Zobrazeno 1 - 10
of 241
pro vyhledávání: '"Hanlee P. Ji"'
Autor:
Kaishu Mason, Anuja Sathe, Paul R. Hess, Jiazhen Rong, Chi-Yun Wu, Emma Furth, Katalin Susztak, Jonathan Levinsohn, Hanlee P. Ji, Nancy Zhang
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-33 (2024)
Abstract Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the tissue, rather than local gene expression changes driven by cell-cell interactions. We propose a
Externí odkaz:
https://doaj.org/article/584d5b43dfac4a9b8622ba36a4824e07
Autor:
Anuja Sathe, Carlos Ayala, Xiangqi Bai, Susan M. Grimes, Byrne Lee, Cindy Kin, Andrew Shelton, George Poultsides, Hanlee P. Ji
Publikováno v:
Genome Medicine, Vol 15, Iss 1, Pp 1-25 (2023)
Abstract Background Understanding the mechanistic effects of novel immunotherapy agents is critical to improving their successful clinical translation. These effects need to be studied in preclinical models that maintain the heterogenous tumor microe
Externí odkaz:
https://doaj.org/article/8cfb40beda144e8e8bef760c00d5144c
Autor:
Ho Jung An, Mira A. Partha, HoJoon Lee, Billy T. Lau, Dmitri S. Pavlichin, Alison Almeda, Anna C. Hooker, Giwon Shin, Hanlee P. Ji
Publikováno v:
Frontiers in Oncology, Vol 13 (2024)
BackgroundColon microbiome composition contributes to the pathogenesis of colorectal cancer (CRC) and prognosis. We analyzed 16S rRNA sequencing data from tumor samples of patients with metastatic CRC and determined the clinical implications.Material
Externí odkaz:
https://doaj.org/article/f36916f7469247408cf94f0de232d4f5
Autor:
Billy Lau, Shubham Chandak, Sharmili Roy, Kedar Tatwawadi, Mary Wootters, Tsachy Weissman, Hanlee P. Ji
Publikováno v:
Scientific Reports, Vol 13, Iss 1, Pp 1-15 (2023)
Abstract The storage of data in DNA typically involves encoding and synthesizing data into short oligonucleotides, followed by reading with a sequencing instrument. Major challenges include the molecular consumption of synthesized DNA, basecalling er
Externí odkaz:
https://doaj.org/article/e05020c8bf364082b0fa245011539ba0
Autor:
Billy T. Lau, Alison Almeda, Marie Schauer, Madeline McNamara, Xiangqi Bai, Qingxi Meng, Mira Partha, Susan M. Grimes, HoJoon Lee, Gregory M. Heestand, Hanlee P. Ji
Publikováno v:
Genome Medicine, Vol 15, Iss 1, Pp 1-13 (2023)
Abstract Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This
Externí odkaz:
https://doaj.org/article/e323638932ce446b90aecb9fb1f4e521
Autor:
Stephanie U. Greer, Jiamin Chen, Margret H. Ogmundsdottir, Carlos Ayala, Billy T. Lau, Richard Glenn C. Delacruz, Imelda T. Sandoval, Sigrun Kristjansdottir, David A. Jones, Derrick S. Haslem, Robin Romero, Gail Fulde, John M. Bell, Jon G. Jonasson, Eirikur Steingrimsson, Hanlee P. Ji, Lincoln D. Nadauld
Publikováno v:
Scientific Reports, Vol 12, Iss 1, Pp 1-15 (2022)
Abstract Autophagy is a housekeeping mechanism tasked with eliminating misfolded proteins and damaged organelles to maintain cellular homeostasis. Autophagy deficiency results in increased oxidative stress, DNA damage and chronic cellular injury. Amo
Externí odkaz:
https://doaj.org/article/07556fe7ab554218a24d01d6e4b51299
Publikováno v:
npj Precision Oncology, Vol 6, Iss 1, Pp 1-11 (2022)
Abstract Deep-learning classification systems have the potential to improve cancer diagnosis. However, development of these computational approaches so far depends on prior pathological annotations and large training datasets. The manual annotation i
Externí odkaz:
https://doaj.org/article/a21435a0720d4fe6b08b5a429358461d
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-16 (2021)
Abstract We developed a single-cell approach to detect CRISPR-modified mRNA transcript structures. This method assesses how genetic variants at splicing sites and splicing factors contribute to alternative mRNA isoforms. We determine how alternative
Externí odkaz:
https://doaj.org/article/8e4adc221d104b4abcfdbff4a0f35b39
Autor:
GiWon Shin, Stephanie U. Greer, Erik Hopmans, Susan M. Grimes, HoJoon Lee, Lan Zhao, Laura Miotke, Carlos Suarez, Alison F. Almeda, Sigurdis Haraldsdottir, Hanlee P. Ji
Publikováno v:
Genome Medicine, Vol 13, Iss 1, Pp 1-18 (2021)
Abstract We developed a sensitive sequencing approach that simultaneously profiles microsatellite instability, chromosomal instability, and subclonal structure in cancer. We assessed diverse repeat motifs across 225 microsatellites on colorectal carc
Externí odkaz:
https://doaj.org/article/f712076aec7c479ebafdae1d3b8bdf16
Autor:
Andrew M. K. Law, Jiamin Chen, Yolanda Colino‐Sanguino, Laura Rodriguez de la Fuente, Guocheng Fang, Susan M. Grimes, Hongxu Lu, Robert J. Huang, Sarah T. Boyle, Jeron Venhuizen, Lesley Castillo, Javad Tavakoli, Joanna N. Skhinas, Ewan K. A. Millar, Julia Beretov, Fernando J. Rossello, Joanne L. Tipper, Christopher J. Ormandy, Michael S. Samuel, Thomas R. Cox, Luciano Martelotto, Dayong Jin, Fatima Valdes‐Mora, Hanlee P. Ji, David Gallego‐Ortega
Publikováno v:
Advanced Science, Vol 9, Iss 21, Pp n/a-n/a (2022)
Abstract To fully investigate cellular responses to stimuli and perturbations within tissues, it is essential to replicate the complex molecular interactions within the local microenvironment of cellular niches. Here, the authors introduce Alginate
Externí odkaz:
https://doaj.org/article/7c01605cf8c442bb9c5423b06b6545f3