11 Jun 2020

Oral Defense of the

Dissertation of

GEOFFREY ASERIOS SOLANO

entitled

Clique Finding Approaches for Discovering Approximate Gene Clusters

For the degree of

DOCTOR OF PHILOSOPHY

(COMPUTER SCIENCE)

on

23 JUNE 2020, 10:00 (Manila Time)

https://up-edu.zoom.us/j/5110149016?pwd=d2RTbFY2T0Y0YUswSnFrai9pVUZOdz09 

Meeting ID: 511 014 9016

Password: 05721723

________________

Panel Members

Dr. Jaime DL. Caro, Adviser

Dr. Alex Gonzaga, Panel Chairman

Dr. Henry N. Adorna, Reader

Dr. Polly W. Sy, Panel Member

Dr.Wilson Tan, Panel Member

ABSTRACT

A gene cluster is a group of two or more genes found within an organism’s DNA that encode similar polypeptides or proteins. Genes belonging to a cluster may share functional dependencies and may be involved in the expression of a specific trait. Identifying these clusters is essential in establishing relationships between organisms as well as in the discovery of drugs and disease treatments. The biological problem of identifying associations among genes across genomes can be formalized as searching for cliques on undirected weighted graphs. This dissertation explores algo- rithmic approaches to two of these clique-finding optimization problems, particularly the Minimum Weight t-partite Clique Problem (MWtCP) and the Minimum Edge- Weighted Clique Problem (Min-EWCP). It was shown that MWtCP is NP- Hard as well as APX-Hard. Approximation algorithms were then presented on the two problems as well as their constant factor approximation ratios in the metric case as well as the ultrametric case of inputs. An additional performance guarantee is shown when a variable σ is provided for varying the metricity property on inputs. Finally, experimental results were presented where algorithmic solutions to the two problems were applied to the problem of discovering approximate gene clusters. A data set composed of 1406 putative orthologous genes of the genomes E. coli str. K-12 and B. subtilis. Another data set composed of 25 gene clusters corresponding to 33 different biological pathways of the same set of species was used to benchmark the results.

24 Mar 2020

March 10, 2020 | Written by Khalil Ismael Michael G. Quilinguing

``On February 13, 2020, President Rodrigo R. Duterte addressed the nation on television as fears over the spread of the Novel Coronavirus 2019 or Corona Virus Disease 2019 (COVID-19) gripped many. Speaking in a video message recorded at the Malacañang Palace, he assured the public that his administration was taking all the necessary measures to limit the spread of the disease. “I call on our people to remain calm, vigilant, responsible. And I also ask [for] your trust and cooperation, support as we face the challenge,” he said.

Earlier during the day, the Manila HealthTek Inc. posted on its official Facebook page a photo of the COVID-19 test kit developed by experts from the Philippine Genome Center and the National Institutes of Health of the University of the Philippines Manila.

... After a specimen is sequenced, it is then forwarded to another unit of the PGC called the Core Facility for Bioinformatics. The unit, according to its supervisor, Dr. Jan Michael Yap, will subject the sequenced samples to a verification process to establish its proper attributes.

''

More information here: https://www.up.edu.ph/the-philippine-genome-center-stockpiling-for-covid-19/

6 Feb 2020

Davinci Maru, ABS-CBN News

Posted at Jan 30 2020 08:19 PM

MANILA - A research facility in the University of the Philippines (UP) said Thursday it would help health authorities confirm cases of the 2019 novel coronavirus (2019-nCoV) in the country.

"The Philippines has the tools and cutting-edge equipment, trained DNA sequencing staff, and scientists to help validate the presence of 2019-nCoV in the country by sequencing the whole viral genome from samples collected from patients," Dr. Cynthia Saloma, executive director of the Philippine Genome Center (PGC), said in a statement.

The facility will assist the Department of Health (DOH) and Research Institute for Tropical Medicine (RITM) on diagnosing possible cases of the illness, which has killed at least 170 in China as of Thursday. Some 81,000 others globally are under observation for possible infection.

China virus death toll rises to 170, more than 1,700 new cases

Using a Next Generation DNA/RNA Sequencing (NGS) equipment, the Philippines will no longer have to send samples of suspected 2019-nCoV cases abroad, said Dr. Jan Michael Yap, head of PGC's core facility for bioinformatics.

"We can do it here," he told ABS-CBN News in a phone interview, adding the results could be released after 3 days.

The equipment, Yap said, is a fast, accurate way of identifying the genetic information of viruses.

The Philippine government already confirmed the country's first case, a 38-year-old woman from Wuhan, China who arrived in Manila on January 21. 

Philippines confirms first case of new coronavirus

The woman arrived in Manila via Hong Kong on Jan. 21. She is now in an undisclosed government hospital.

The Philippines had been sending specimen samples to the Victorian Infectious Disease Reference in Australia to confirm if the patient is infected with the new coronavirus.

"Before wala pa kasing existing data on what the 2019-nCov looks like," Yap said.

The facility is also in talks with the DOH of creating confirmatory test kits to swiftly identify patients carrying the strain, he added.

"We are now preparing our materials, tools and equipment. We are ready to assist at any moment," Yap said.

The World Health Organization (WHO) had said coronaviruses were a large family of viruses ranging from the common cold to more severe diseases such as the Middle East Respiratory Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome (SARS).

Fever, cough and breathing difficulties are among its symptoms, the UN health agency added.

"

source: https://news.abs-cbn.com/news/01/30/20/filipino-scientists-offer-help-in-detecting-2019-ncov-in-ph