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Mihai Pop co-organizes Dagstuhl workshop

Fri Sep 02, 2016
Mihai Pop co-organized a workshop on "Next Generation Sequencing - Algorithms, and Software For Biomedical Applications" at the Schloss Dagstuhl Leibniz Zentrum fur Informatik in Dagstuhl, Germany. The other co-organizers were Gene Myers from the Max Planck Institute in Dresden,, Knut Reinert from the Freie Universitaet in Berlin, and Tandy Warnow, from the University of Illinois, Urbana Champaign. The workshop brought together a broad group of scientists from Europe an the US who worked together for a week to identify computational challenges and opportunities due to the rapidly increasing volumes of sequencing data and emerging experimental technologies.

CBCB scientist Todd Treangen and CBCB alumni Adam Phillippy and Sergey Koren publish a paper in Genome Biology describing Mash, a new software tool for fast genome and metagenome estimation based on MinHash dimensionality-reduction

Wed Jun 29, 2016

CBCB faculty Todd Treangen and CBCB alumni Adam Phillippy and Sergey Koren have published a paper titled “Mash: fast genome and metagenome distance estimation using MinHash” in Genome Biology on June 20, 2016.

In the paper, they demonstrate several use cases of Mash, including the clustering of all 54,118 NCBI RefSeq genomes in 33 CPU h; real-time database search using assembled or unassembled Illumina, Pacific Biosciences, and Oxford Nanopore data; and the scalable clustering of hundreds of metagenomic samples by composition.

The paper can be found here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x

CBCB scientists Mahfuza Sharmin, Hector Corrada Bravo, and Sridhar Hannenhalli publish a paper in Genome Research on heterogeneity of transcription factor binding specificity models

Thu Jun 23, 2016

CBCB graduate student and lead author Mahfuza Sharmin, and CBCB faculty Hector Corrada Bravo and Sridhar Hannenhalli, have published a paper titled "Heterogeneity of Transcription Factor binding specificity models within and across cell lines" in Genome Research on June 16, 2016.

In this paper, they develop an ensemble based approach (TRISECT) to identify heterogeneous binding rules of cell-type specific TF occupancy and analyze the inter-cell-type sharing of such rules. Their novel ensemble-based approach reveals, for the first time, a widespread heterogeneity of binding rules, comprising interaction partners within a cell-type, many of which nevertheless transcend cell-types. Notably, the putative targets of shared binding rules in different cell-types, while distinct, exhibit significant functional coherence.

The paper can be found here: http://genome.cshlp.org/content/early/2016/06/16/gr.199166.115?top=1

Free Bioinformatics, Computational Biology, and Genomics Workshop on June 15

Thu Jun 02, 2016

Registration is now open for the ISCB DC area regional student group summer workshop on bioinformatics, computational biology and genomics!

The meeting will take place in the Biosciences Research Building (BRB) at the University of Maryland, College Park campus. The goal of the meeting is to bring together researchers from different institutions around the region to share ideas and learn from one another, and to foster collaborations across organizations.

Topics include:

◦ Genome-scale metabolic modeling

◦ Web application development for computational biology

◦ Bacterial genome assembly & annotation

◦ Analyzing sequence motifs through maximum entropy modeling

◦ Obtaining and Analyzing Data from the The Cancer Genome Atlas Project

◦ Co-expression network analysis using RNA-Seq data

Registration is FREE and includes lunch, kindly provided by the Center for Bioinformatics and Computational Biology.

Registration: http://tinyurl.com/iscb-dc-2016

Deadline : June 10, 2016

For more information about the meeting, including detailed schedule information, check out the meeting website at: http://iscb-dc-rsg.github.io/2016-summer-workshop/

Feel free to contact Keith Hughitt at khughitt@umd.edu if you have any questions or suggestions regarding the meeting.

CBCB Alumn Michael Schatz named the 21st Bloomberg Professor at Johns Hopkins University

Thu May 26, 2016
Michael Schatz (PhD in Computer Science, 2010) has received an endowed Bloomberg Distinguished Professorship in the department of Computer Science at Johns Hopkins University, becoming the 21st recipient of the prestigious endowed professorship.

CBCB researchers Jessica Goodheart and Keith Hughitt have received the 2015-2016 BISI Merit Award

Fri May 06, 2016
CBCB doctoral students Jessica Goodheart and Keith Hughitt have received the 2015-2016 BISI Merit Award. This award is presented to BISI students that excel in scholarship, teaching, and service. The award comes with an honorarium of $2200.

CBCB scientists Joo Sang Lee, Avinash Das Sahu, and Eytan Ruppin are Invention of the Year award nominees

Wed Apr 13, 2016

Each year, UMD honors exceptional inventions that have the potential to make an important impact on science, society, and the free market. The Invention of the Year award nominees come from three categories: Physical Sciences, Life Sciences, and Information Sciences. One invention from each category is selected to win the Invention of the Year Award.

CBCB postdocs Joo Sang Lee and Avinash Das Sahu, and CBCB faculty Eytan Ruppin, are finalists in the Physical Sciences category.

For more information, please see: http://research.umd.edu/news/news_story.php?id=9587

CBCB faculty Eytan Ruppin's group publishes a paper in Cell Systems on predicting drug side effects

Mon Apr 11, 2016

CBCB faculty Eytan Ruppin's group has published a paper titled "Metabolic Network Prediction of Drug Side Effects" on March 23, 2016 in the journal Cell Systems .

For further information, please see: https://www.cs.umd.edu/article/2016/03/professor-eytan-ruppin-publishes-...

Metabolic Network Prediction of Drug Side Effects" article: http://www.sciencedirect.com/science/article/pii/S2405471216300734

Recent Promotions for CBCB Faculty

Mon Apr 11, 2016

Congratulations to the following mentioned faculty:

Dr. Hector Corrada Bravo has been promoted to Associate Professor. Additionally, Dr. Mihai Pop, Dr. Najib El-Sayed, and Dr. Michael Cummings have been promoted to Professor.

Adam Phillippy quoted in the NY Times

Apr 03, 2016
CBCB alumnus Adam Phillippy, now Head of the Genomics Informatics Section of the Computational within Statistical Genomics Branch at the National Human Genome Research Institute (NIHGRI), was quoted in the NY Times on the challenges involved in the reconstruction of the genome of Aedes aegypti - the mosquito that carries, among other diseases, the Zika virus.

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