Trainee, Visitor and Volunteer Onboarding
New Publication from Johnson Lab and Collaborators
A new publication on profiling Tuberculosis Signatures from the Johnson lab is now available in BMC Infectious Diseases (part of Springer Nature). Click here to read the full article.
Dr. Sarah Mazzilli to Present at The Innovator’s Journey: Embracing Creativity & Discomfort in Pursuit of Impact
Source: Boston University Office of Research
Thursday, February 25, 2021 | 3-4:30 pm
In this series of lightning talks, faculty innovators from across BU schools and colleges will share their diverse paths from invention to market to impact. Featured speakers include Dr. Sarah Mazzilli, Assistant Professor of Medicine in the Section of Computational Biomedicine. The session will touch on the challenges and opportunities of navigating the world of business as an academic researcher, the importance of setting a personal objective and assessing market need, and the concepts of creativity and innovation in the context of translational research. The talks will be followed by a moderated Q&A led by Rana K. Gupta, Director of Faculty Entrepreneurship.
The event will also include the presentation of the BU Innovator of the Year Award to Dr. Jerome Mertz, Professor of Biomedical Engineering and Electrical & Computer Engineering (ENG) and Physics (CAS).
Click here to read more about featured speakers and to register.
Dr. Stefano Monti and Collaborators Awarded NIDCR R01 Grant
Source: Boston University School of Medicine
Researchers at the Henry M. Goldman School of Dental Medicine and the School of Medicine have received a five-year, $3.2 million National Institute of Dental and Craniofacial Research (NIDCR) R01 grant. This grant will fund research into the role of b-catenin/CBP signaling in the epigenetic regulation of cellular plasticity in head and neck cancer progression.
The project is led by the Multiple Principal Investigator team comprised of Drs. Maria Kukuruzinska (contact PI, Translational Dental Medicine, GSDM), Stefano Monti (Computational Biomedicine, BUSM), and Xaralabos Varelas (Biochemistry, BUSM). Other investigators on the project include Drs. Manish Bais (Translational Dental Medicine, GSDM), Vikki Noonan (Oral & Maxillofacial Pathology, GSDM), Andrew Salama (Oral and Maxillofacial Surgery, GSDM), Catherine Costello (Biochemistry, BUSM), and Dennis Jones (Pathology, BUSM).
Click here to read more.
Past Event – Dr. Vijaya Kolachalama at BU AHA-GV Lecture
On January 25, 2021 from 2:00-3:00PM, CBM's Vijaya Kolachalama presented "Unsupervised Machine Learning" at the Bu AHA-GV Lecture. Click here for additional lecture materials.
Maria Perez Cardenas joins CBM as Scientific Program Manager
Maria Perez Cardenas, PhD has joined the Section of Computational Biomedicine as a Scientific Program Manager to support ongoing and new research in early detection of lung cancer with Drs. Spira, Lenburg and Billatos. Maria received her Ph.D. in Chemistry from the University of Maryland, College Park, MD and most recently worked as a Partnership Manager at the European Institute of Innovation & Technology, Silicon Valley Hub San Francisco, CA. We welcome Maria and look forward to having her as a member of our team.
Dr. Joshua Campbell Receives Award from Lung Cancer Research Foundation
Joshua Campbell, PhD, Assistant Professor has received an award from the Lung Cancer Research Foundation. The award will provide support for two years to research “Determining differences in immunotherapy outcomes and immunobiology in African American patients with NSCLC”.
New Publication – Contextualized Protein-Protein Interactions
Source: Patterns
Highlights
We present PPI Context: contextualization of existing literature-curated PPIs
A resource for filtering PPIs by cell-line information mined from reporting studies
A fast and flexible pipeline implementing the presented data mining method
The Bigger Picture
Existing literature-curated protein-protein interaction (PPI) databases usually aggregate cell-type-agnostic interactions, yet PPIs are dependent on environmental conditions. Thus, new methods and resources for inferring the context in which a PPI is reported will extend their application and use in disease-centric modeling. We expect the resource presented in this article to be of high interest to those querying known interactions of proteins of interest, reconstruction and analyses of molecular interaction networks, and multi-omics data integration approaches.
Summary
Protein-protein interaction (PPI) databases are an important bioinformatics resource, yet existing literature-curated databases usually represent cell-type-agnostic interactions, which is at variance with our understanding that protein dynamics are context specific and highly dependent on their environment. Here, we provide a resource derived through data mining to infer disease- and tissue-relevant interactions by annotating existing PPI databases with cell-contextual information extracted from reporting studies. This resource is applicable to the reconstruction and analysis of disease-centric molecular interaction networks. We have made the data and method publicly available and plan to release scheduled updates in the future. We expect these resources to be of interest to a wide audience of researchers in the life sciences.
Click here to read the full article.
Evans Days of Research – Dr. Vijaya Kolachalama Receives Outstanding Research Collaborator Award
Vijaya B. Kolachalama, PhD, FAHA, Assistant Professor of Medicine in the Section of Computational Biomedicine was awarded an Outstanding Research Collaborator Award as part of the Annual Department of Medicine Evans Days. Dr. Kolachalama’s research interests include phenotyping neurodegeneration, digital pathology, as well as musculoskeletal and cardiovascular diseases, with a specific focus on machine learning. He is a faculty member of the Department of Computer Science, Boston University and a Founding Member of the Faculty of Computing & Data Sciences at Boston University. Congratulations to Dr. Kolachalama.
Dr. Joshua Campbell Receives Shipley Prostate Cancer Pilot Grant Award
Source: BU School of Medicine
Dr. Joshua Campbell, Assistant Professor Medicine/Computational Biomedicine, received a Shipley Prostate Cancer Pilot Grant Award. Please see below for more information on Dr. Campbell's joint project with Drs. Gerald Denis and Andrew Emili:
Protein-protein interactions (PPIs), which constitute an essential step in cell biology that, when disrupted, can cause profound functional abnormalities, are important to understand. Drs. Campbell and Denis will work with Pathology & Laboratory Medicine to grow organoid cultures from prostatectomy derived from patients with low- and high-grade disease. Specific subpopulations of epithelial cells will be sorted using flow cytometry and then profiled with mass spectrometry using Dr. Emili’s precision facilities of the BU Center for Network Systems Biology to identify differences in protein abundance or connectivity in protein interaction networks between grades in each cell type. Overall these data will identify key cofactors for aggressive disease.
Bioinformatics Analyst – Darren Chiu
Darren Chiu, of the Mazzilli Lab, recently transitioned from Research Technician to Bioinformatics Analyst. Before joining the lab, Darren completed his master’s degree in Immunology at Harvard University, where his research focused on discovering non-coding functional single nucleotide polymorphisms (SNPs) associated with autoimmune diseases and investigating the regulatory mechanism of each SNP on gene expression.
His research and technical projects in the lab previously focused on studying lung pre-cancer, including characterizing the impact of carcinogens on lung epithelium and developing methods for single nuclei sequencing. The other focus of his research was to develop single nuclei isolation protocol for airway brushes and small lung tissue samples. He also developed a protocol to treat cells with carcinogens associated with tobacco cigarettes, the known cause of lung cancer.
Fascinated by the capability of bioinformatics/computational analysis to decipher the biological messages hidden in the samples generated, he decided to pursue an opportunity to learn more computational skills. The current focus of his new role is working with single nuclei and bulk transcriptomics data from lung cancer patient samples to gain biological insights about the cell types and states that drive lung cancer development and pathogenesis. He is also involved in analysis of the targeted B-cell receptor sequencing data to explore the role of B cells in premalignant lung lesions.