New Publication from Campbell Lab
(source: Nature Communications) The Campbell lab, led by its Bioinformatics students, has just been published for SCTK-QC, a pipeline for comprehensive QC of single-cell RNA-seq data. This pipeline will help with reprocessing and QC efforts in consortiums. Click here to read the full publication.
Detection of dementia on voice recordings using deep learning: a Framingham Heart Study
(Source: BMC Alzheimer’s Research and Therapy) New publication from Chonghua Xue, Bioinformatics Analyst and Dr. Vijaya Kolachalama, Assistant Professor of Medicine in the Section of Computational Biomedicine. See below for a brief summary and click the link to read the whole article. Background Identification of reliable, affordable, and easy-to-use strategies for detection of dementia is […]
Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data
(Source: Oxford Academic) New publication from Dr. Stefano Monti, Associate Professor of Medicine in the Section of Computational Biomedicine. See below for a brief summary and click the link to read the whole article. As high-throughput genomics assays become more efficient and cost effective, their utilization has become standard in large-scale biomedical projects. These studies […]
Deep learning-driven quantification of interstitial fibrosis in digitized kidney biopsies
(Source: The American Journal of Pathology) New publication from Dr. Vijaya Kolachalama, Assistant Professor of Medicine in the Section of Computational Biomedicine. See below for a brief summary and click the link to read the whole article. Interstitial fibrosis and tubular atrophy (IFTA) on a renal biopsy are strong indicators of disease chronicity and prognosis. […]
Subchondral bone length in knee osteoarthritis: A deep learning derived imaging measure and its association with radiographic and clinical outcomes
(Source: Wiley Online Library) New Publication from Dr. Vijaya Kochalama, Assistant Professor of Medicine in the Section of Computational Biomedicine. Please see below for a brief summary and click the link to read the full article. Objective Develop a bone shape measure that reflects the extent of cartilage loss and bone flattening in knee osteoarthritis […]
Animalcules: interactive microbiome analytics and visualization in R
Source: BMC (Part of Springer Nature) New publication from Dr. Evan Johnson, Dr. Stefano Monti, Anthony Federico and collaborators – see below for the abstract and to read more. Background Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled […]
Enhancing magnetic resonance imaging-driven Alzheimer’s disease classification performance using generative adversarial learning
Source: BMC (Part of Springer Nature) New publication from Dr. Vijaya Kolachalama and collaborators – see below for the abstract and to read more. Background Generative adversarial networks (GAN) can produce images of improved quality but their ability to augment image-based classification is not fully explored. We evaluated if a modified GAN can learn from […]
Protein signatures of centenarians and their offspring suggest centenarians age slower than other humans
Source: Aging Cell New publication from Dr. Stefano Monti, Associate Professor of Medicine, in collaboration with Dr. Thomas Perls and Dr. Paola Sebastiani of the New England Centenarian Study. See below for a brief summary and click the link to read more. Using samples from the New England Centenarian Study (NECS), we sought to characterize […]
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.
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. […]