if it
happens in a significant fraction of the patients, and if it is strong.
Also, a longer aberration is less likely to be attributable to measurement
error. We define V, the “volume”
associated with an aberration as the product of three factors: (a)
fraction of patients with the aberration, (b) the aberration’s
length and (c) its amplitude. Our algorithm compares the volume V
derived from the real data to a random model obtained by permutations,
and yields the statistical significance (p-value) of the measured
value of V. We applied the method on different aCGH datasets, including Glioblastoma,
Medulloblastoma, and Neuroblastoma,
and detected genetic locations that were significantly aberrant. Previously
observed genomic aberrations as well as new ones were detected. We
explored the relationships between whole chromosome events and different
local DNA aberrations, trying to refine clinical subgroups. |
| 04/02 |
http://www.sunysb.edu/chemistry/faculty/jwang.htm |
Landscape Theory of Cellular Networks |
| 04/09 |
Bonneau, Richard - Visiting Scientist, Courant Institute, NYU - James Library |
Learning global transcriptional dynamics with the Inferelator and cMonkey Abstract cMonkey groups genes and conditions into biclusters on the basis of 1) coherence in expression data across subsets of experimental conditions, 2) co-occurrence of putative cis-acting regulatory motifs in the regulatory regions of bicluster members and 3) the presence of highly connected sub-graphs in metabolic and functional association networks. We describe the algorithm and the results of extensive tests of several previously described methods, showing that cMonkey has several advantages in the context of regulatory network inference. The Inferelator is a network inference algorithm that infers regulatory influences for genes and/or gene clusters from mRNA and/or protein expression levels. The procedure can simultaneously model equilibrium and time-course expression levels, such that both kinetic and equilibrium expression levels may be predicted by the resulting models. Through the explicit inclusion of time, and gene-knockout information, the method is capable of learning causal relationships. It also includes a novel solution to the problem of encoding interactions between predictors.
http://www.cell.com/content/article/abstract?uid=PIIS009286740701416X |
| 04/16 |
Li, Wen-Hsiung
- Visiting Scientist, |
Protein evolution in terms of structure |
| 04/23 |
|
Efficient
genome methylation profiling using next-generation
sequencing |
| 04/30 |
Muthuswamy, Lakshmi |
Statistical interpretation of copy number variations in genetic diseases |
| 05/07 |
Smith Andrew - McClintock Conference Room |
Identifying functional domains of diffuse epigenomic marks from ChIP-seq data |
Other Resources:
Last updated September 13, 2006