On Friday, March 6,  the Computer Science Department will host its next colloquium for the Spring 2020 semester. Angela Huang (TCNJ Class of 2017) from the University of Pennsylvania will give a technical talk on bioinformatics entitled “A Subspace Clustering Algorithm for Identifying Cell Populations with scRNA-seq”.  An abstract of her talk can be found below.

Abstract:

Background: With the advent of single-cell RNA-sequencing (scRNA-seq), researchers now have the ability to define cell types from large amounts of transcriptome information. Over the years, various clustering algorithms have been designed. Motivation for such work can be seen in Cell Atlas projects, which aim to depict cell types present in an organism across its stages of development. Currently, most clustering algorithms measure cell-to-cell similarities using distance metrics on the full set of genes (after the optional step of dimension reduction). This requires clusters to be both compact and far enough apart that the algorithms can recover them. However, for developmental data, the clusters may not be compact; cells may be well spread out across developmental trajectories. The clusters may also not be very far apart; the developmental trajectories may intersect.

Methods: In our work, we propose to model each cell population with a single affine subspace, where all cells of the same type share a common set of constraints.

Results: We present an algorithm that leverages this subspace structure and learns a cell-to-cell affinity matrix based on notions of subspace similarity. We simulate scRNA-seq data according to the subspace model and benchmark the performance of our algorithm against pre-existing methods. We further test our algorithm on an in-house C. elegans dataset and other developmental datasets.

Significance: We show how our algorithm is able to recover information on both cell type and developmental time. Lastly, we demonstrate how the subspace model allows us to compactly recover the major genes involved in an organism’s development.

Bio:
Angela Huang is a Computer Science alumni of CS @ TCNJ. She is currently pursuing her PhD in Computer Science at The University of Pennsylvania. Her research interests are broadly in the areas of Computational Biology and Data Analysis. Prior to graduate school, her interest in Computational Biology grew through her research experiences in Dr. Dimitris Papamichail’s laboratory at TCNJ, Dr. Xin Li’s laboratory at Louisiana State University, and Dr. Michael Brent’s laboratory at Washington University, St. Louis. In her free time, Angela enjoys nature, art, choreography, and exploring new exhibits around Philadelphia.

On Friday, February 7,  the Computer Science Department will host its first colloquium of the Spring 2020 semester.  Jesse Cerutti of Pfizer will give a technical talk on data management skills in pharmaceutical industry entitled “Enterprise Data Lakes: The backbone of next-gen analytics”.  An abstract of his talk can be found below.

Abstract:
Successfully executing on a data lake strategy at an enterprise level requires multiple teams with varying technical skillsets. The architecture of the solution can quite literally make or break the success of the project. In this talk I will discuss the background of our Pfizer manufacturing application landscape and why a data lake is critical to future success. I will also get into the details of the architecture, application design challenges and considerations as well as technologies required in the implementation of the project. Finally, when completed successfully I will discuss how this enables next-gen analytics for our manufacturing sites and the wider organization.

Bio:
Jesse Cerutti currently leads the Solution Engineering practice within the Digital Quality Manufacturing group. Within this role his responsibilities include architecting and guiding engineering practices for all global applications that are used within the laboratories across the Pfizer manufacturing network. Jesse has over 18 years experience working in technology either for or associated with the Pharmaceutical industry and has spent the last 10 years at Pfizer in various roles. Prior to his role in Solution Engineering, Jesse has held roles that include web development, AWS infrastructure design, and Laboratory Information Management solution development. Jesse’s education includes a B.S. in Computer Science from The College of New Jersey, an MBA from William Paterson University.

Congratulations to the 27 presenters at this fall’s Celebration of Computing, held on Wednesday, December 4!

Gallery of Photos (Taken by Computer Science Department Faculty & Staff)

On Tuesday, November 19,  the Computer Science Department will host its final colloquium of the Fall 2019 semester.  Matt Cesari, TCNJ’s Chief Information Security Officer, will give a technical talk entitled “TCNJ Cybersecurity Layers of Defense”.  An abstract of his talk can be found below.

Abstract:
A detailed overview of the security layers protecting TCNJ digital assets, networks, and community members. Review the TCNJ network design and network security devices. Learn how encrypted traffic limits network security tools and how endpoint security must evolve to fill the gap. Discuss how threat intelligence plays a crucial role in security operations, and the unique challenges and opportunities in the Higher Education cybersecurity space.

Bio:
Jesse Cerutti currently leads the Solution Engineering practice within the Digital Quality Manufacturing group. Within this role his responsibilities include architecting and guiding engineering practices for all global applications that are used within the laboratories across the Pfizer manufacturing network. Jesse has over 18 years experience working in technology either for or associated with the Pharmaceutical industry and has spent the last 10 years at Pfizer in various roles. Prior to his role in Solution Engineering, Jesse has held roles that include web development, AWS infrastructure design, and Laboratory Information Management solution development. Jesse’s education includes a B.S. in Computer Science from The College of New Jersey, an MBA from William Paterson University.