Sushmita Roy

About

Sushmita Roy is a Professor in the Department of Biostatistics and Medical Informatics and the Department of Computer Science at the University of Wisconsin, Madison. She is also affiliated with the Wisconsin Institute for Discovery (WID). The page lists her as a current member of the research community, but does not provide specific details about her research focus, background, or key contributions.

Research topics

• Genetics
• Biology
• Computer Science
• Computational biology
• Data science
• Evolutionary biology
• Neuroscience
• Cell biology
• Botany

Selected publications

• The NIH Somatic Cell Genome Editing program

  Nature · 2021 · 130 citations

  The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium's plans to develop and benchmark approaches to induce and measure genome modifications…

  PublisherOA PDFDOI

• Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

  Nature Communications · 2023-05-27 · 112 citations

  articleOpen accessSenior author

  Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and signaling proteins to target genes. Single-cell technologies such as single cell RNA-sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), can examine cell-type specific gene regulation at unprecedented detail. However, current approaches to infer cell type-specific GRNs are limited in their ab…

  PublisherOA PDFDOI

• Current and future directions in network biology

  Bioinformatics Advances · 2024-01-01 · 92 citations

  editorialOpen access

  Summary: Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data…

  PublisherDOI

• Identification of FMR1-regulated molecular networks in human neurodevelopment

  Genome Research · 2020 · 67 citations

  gene deletion. We discovered that FMR1 preferentially binds long transcripts in human neural cells. FMR1 targets include genes unique to human neural cells and associated with clinical phenotypes of FXS and autism. Integrative network analysis using graph diffusion and multitask clustering of FMR1 CLIP-seq and transcriptional targets reveals critical pathways regulated by FMR1 in human neural development. Our results demonstrate that FMR1 regulates a common set of targets among different neural…

  DOI

• Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in <i>Populus</i>

  Development · 2022 · 62 citations

  Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. Presently, we lack a lineage map of the shoot apex cells in woody perennials - a crucial gap considering their role in determining primary and secondary growth. Here, we used single-nuclei RNA-sequencing to determine cell type-specific transcriptomes of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally…

  PublisherOA PDFDOI

Recent grants

• CAREER: Comparative Network Biology to Study the Evolution of Regulatory Networks

  NSF · $507k · 2014–2020

• Computational Inference of Regulatory Network Dynamics on Cell Lineages

  NIH · $1.5M · 2016–2023

• Computational approaches for comparative regulatory genomics to decipher long-range gene regulation

  NIH · $1.4M · 2018–2024

Frequent coauthors

• Alireza Fotuhi Siahpirani

  University of Tehran

  110 shared

• Shilu Zhang

  University of Science and Technology of China

  74 shared

• Deborah Chasman

  University of Wisconsin–Madison

  68 shared

• Sara Knaack

  Wisconsin Institutes for Discovery

  66 shared

• Sunnie Grace McCalla

  University of Wisconsin–Madison

  60 shared

• Junha Shin

  52 shared

• Rupa Sridharan

  University of Wisconsin–Madison

  47 shared

• Saptarshi Pyne

  Wisconsin Institutes for Discovery

  38 shared

Labs

• Roy LabPI

Education

• Ph.D., Biostatistics

  University of Wisconsin-Madison

  2005

• M.S., Biostatistics

  University of Wisconsin-Madison

  2001

• B.S., Statistics

  University of Calcutta

  1998

Similar researchers at University of Wisconsin-Madison

• Ron Gangnonh-85
• Karl Bromanh-68
• Michael A. Newtonh-62