Blogs (4) >>

Protein interactions and cellular responses are fundamental pillars of molecular systems biology. Decoding these complex signaling pathways requires advanced computational methods. One promising direction of algorithm development is using graph algorithms to identify proteins involved in signaling pathways. Despite the availability of tools, many researchers grapple with software and user experience constraints. In response, we have developed the Signaling Pathway Reconstruction Analysis Streamliner (SPRAS), a robust containerized framework that enables users to easily reconstruct signaling pathways by connecting proteins of interest within molecular interaction networks. It seamlessly integrates graph algorithms designed for pathway reconstruction with downstream visualization and clustering analysis.

In this paper, we contribute and integrate three random-walk-based algorithms to SPRAS, including one we developed and two that appear in the literature. Random walk approaches have been highly successful in predicting candidate proteins involved in a signaling pathway, and integrating them into SPRAS will greatly expand the framework’s ability for pathway reconstruction. We illustrate their importance by using the random walk algorithms now available in SPRAS to explore potential proteins involved in cell-cell fusion in flies. With the addition of these new algorithms, SPRAS will become an essential tool for unraveling the mysteries of biological interactions.

Thu 21 Mar

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15:00 - 17:00
ACM Student Research Competition - PostersACM Student Research Competition at Exhibit Hall E - Posters
Chair(s): Mohammed Seyam Virginia Tech, Timothy Yuen University of Texas at San Antonio
15:00
2h
Talk
Ethics vs. Abstraction: Comparing Learning Outcomes from Ethics-Integrated and Technical-Only Instruction
ACM Student Research Competition
Noelle Brown University of Utah
15:00
2h
Talk
SQL Query Evaluation with Large Language Model and Abstract Syntax Trees
ACM Student Research Competition
Lili Xiang Northeastern University
15:00
2h
Talk
Enhancing Scratch Programming with Autograding
ACM Student Research Competition
Herart Dominggus Nurue The University of Alabama
15:00
2h
Talk
Askers, Answerers, Non-Answerers, and Lurkers: Investigating Online Q&A Platforms Personas and Success in a CS1 Course
ACM Student Research Competition
Nigel Newby University of Pennsylvania
15:00
2h
Talk
Cloud-Secure: An Investigation into Firefly and Grey Wolf Optimization Algorithms for Phishing Detection with Machine Learning Classifiers
ACM Student Research Competition
Kelvin Ovabor Computer science Department,The University of Alabama
15:00
2h
Talk
A Web Development and Cloud Deployment Framework for a Software Engineering Course
ACM Student Research Competition
Michael Wilkinson Worcester Polytechnic Institute, Ariel Schechter Worcester Polytechnic Institute, Bryce Lukens Worcester Polytechnic Institute, Ian Wright Worcester Polytechnic Institute, Joseph Cardarelli Worcester Polytechnic Institute
15:00
2h
Talk
Creating Instructional Elementary Programming Videos for Use in an Adaptive Testing and Remediation System
ACM Student Research Competition
Abigail Jones Northern Kentucky University, Manogya Aryal Northern Kentucky University, Justin Selby Northern Kentucky University, Seth Adjei Northern Kentucky University
15:00
2h
Talk
Accessing and Democratizing AI for Whom? Student Learning through an Algorithm-Centered Supply Chain Case Study
ACM Student Research Competition
Ashish Hingle George Mason University
15:00
2h
Talk
Understanding support needs in computer science labs
ACM Student Research Competition
Weiyin Xu University of San Diego
15:00
2h
Talk
Towards a Verified Implementation of a Network Stack
ACM Student Research Competition
Caitlyn Wilde Lewis and Clark College, Wyeth Greenlaw Rollins Lewis and Clark College, Levi Overcast Evergreen State College
15:00
2h
Talk
Exploring K-12 Teachers' Trajectories of Engagement with Critically Conscious Computing
ACM Student Research Competition
Brendan Henrique University of California, Berkeley
15:00
2h
Talk
Energizing Web Development in the Exploring Computer Science Curriculum
ACM Student Research Competition
Samuel Mazzone Marquette University
15:00
2h
Talk
Revolutionizing Student Engagement and Enrollment through Personalized, AI-Driven Dialog Systems in Higher Education
ACM Student Research Competition
Alexander Fox Elizabethtown College, Joshua Stoner Elizabethtown College, Jingwen Wang Elizabethtown College
15:00
2h
Talk
Understanding Engineering Students’ Ethical and Algorithmic Decision Preferences through a Consequentialist Framework
ACM Student Research Competition
Edward Kempa University of Florida, Ashish Aggarwal University of Florida
15:00
2h
Talk
The Future of the Error Message: Comparing Large Language Models and Novice Programmer Effectiveness in Fixing Errors
ACM Student Research Competition
Brij Howard-Sarin Williams College
15:00
2h
Talk
Learning with the Rashomon Augmented Reality Cube (RARc)
ACM Student Research Competition
Candy Arce New Mexico State University, Angie Hernandez New Mexico State University, Ruth Torres Castillo New Mexico State University, Tomas Valdez New Mexico State University, Raena Cota New Mexico State University, Enrico Pontelli
15:00
2h
Talk
Mining students’ mastery levels from CS placement tests via LLMs
ACM Student Research Competition
Yi Li Boston College, Riteng Zhang Boston College, Danni Qu Boston College, Marques Samary Maíra  Boston College
15:00
2h
Talk
Understanding Outcome Expectancy in a CS1 Course
ACM Student Research Competition
Griffin Pitts University of Florida, Ashish Aggarwal University of Florida
15:00
2h
Talk
Enhancing American Sign Language Classification by Leveraging Hand Landmark Extraction
ACM Student Research Competition
Benjamin Guerrieri The College of New Jersey
15:00
2h
Talk
A Comparative Study of Few-Shot vs. Zero-Shot Prompting to Generate Quick and Useful Responses to Students’ Periodic Reflections
ACM Student Research Competition
Ethan Hurley UNC Charlotte - College of Computing and Informatics, Joel Okyere-Badoo UNC Charlotte - College of Computing and Informatics
15:00
2h
Talk
Simplifying Signaling Pathway Reconstruction with Containerized Random Walk Algorithms
ACM Student Research Competition
Yancheng Liu Reed College, Anna Ritz Reed College
15:00
2h
Talk
Is ChatGPT the academic Catalyst we’ve all been waiting for?
ACM Student Research Competition
Raneem Mousa Simmons university, Nanette Veilleux Simmons University
15:00
2h
Talk
Undergraduate Facilitators as Role Models for Middle School Learners within an AI Summer CampK12
ACM Student Research Competition
Carly Solomon University of Florida
15:00
2h
Talk
Understanding Undergraduate Students’ Participation in Computing Clubs
ACM Student Research Competition
Brooke Nelson University of Florida, Amanpreet Kapoor University of Florida, USA, Christina Gardner-McCune Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
15:00
2h
Talk
Recommendation System Algorithm Application to Increase Interdisciplinary Undergraduate Course Collaborations
ACM Student Research Competition
Julianna Iannini The College of New Jersey, Kyla Ramos The College of New Jersey, Joe Petrecca The College of New Jersey
15:00
2h
Talk
Edit, Run, Error, Repeat: Learning Analytics To Find The Most Improved Programming Student
ACM Student Research Competition
Johan Snider Uppsala University