Hongfu Liu Joins Computer Science as Assistant Professor

Dr. Hongfu Liu has joined the Michtom School of Computer Science at Brandeis University as a tenure-track assistant professor. He received his Ph.D. in the Department of Electrical & Computer Engineering, Northeastern University (NEU), supervised by Prof. Yun (Raymond) Fu within 3.5 years. Before joining NEU, he earned his master and bachelor degrees in management from the Beihang University with Prof. Junjie Wu. He also received two minor bachelor degrees in applied mathematics and laws.

His current research interests lie in data mining, machine learning  and related applications on business intelligence, computer vision and bioinformatics. He has published several papers in top conferences and journals, such as KDD, ICDM, SDM, AAAI, IJCAI, T-PAMI, T-KDE, T-IP, DMKD, BMC and so on. He is also the reviewer for several top conferences and journals. He has been nominated as KDD Top 20 rising star all over the world in 2016.

TIDAL-Fly: a new database resource of Transposon Landscapes for understanding animal genome dynamics.

We tend to think of our genomes as nicely-ordered encyclopedias,  curated with only useful information that makes up our genes.  In actuality, nature and evolution is extremely sloppy.  All animal genomes, from us humans to the simple fruit fly, are littered with genetic baggage.  This baggage is sizeable, making up at least 11% of the fly genome and more than 45% of our genome.  The scientific term for this baggage is transposable elements (TEs) or transposons, which are mobile entities that must copy themselves to other places of the genome to ensure their survival during animal evolution.

Because there are so many copies of transposons, they can be difficult to analyze by most standard genetic methods. Brandeis postdoctoral fellow Reazur Rahman and a team in Nelson Lau’s lab have formulated a new tool called the Transposon Insertion and Depletion AnaLyzer (TIDAL). TIDAL aims to provide an accurate and user-friendly program to reveal how frequently transposons can move around in animal genomes.  Currently, the TIDAL tool has been applied to over 360 fruit fly genomes that have been sequenced and deposited in the NIH NCBI Sequencing Read Archive.  The outputs from this program are available to the whole genetics community through the TIDAL-FLY database.

tidal fly banner

The TIDAL-Fly database will allow geneticists to pick their favorite fly strain and see if a transposon has landed near to their gene and perhaps affect gene expression. Fruit flies are key model organisms utilized by many researchers, including here at Brandeis, to study human diseases, from infertility to insulin signaling to aging to sleep disorders.  Since these new transposon insertions are not available in the standard genome databases, this tool and website may provide answers to previously puzzling genetic effects not revealed by typical DNA sequencing studies.  It is Reazur’s and the Lau lab’s goal to continue updating the TIDAL-Fly database with more genomes as fly genome re-sequencing becomes easier and easier to perform.

see also: Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, Lau NC. Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Res. 2015.

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