Is this you? As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.
Claim your profile
Articles by Robert Sebra
Plasticity of human microglia and brain perivascular macrophages in aging and Alzheimer’s disease
Abstract Myeloid cells, including microglia and perivascular macrophages, are central to Alzheimer’s disease (AD) neurobiology, yet their role remains incompletely understood. We profiled 832,505 human myeloid cells from the prefrontal cortex of 1,607 donors spanning the lifespan and showing varying degrees of AD neuropathology. We delineated six subclasses comprising 13 transcriptionally distinct subtypes and identified adaptive changes associated with aging and AD progression.
Author Correction: A streamlined base editor engineering strategy to reduce bystander editing - Nature Communications
Correction to: Nature Communications https://doi.org/10.1038/s41467-025-63609-6, published online 30 August 2025 In the version of the article initially published, there were typos in Fig. 1c and Supplementary Fig. 1a, where the mutation annotations of ABE-NW3 now reading “Y149Q” appeared originally as “Y149N.” The figures are updated in the HTML and PDF versions of the article.
Author Correction: A streamlined base editor engineering strategy to reduce bystander editing - Nature Communications
Correction to: Nature Communications https://doi.org/10.1038/s41467-025-63609-6, published online 30 August 2025 In the version of the article initially published, in the second paragraph of the Results, the sentence “Some of the amino acid changes, such as N108Q and V28C, have been previously reported to attenuate bystander editing” was missing and has now been added alongside a new reference: “Perrotta, R. M. et al. Machine learning and directed evolution of base editing enzymes.
A streamlined base editor engineering strategy to reduce bystander editing - Nature Communications
Abstract Base editing (BE) can permanently correct over half of known human pathogenic genetic variants without requiring a repair template, thus serving as a promising therapeutic tool to treat a broad spectrum of genetic diseases. However, the broad activity windows of current base editors pose a major challenge to their therapeutic application.
A study of gene expression in the living human brain - Molecular Psychiatry
Abstract A goal of psychiatric research is to determine the molecular basis of human brain health and illness. One way to achieve this goal is through studies of gene expression in human brain tissue. Due to the unavailability of brain tissue from living people, most such studies are performed using tissue from postmortem brain donors.
Regulation of airway fumarate by host and pathogen promotes Staphylococcus aureus pneumonia - Nature Communications
Abstract Staphylococcus aureus is a leading cause of healthcare-associated pneumonia, contributing significantly to morbidity and mortality worldwide. As a ubiquitous colonizer of the upper respiratory tract, S. aureus must undergo substantial metabolic adaptation to achieve persistent infection in the distinctive microenvironment of the lung. We observed that fumC, which encodes the enzyme that converts fumarate to malate, is highly conserved with low mutation rates in S.
Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures
|
Keywords proteogenomics lung adenocarcinoma genomics mass spectrometry PTMs biomarkers smokers never-smokers CPTAC ICPC Introduction Lung adenocarcinomas (LUAD), the most prevalent subtype of non-small cell lung cancers (NSCLC), represent a significant global health challenge with marked geographical and epidemiological diversity in incidence and disease progression.1 Despite advances in targeted therapies and improved diagnostic techniques, LUAD continue to exhibit high mortality rates,2...
By Shankha Satpathy, Natalie Clark, Yi-Ju Chen, Noshad Hosseini, Ya-Hsuan Chang, Yi Hsiao, Jonathan T. Lei, Francesca Petralia, Jin-Shing Chen, Yifat Geffen, David Heiman, Indranil Paul, Hanbyul Cho, Michelle Hollenberg, Giacomo B Marino, Kuen-Tyng Lin, Rahul Mannan, C. White, Joe Allen, Shayan C. Avanessian, M. Kane, Ashley Wolfe, Wenke Liu, Shankara Anand, Mong-Wei Lin, Moe Haines, Erik Bergström, Grant A. Hussey, Ginny Xiaohe Li, Deepak Mani, Hao Fang, Eric J. Jaehnig, Hasmik Keshishian, Kang-Yi Su, Yi-Jing Hsiao, Hsao-Hsun Hsu, Min-Shu Hsieh, Kuo-Hsuan Hsu, Simone Gohsman, John R. Thorup, Yamei Deng, Yo Akiyama, Eden Z. Deng, Eric Chen, Azra Krek, Rodrigo Espinoza, Weiping Ma, Daniel Charytonowicz, Robert Sebra, Jyun-Hong Lin, Yin-Chen Hsu, Kun-Chieh Chen, Yu-Tai Wang, Alexander J. Lazar, Mehdi Mesri, Xu Zhang, Karl R. Clauser, David Fenyö, Arul M. Chinnaiyan, Bing Zhang, Kelly V. Ruggles, Chelsea Newton, Pei Wang, Galen Hostetter, Gilbert S. Omenn, Chandan Kumar-Sinha, Ramaswamy Govindan, Paul K. Paik, Abhijit Parolia, QING LI, Avi Ma’ayan, Gad Getz, Saravana M. Dhanasekaran, Ana I. Robles, Gee-Chen Chang, Pan-Chyr Yang, Sung-Liang Yu, Hsuan-Yu Chen, Alexey I. Nesvizhskii, Steven Carr, D.R. Mani, Marcin Cieslik, Yu-Ju Chen, Michael Gillette, Chao-Wen Lu, Cheng-Hsiang Chu, Chia-Li Han, Chien-Yu Lin, Ching-Wen Chen, Chung-Hsien Lin, Hsiang-En Hsu, Jia-Jun Wu, Pei-Hsing Chen, Pei-Rong Huang, Wan-Chun Lai, Xu-Heng Chiang, Ya-Ling Chang, Yan-Ming Chen, Yi-Ling Chen, Yi-Wen Wang, Yi-Wei Lin, Yu-Cheng Chang, Yu-Ting Huang, Zhe-Rong Zheng, Akhilesh Pandey, Alexander Pilozzi, Alex Webster, Amanda G. Paulovich, Andrew Godwin, Barbara L Pruetz, Bart O. Williams, Brian Druker, Daniel Rohrer, Daniel Chan, Danail Petrov, Elizabeth Duffy, George Wilson, Grace Zhao, Jan Lubinski, Jasmine Huang, Jason M. Hafron, Jeffrey W. Tyner, John M. Koomen, Maciej Wiznerowicz, Marcin Domagalski, Meenakshi Anurag, Nathan Edwards, Paul D Piehowski, Qin Li, Rafael Fonseca, Rashna Madan, Ross Bremner, Sandra López Cerdá, Shuang Cai, Tao Liu, Thomas A. Bauer, Xiaojun Jing, Yuping Zhang, Zoran Andrić, Miloni Kinarivala, Brecca Miller, Alexi Monovoukas, Yan-Si Chen, Ze-Shiang Lin, Chang-Wei Yeh, Eunkyung An, Mathangi Thiagarajan, Chi-Ya Shen, Chien-Chia Lin, Hsing-Jui Tsai, Jing-Wei Lin, Juani Waniwan, Ki-Hok Liao, Sin-Ming Huang, Tai-Ching Lin, Wei-Tzu Chiu, Yuju Lien, Abdul Samad Hashimi, Adrij Mohan, Aniket Dagar, David Chesla, Diwakar Davaar, Iga Kołodziejczak, Kakhaber Zaalishvili, Karen A. Ketchum, Melissa Borucki, Negin Vatanian, Pamela Grady, Popovici Bogdan, Ratna R. Thangudu, Reese Crispen, Ronald Matteotti, Sandra L. Cottingham, Shirley Tsang, William W. Maggio, Yvonne Shutack
|
Cell Press
Verified
Atezolizumab plus personalized neoantigen vaccination in urothelial cancer: a phase 1 trial - Nature Cancer
Abstract Features of constrained adaptive immunity and high neoantigen burden have been correlated with response to immune checkpoint inhibitors (ICIs). In an attempt to stimulate antitumor immunity, we evaluated atezolizumab (anti-programmed cell death protein 1 ligand 1) in combination with PGV001, a personalized neoantigen vaccine, in participants with urothelial cancer.
Tracking HIV persistence across T cell lineages during early ART-treated HIV-1-infection using a reservoir-marking humanized mouse model - Nature Communications
Abstract Human immunodeficiency virus (HIV) infection depletes CD4 T-cells, and long-term persistence of latent virus prevents full clearance of HIV even in the presence of effective antiretroviral therapy (ART), Here we present the HIV-1-induced lineage tracing (HILT) system, a model that irreversibly marks infected cells within a humanized mouse model, which detects rare latently infected cells.
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing - Nature Genetics
|
Abstract Microglia, the innate immune cells of the central nervous system, have been genetically implicated in multiple neurodegenerative diseases. Mapping the genetics of gene expression in human microglia has identified several loci associated with disease-associated genetic variants in microglia-specific regulatory elements. However, identifying genetic effects on splicing is challenging because of the use of short sequencing reads.
By Jack Humphrey, Elena Coccia, Tatsuhiko Naito, Benjamin Müller, Alexandra E. Münch, Reta Birhanu Kitata, Nancy J. Francoeur, Marina A. Gritsenko, Matthew Monroe, Vanessa L Paurus, Karl K. Weitz, Robert Sebra, Tao Liu, Alison Goate, Vahram Haroutunian, Gabriel Hoffman, John F. Fullard, Panos Roussos, Periklis Malakates, Konstantina Psychogyiou
|
Nature
Verified
Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer - Nature Genetics
Abstract Targeting cancer stem cells (CSCs) is crucial for effective cancer treatment, yet resistance mechanisms to LGR5+ CSC depletion in WNT-driven colorectal cancer (CRC) remain elusive. In the present study, we revealed that mutant intestinal stem cells (SCs) depart from their canonical identity, traversing a dynamic phenotypic spectrum.
Multiscale mapping of transcriptomic signatures for cardiotoxic drugs - Nature Communications
Abstract Drug-induced gene expression profiles can identify potential mechanisms of toxicity. We focus on obtaining signatures for cardiotoxicity of FDA-approved tyrosine kinase inhibitors (TKIs) in human induced-pluripotent-stem-cell-derived cardiomyocytes, using bulk transcriptomic profiles. We use singular value decomposition to identify drug-selective patterns across cell lines obtained from multiple healthy human subjects.
Author Correction: Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer: a phase 2 trial - Nature Medicine
Correction to: Nature Medicine https://doi.org/10.1038/s41591-023-02568-1, published online 2 October 2023. In the version of the article initially published, Diane M.
Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer: a phase 2 trial - Nature Medicine
Abstract Cystectomy is a standard treatment for muscle-invasive bladder cancer (MIBC), but it is life-altering. We initiated a phase 2 study in which patients with MIBC received four cycles of gemcitabine, cisplatin, plus nivolumab followed by clinical restaging. Patients achieving a clinical complete response (cCR) could proceed without cystectomy.
MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping - Nature Cell Biology
Abstract MacroH2A has established tumour suppressive functions in melanoma and other cancers, but an unappreciated role in the tumour microenvironment. Using an autochthonous, immunocompetent mouse model of melanoma, we demonstrate that mice devoid of macroH2A variants exhibit increased tumour burden compared with wild-type counterparts.
Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants - Nature Communications
Abstract Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, direct evidence of subsequent transmission and continued stepwise adaptation is lacking.
Interpretable and context-free deconvolution of multi-scale whole transcriptomic data with UniCell deconvolve - Nature Communications
In this work, we presented UniCell: Deconvolve Base, a universal, context-free cell type deconvolution tool for transcriptomic data that integrates the entirety of publicly-available scRNA-Seq data into a single unified training dataset for deep learning applications.
Application of Single-Cell Sequencing to Immunotherapy
Yadav S.S. Stockert J.A. Hackert V. et al. Intratumor heterogeneity in prostate cancer. Urol Oncol. 2018; 36: 349-360 Riaz N. Havel J.J. Makarov V. et al. Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab. Cell. 2017; 171: 934-949.e16 da Costa J.B. Gibb E.A. Nykopp T.K. et al. Molecular tumor heterogeneity in muscle invasive bladder cancer: Biomarkers, subtypes, and implications for therapy. Urol Oncol. 2018; https://doi.org/10.1016/j.urolonc.2018.11.015 Cote R.J. Esrig D. Groshen S.
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles
Li Wang1,2,3, Robert P. Sebra1,2,3, John P. Sfakianos4, Kimaada Allette1,2, Wenhui Wang1,2, Seungyeul Yoo1,2, Nina Bhardwaj5,6, Eric E. Schadt1,2,3,6, Xin Yao7, Matthew D. Galsky5,6 & Jun Zhu ORCID: orcid.org/0000-0003-0834-81781,2,3,6 Genome Medicine volume 12, Article number: 24 (2020) Cite this article Abstract Background Patient stratification based on molecular subtypes is an important strategy for cancer precision medicine.
DNA sequencing at ultra-high fidelity
Now that next-generation DNA sequencing has thoroughly permeated the life sciences, it is easy to overlook the remaining technical challenges of this foundational tool. Continued research is needed to increase sequencing read lengths, reduce error rates, and further increase throughput. In this issue, Chen et al.1 present a method for improving read quality through molecular and error-correction methods.
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis
For a comprehensive evaluation, we used diverse types of RNA-seq data in our analysis. Supplementary Table 1 summarizes the data sets used in this study. These data sets include 15 Illumina and Pacific Biosciences (PacBio) data sets from normal human sample NA1287810, human MCF-7 breast cancer cell11, H1 human embryonic stem cell (hESC)12, and the Sequencing Quality Control Consortium (SEQC) data set8.
Assay Development for Clinical Genomics
SMRT sequencing enables the detection of genomic variants for a wide range of clinical applications The Mount Sinai Health System in New York serves some 3.5 million patients each year. In doing so, its 7,000-plus physicians rely heavily on clinical laboratory testing to diagnose patients and make critical treatment decisions. Some of the earliest incarnations of genetic assays used in such applications are born in the technology development lab of the Icahn School of Medicine at Mount Sinai.
Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in Vibrio cholerae and Vibrio fischeri
AbstractThe vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae.
Use of multiple sequencing technologies to produce a high-quality genome of the fungus
Use of multiple sequencing technologies to produce a high-quality genome of the fungus Pseudogymnoascus destructans, the causative agent of bat White-Nose syndrome Genome Announcements By: Kevin P. Drees, Jonathan M. Palmer, Robert Sebra, Jeffrey M. Lorch, Cynthia Chen, ChengCang Wu, Jin Woo Bok, Nancy F. Keller, David Blehert, Christina A. Cuomo, Daniel L. Linder, and Jeffrey T.
Show More
loading
Actions
Is this you?
As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.Get in touch with Robert
Contact Robert, search articles and posts on X, monitor coverage, and track replies from one place.
Learn more about Muck Rack