[2024/04/18] SComB Celebrates Bioinfo-AMR team’s Best Presentation & Jiaan’s Birthday

Congratulations to Micah, Yurik, Joachim, Raissa, Kath, and their adviser Dr. Llewelyn Espiritu for being selected as one of the best presentations in the THBIOL1 thesis proposal. Their thesis proposal is entitled “Genome analysis of Escherichia coli isolated from environmental wastewater.”

The team gathered at Crabs N Crack, Aseana Parqal Mall, to celebrate. Additionally, we jointly celebrated the birthday of our SComB RA, Jiaan Santos.


[2024/03/13] JP Defends His MS Mathematics Thesis

Congratulations to Mr. John Paul Guzman for successfully defending his MS Mathematics thesis entitled “Aspect-Based Sentiment Analysis of Filipino COVID-19 Tweets with Memory Networks.”

ABSTRACT

Sentiment analysis is the process of extracting opinions from text. It has a wide variety of applications, such as monitoring social media, processing customer reviews, and improving health communication. Aspect-based sentiment classification (ABSC) is a type of sentiment analysis that determines sentiments toward specified aspects in a given text. Knowledge about the specific target of the opinion allows for a more fine-grained analysis of sentiments. This results in richer insights that can lead to further applications.

In this paper, the goal is to model the ABSC task to be applicable to texts in various languages and topics. To achieve this, we study the mathematical foundations of machine learning and deep learning. We explore techniques to overcome the challenges associated with multilingual ABSC, such as working with limited data, varying grammar structures, and out-of-vocabulary words. Then, we construct a memory network as a mathematical model for the task of multilingual ABSC. Our model is evaluated on four datasets to demonstrate its capacity to learn the grammatical rules pertinent to ABSC across various languages and topics. Three benchmark datasets in English are used to compare our model with existing ones. Additionally, we created a multilingual dataset referred to as the FHT dataset. This dataset consists of health-related tweets published in the Philippines during the COVID-19 pandemic. The tweets are written in English and Filipino, with possible code-switching. Our model achieved slight improvements over similar models in the benchmark datasets. Meanwhile, its performance in the FHT dataset is comparable to that observed in the benchmark datasets. Finally, we demonstrated potential applications that utilize insights from an ABSC model. This includes using ABSC to analyze the sentiments gathered during the COVID-19 pandemic.

Keywords: Machine Learning, Sentiment Analysis, Aspect-Based Sentiment Classification, Twitter


[2024/02/27-29] SComB Attends eAsia-AMR Hands-on Workshop

SComB members attended the eAsia-AMR hands-on workshop on phylogenetic tress in R at Keio University SFC Campus hosted by Dr. Haruo Suzuki, who is an expert in the field of bioinformatics and genome microbiology.


[2024/02/23] SComB Attends eAsia-AMR Meeting

SComB members attended the eAsia-AMR meeting at Keio University Mita Campus, Tokyo organized by the Japan team. Teams from Thailand, Australia, and the Philippines were physically present while the US team and some members who were not able to attend in person attended the meeting virtually. Our Year 2 eAsia research on exploring alternative non-antibiotic treatments to tackle AMR (ATTACK-AMR) has made significant strides, particularly the broadening of our collaboration. This year, we extend a warm welcome to the EnD-AMR-Asia consortium, facilitated by Prof. Ryo Honda, to contribute their perspectives and efforts towards local and global AMR surveillance.

During the morning session, all teams presented their progress updates followed by the introduction of the EnD-AMR-Asia consortium. In the afternoon session, Dr. Haruo Suzuki held a workshop on Introduction to R and phylogenetic analysis. After the workshop, the team had a gathering at a nearby izakaya.


[2024/02/16] SComB Participates in PGL’s Seminar

Prof. Angelyn Lao and Dr. Anish Shrestha participated as panelists in the PGL (Practical Genomics Laboratory) seminar entitled “Toward a World of Precision Everything: Data Distillation and Prediction in the Life Sciences.” The keynote speaker is Prof. Fred Wright, the Director of the Bioinformatics Research Center at the North Carolina State University. The moderator is PGL’s head Prof. Ma. Carmen Lagman. SComB members Paul Yu, Feeroz Yusoph, and Paul Capule also attended the event.


[2024/02/01] SComB Head Elected as PSMB VP

Congratulations! Prof. Angelyn Lao for being elected as the Philippine Society for Mathematical Biology Vice President.


[2024/01/31] DLSU SHS Interns at SComB

De La Salle University senior high school student interns met with SComB head Prof. Angelyn Lao and SComB research fellow Paul Yu to present the progress updates of their respective projects on “Meta-Analysis on the Removal of Microplastics of Biological and Chemical Wastewater Treatment” and “Understanding Filipino’s Communication Dynamics Through Topic Modeling Analysis.”


[2024/01/27] SComB Attends PSM Cluster 1 Symposium

SComB members attended the Philippine Society for Microbiology, Inc. (PSM) Cluster 1 Symposium, headed by Dr. Llewelyn Espiritu, with the theme of “Computational microbiology and biotechnology in an evolving microbial world.” One of the speakers is Dr. Anish Shrestha, who talked about “Understanding life through enormous piles of sequence data.” This was held at the University Theatre, Trinity University of Asia, Quezon City.


[2024/01/22-25] SComB Attends IWOMB 2024

SComB head Prof. Angelyn Lao attended the Philippine Society for Mathematical Biology 2024 International Workshop on Mathematical Biology (IWOMB 2024). She is also part of the organizing committee of the conference. This was held at the Paradise Garden Resort Hotel and Convention Center Boracay, Boracay Island, Philippines.


[2023/12/12] SComB Attends CENSER Christmas Party

SComB members Paul Yu, Robert Unciano, and Paul Rainier Capule attended the CENSER Christmas party. Paul Yu also did a three-minute flash presentation of the study entitled “Mathematical modeling of fluconazole resistance in the ergosterol pathway of Candida albicans.”

The submitted poster is as shown below:


[2023/12/07] SComB Attends DLSU OVPRI Christmas Party

SComB members Paul Yu, Robert Unciano, and Lara Lim attended the De La Salle University Office of the Vice President for Research and Innovation Christmas party.


[2023/12/06] SComB’s Year-End Gathering

SComB held its year-end gathering at The Barn by Borro.


[2023/12/01] ATTACK-AMR Member Wins 2nd Prize in 2023 MFET Award

ATTACK-AMR student member Mark Edward Gonzales bagged 2nd prize in 2023 Magsaysay Future Engineers/Technologists (MFET) Award, organized by the National Academy of Science and Technology, Philippines (NAST PHL). It aims to recognize outstanding research outputs on engineering and technology at the collegiate level and to encourage young Filipino students to pursue a career in science.

Mark presented his research paper entitled “Protein embeddings improve phage-host interaction prediction” in front of a jury composed of esteemed NAST members. This was held at Century Park Hotel, Manila. The recording can be viewed here.


[2023/11/22-2023/12/01] SComB Attends SEAMS School 2023

SComB research fellows, Paul Yu and Feeroz Yusoph, attended the SEAMS School 2023 Scientific Computing for Differential Equations and Applications.


[2023/11/19] SComB Paper Published in Journal of Theoretical Biology (Scopus Q1-91th)

The paper entitled “Comparative analysis of kinetic realizations of insulin signaling” was published in Journal of Theoretical Biology. The authors are Patrick Vincent N. Lubenia, Eduardo R. Mendoza, and Angelyn R. Lao.


[2023/09/29-2023/10/01] SComB Attends Philippine Datathon 2023

SComB head Prof. Angelyn Lao is part of the organizing committee of the Philippine Datathon 2023 and served as the emcee of the event. SComB research fellow Paul Yu assisted in the ushering, documentation, and logistics of the said event.


[2023/09/25-2023/09/27] SComB Visits Taiwan Universities

SComB head Prof. Angelyn Lao presented in National Tsing Hua University and National Taiwan Normal University as part of the 2023 Research and Education Forum of Japan, Philippines and Taiwan.


[2023/08/21] SComB Visits SBI Tokyo

SComB head Prof. Angelyn Lao and member Paul Yu visited The Systems Biology Institute Tokyo headquarters in Japan. We had a meeting with Dr. Samik Ghosh to discuss about a possible collaboration. Dr. Anish Shrestha also attended the meeting virtually.


[2023/08/20-2023/08/25] SComB Presents at ICIAM2023 Tokyo

SComB members Paul Yu and Feeroz Yusoph presented their poster on Day 3 of the ICIAM2023 conference. SComB head Prof. Angelyn Lao presented in the EASIAM minisymposium on Day 5.


[2023/08/17] SComB Visits Mahidol University

SComB member Dr. Llewelyn Espiritu visited the ATTACK-AMR Thailand counterpart, Dr. Janvilisri Tavan at Mahidol University. She presented a talk on Antimicrobial Resistance, followed by a tour of the facility at Dr. Tavan’s lab. Shown below are Dr. Tavan (4th from the left), members of his lab, and Dr. Espiritu (6th from the left).


[2023/07/24] ATTACK-AMR Paper Published in PLoS ONE (Scopus Q1-87th)

The ATTACK-AMR paper entitled “Protein embeddings improve phage-host interaction prediction” was published in PLoS ONE. The authors are Mark Edward M. Gonzales, Jennifer C. Ureta, and Anish M.S. Shrestha. To know more, see Projects.


[2023/07/19] SComB x BioinfoLab Organizes R for Computational Biology Workshop

SComB organized a two-part R workshop series. This workshop is the second part entitled “R for Computational Biology Workshop.” The speakers for this workshop are Mr. Jiaan Carlo Santos, MS Biology student and Mr. Paul Yu, MS Mathematics student. It was held in hybrid format via Zoom and at the Research Commons, 2nd Flr. Br. Andrew Gonzalez Bldg., De La Salle University. Shown below are our on-site participants from our upcoming collaborators from the DOST-FNRI.

The training materials can be accessed from this Kaggle notebook.


[2023/07/16-2023/07/21] SComB Presents at the SMB 2023

SComB presented at the Society for Mathematical Biology Annual Meeting 2023: Celebrating SMB’s 50th Anniversary, held at the Ohio State University, Columbus, Ohio. Prof. Angelyn Lao presented at the Minisymposium (MS01), entitled “A reaction network analysis of insulin signaling,” and at the Poster Session (PS01), entitled “Systems biology approach to understanding azole resistance mechanisms in Candida albicans.”


[2023/07/12] SComB x BioinfoLab Organizes Basic R Workshop

SComB organized a two-part R workshop series. This workshop is the first part entitled “Basic R Workshop.” The speakers for this workshop are BS/MS Computer Science students, Ms. Daphne Janelyn Go and Mr. Mark Edward Gonzales. It was held in hybrid format via Zoom and at the Research Commons, 2nd Flr. Br. Andrew Gonzalez Bldg., De La Salle University. Shown below are our on-site participants from our upcoming collaborators from the DOST-FNRI.

The training materials can be accessed from this Kaggle notebook.


[2023/06/05] SComB Presents at the HKUST SIAM Student Chapter Annual Meeting

SComB presented their study entitled “Mathematical modeling of fluconazole resistance in the ergosterol pathway of Candida albicans” at the Hong Kong University of Science and Technology (HKUST) Society for Industrial and Applied Mathematics (SIAM) Student Chapter Annual Meeting virtually


[2023/05/31] SComB Attends Systematic Review & Statistical Analysis Workshop

SComB members attended a workshop organized by the Department of Biology, De La Salle University. The workshop is entitled “Overview of systematic review and statistical analysis in basic sciences.” The resource speaker is Dr. Ourlad Alzeus Tantengco, a faculty of the DLSU Department of Biology and a recipient of the National Academy of Science and Technology’s (NAST) 2023 Outstanding Young Scientist (OYS) Award.


[2023/05/31] SComB Meets with DOST-FNRI and Duke University for Collaboration

SComB had a virtual meeting with the DOST-FNRI team and Dr. Lawrence David, Associate Director of the Duke Microbiome Center, to plan the possible collaboration among the three institutions.


[2023/04/22] SComB Hosts Graduate Seminar for Mr. John Paul Guzman

SComB hosted a virtual graduate seminar for Mr. John Paul Guzman entitled “The mathematics of attentive neural turing machines (ANTM)”, which explores the mathematical aspects of the ANTM, a neural network architecture applied to an aspect-based sentiment classification (ABSC) task for sentiment analysis.


[2023/04/21] SComB Meets with Duke University

SComB had a virtual meeting with Dr. Lawrence David, Associate Director of the Duke Microbiome Center, to discuss a possible workshop activity and future collaboration on the computational analysis of the human gut microbiome.


[2023/04/17-2023/04/19] ATTACK-AMR Team Attends QIAGEN Workshop

The ATTACK-AMR team attended the AMR workshop conducted by QIAGEN Singapore. The workshop covers an end-to-end AMR workflow covering library preparation up to bioinformatics analysis. This was held at the Philippine Genome Center, UP Diliman.


[2023/04/13] ATTACK-AMR Team Starts Sample Collection

The ATTACK-AMR Team started the sample collection and processing in preparation for DNA extraction and metagenomic sequencing. This will be conducted weekly for six months by the SComB research assistants and graduate students from the Department of Biology, De La Salle University. They were supervised by Dr. Llewelyn Espiritu, Associate Professor of the Department of Biology, De La Salle University during sample processing.


[2023/03/17] ATTACK-AMR Seminar by Dr. Lawrence David

The ATTACK-AMR team organized a seminar entitled “Genomic studies of nutrition and the gut microbiome” by Dr. Lawrence David, Co-director of Duke Microbiome Center, Molecular Genetics & Microbiology, Duke University, Durham, North Carolina. It was held at the Yuchengco Hall, De La Salle University.


[2023/03/13] ATTACK-AMR Team Visits Chinese General Hospital

The ATTACK-AMR team visited Chinese General Hospital for the collection site visit and a quick tour by the engineers at the sewage treatment plant.


[2023/03/02] ATTACK-AMR Team Visits St. Luke’s Medical Center - Quezon City

The ATTACK-AMR team visited St. Luke’s Medical Center - Quezon City for a courtesy call with Associate Director Dr. Mark Pierre Dimamay and Vice President Dr. Rodolfo Pagcatipunan of the Research and Biotechnology Division. The team also visited the collection site at the said hospital.


[2023/02/17] ATTACK-AMR Team Attends PacBio Seminar at PGC, UP Diliman

The ATTACK-AMR team attended the PacBio Seminar entitled “Unlock the promise of genomics through HiFi sequencing,” hosted by PGC’s DNA Sequencing Core Facility and Noveaulab. The speaker is Dr. Zuwei Qian, Director of Marketing - APAC region for PacBio. This was held at the Philippine Genome Center, UP Diliman


[2023/02/01] ATTACK-AMR Team Visits UST Team

The ATTACK-AMR team visited the UST team for a face-to-face meeting.


[2023/02/01] DLSU-URCO Recognition to SComB Members

SComB members got recognized at the DLSU-URCO Research Recognition 2023 held at The Verdure, Henry Sy Sr. Hall, De La Salle University.


[2023/01/27] ATTACK-AMR Team Visits UST Team

The ATTACK-AMR team visited the UST team and the collection site at the UST hospital.


[2023/01/25] ATTACK-AMR Seminar by Dr. Windi Musiazari

The ATTACK-AMR team organized a seminar entitled “Monitoring antibiotic resistance and bacterial pathogens in the environment” by Dr. Windi Muziasari, Founder & CEO of Resistomap, Helsinki, Finland. It was held at the Yuchengco Hall, De La Salle University.


[2022/12/15] ATTACK-AMR Christmas Party

The ATTACK-AMR team had a Christmas Party at Romantic Baboy.


[2022/12/15] ATTACK-AMR Workshop by Dr. Llewelyn Espiritu

The ATTACK-AMR team had a workshop on “Antimicrobial resistance and its mechanisms” by Dr. Llewelyn Espiritu. It was held at the Research Commons, De La Salle University.


[2022/12/03] ATTACK-AMR Team Joined in the PSM Cluster 1 Symposium

The ATTACK-AMR team joined in the PSM Cluster 1 Symposium held at the Ricardo & Dr. Rosita Leong Hall, Ateneo de Manila University.


[2022/12/03] ATTACK-AMR Workshop by Dr. Tavan Janvilisri in the PSM Cluster 1 Symposium

In the PSM cluster 1 symposium, Dr. Tavan Janvilisri, Professor, Department of Biochemistry, Faculty of Science Mahidol University, gave a talk on “Alternative Therapeutics to Tackle AMR Pathogens (ATTACK- AMR) A case of Clostridioides difficile”


[2022/12/03] ATTACK-AMR Workshop by Dr. Joy Scaria in the PSM Cluster 1 Symposium

In the PSM cluster 1 symposium, Dr. Joy Scaria, Associate Professor, Department of Veterinary and Biomedical Sciences, South Dakota State University, gave a talk on “Genomics Based Detection of Foodborne Pathogens to Improve Food Safety”


[2022/11/16] ATTACK-AMR Paper Published in mSystems (Scopus Q1-94th)

The ATTACK-AMR paper entitled “Mathematical modeling of fluconazole resistance in the ergosterol pathway of Candida albicans” was published in mSystems journal of the American Society for Microbiology. The authors are Paul K. Yu, Llewelyn S. Moron-Espiritu, and Angelyn R. Lao. To know more, see Projects.


[2022/11/05] SComB’s Poster Entry and Research Splash at the Leave a Nest Hyper Interdisciplinary Conference Philippines 2022

The SComB research unit presented their research at the Leave a Nest Hyper Interdisciplinary Conference Philippines 2022, with a poster entitled “Systems biology approach to understanding azole resistance mechanisms in Candida albicans”.


[2022/10/11] SComB’s Poster Entry to the Annual PAASE Meeting & Symposium 2022

The SComB research unit presented their research at the Annual PAASE Meeting & Symposium 2022, with a poster entitled “Mathematical modeling approach to drug target identification in Candida albicans ergosterol biosynthesis pathway”.


[2022/09/23] SComB Posters won First and Third Place in the 10th DOST-SEI ASTHRDP Graduate Scholars’ Conference

The SComB research unit won the First and Third Place in the technical poster competition under the mathematical and computational sciences category in the 10th DOST-SEI ASTHRDP Graduate Scholars’ Conference. The recording can be seen in the UP Diliman College of Science Facebook page.


[2022/09/22-23] SComB’s Poster Entry to the 10th DOST-SEI ASTHRDP Graduate Scholars’ Conference

The SComB research unit took part in the 10th DOST-SEI ASTHRDP Graduate Scholars’ Conference with two poster entries.


[2022/08/25] ATTACK-AMR Project Meeting with Japanese Counterpart

The ATTACK-AMR Philippine team had an online meeting with Japan and Thailand counterparts about the sample handling and bioinformatics process.


[2022/07/26] ATTACK-AMR Project’s Meet & Greet Session

The DLSU team of the ATTACK-AMR Project had their meet & greet session at Cafe Adriatico, Remedios Circle. In the photo below, from left to right, are Robert Unciano, Llewelyn Moron-Espiritu, Angelyn Lao, Paul Yu, Anish Shrestha.


[2022/07/23] ATTACK-AMR Project Meeting

The ATTACK-AMR Philippine team had an online meeting to discuss about the procurement process and sample collection protocol.


[2022/07/08] ScomB wins the Best Poster Award in the DLSU Research Congress 2022

On Day 3 of the DLSU Research Congress 2022, the Best Poster Award was conferred to the SComB research unit in their poster entry entitled “Identification of drug targets in Candida albicans ergosterol biosynthesis pathway using mathematical modeling”.


[2022/07/07] SComB’s Poster Entry to the DLSU Research Congress 2022

The SComB research unit took part in the DLSU Research Congress 2022 with a poster entry entitled “Identification of drug targets in Candida albicans ergosterol biosynthesis pathway using mathematical modeling”. Using mathematical modeling, we aim to identify possible drug targets in the ergosterol pathway of Candida albicans.


[2022/06/28] LNest Grant Global Challenge Award 2022

Congratulations to Mr. Paul K. Yu, a research assistant at the Systems & Computational Biology (SComB) research unit of the College of Science Center for Natural Sciences and Environmental Research (CENSER) and an MS graduate fellow of the Department of Science and Technology-Science Education Institute (DOST-SEI), for being selected as one of the awardees of the LNest Grant Global Challenge Award 2022. The project title is “Systems biology approach of understanding azole resistance mechanisms in Candida albicans.” The research is in collaboration with Dr. Llewelyn S. Moron-Espiritu from the Department of Biology of De La Salle University and a member of the SComB research unit, and Prof. Angelyn R. Lao from the Department of Mathematics and Statistics of De La Salle University, and the head of the SComB research unit.

Project summary:

Candidiasis is reported as the most common fungal infection in the critical care setting. Its causative agent is an opportunistic fungus belonging to the genus Candida, the most common species of which is the Candida albicans. The current antifungal drug of choice for the treatment of Candidiasis is fluconazole, which is classified under azole antifungals, primarily due to its low cost, limited toxicity, and bioavailability. Its mechanism of action is the inhibition of the C14α-demethylase enzyme, a key enzyme in the ergosterol pathway, thereby blocking the synthesis of ergosterol, which is an integral component of the fungal cell membrane. In recent years, the significant increase of fluconazole-resistant C. albicans in clinical samples calls for a need to search for other possible drug targets. In this study, we constructed a mathematical model of the ergosterol pathway of C. albicans using ordinary differential equations with mass-action kinetics. Using the model, we plan to conduct various simulations to understand fluconazole resistance mechanisms in the ergosterol pathway and look for possible drug targets. The models aim to aid researchers to narrow down the possible drug targets prior to doing costly and time-consuming experiments, and to serve as a cross-validation tool for experimental data.

This news is featured in the 2401 newsletter Vol. 53 No.13, 07/12/2022 of De La Salle University, and also announced in the Leave-a-Nest Website.


[2022/06/20-2022/07/11] DLSU-PSHS Summer Internship Program: Mathematical Modeling

The SComB research unit took part in the 2022 DLSU-PSHS Summer Internship Program. We conducted lecture-based and hands-on workshop on Mathematical Modeling. Three senior high school students from the Philippine Science High School were accepted as our interns. On week 1, lectures were given on introduction mathematical modeling and its workflow, with hands-on workshop on the Python programming language, Wolfram Mathematica software, and LaTeX typesetting using Overleaf. On week 2, the lecture was on scientific communication and the interns were given a problem set on forecasting fuel prices, to be worked as a group. This is to prepare for their final project, to be presented at the last day of the internship program. The interns attended an actual thesis proposal defense by an MS Mathematics student. On week 3, the interns were exposed to various researches at the 2022 DLSU Research Congress. The full details are shown in the Course Syllabus
.

Instructors:

  • Prof. Angelyn R. Lao
  • Paul K. Yu (Teaching Assistant)

Interns:

  • Gerard C. Aurellano (Philippine Science High School - Bicol Region Campus)
  • Megan Marie B. Sio (Philippine Science High School - Western Visayas Campus)
  • Ethan Lestat L. Tiongson (Philippine Science High School - CALABARZON Region Campus)