Mark Gerstein
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Explore the profile of Mark Gerstein including associated specialties, affiliations and a list of published articles.
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Recent Articles
1.
Yang J, Agrawal K, Stanley 3rd J, Stanley J, Li R, Jacobs N, et al.
bioRxiv
. 2025 Feb;
PMID: 39975288
HIV infection exerts profound and long-lasting neurodegenerative effects on the central nervous system (CNS) that can persist despite antiretroviral therapy (ART). Here, we used single-nucleus multiome sequencing to map the...
2.
Wang G, Warrell J, Zheng S, Gerstein M
Cell Rep Phys Sci
. 2025 Jan;
5(11).
PMID: 39866853
Graph neural networks (GNNs) have emerged as powerful tools for representation learning. Their efficacy depends on their having an optimal underlying graph. In many cases, the most relevant information comes...
3.
Moore J, Pratt H, Fan K, Phalke N, Fisher J, Elhajjajy S, et al.
bioRxiv
. 2025 Jan;
PMID: 39763870
Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, The ENCODE consortium mapped biochemical signals across many cell types and tissues and integrated...
4.
Liu J, Borsari B, Li Y, Liu S, Gao Y, Xin X, et al.
Cell
. 2024 Dec;
188(2):515-529.e15.
PMID: 39706190
Psychiatric disorders are influenced by genetic and environmental factors. However, their study is hindered by limitations on precisely characterizing human behavior. New technologies such as wearable sensors show promise in...
5.
Gupta C, Cohen Kalafut N, Clarke D, Choi J, Arachchilage K, Khullar S, et al.
medRxiv
. 2024 Dec;
PMID: 39677458
Neuropsychiatric disorders lack effective treatments due to a limited understanding of underlying cellular and molecular mechanisms. To address this, we integrated population-scale single-cell genomics data and analyzed cell-type-level gene regulatory...
6.
Zhou X, Kedia S, Meng R, Gerstein M
PLoS One
. 2024 Dec;
19(12):e0312848.
PMID: 39630834
The early detection of Alzheimer's Disease (AD) is thought to be important for effective intervention and management. Here, we explore deep learning methods for the early detection of AD. We...
7.
Mudge J, Carbonell-Sala S, Diekhans M, Martinez J, Hunt T, Jungreis I, et al.
Nucleic Acids Res
. 2024 Nov;
53(D1):D966-D975.
PMID: 39565199
GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome...
8.
Kaur G, Perteghella T, Carbonell-Sala S, Gonzalez-Martinez J, Hunt T, Madry T, et al.
bioRxiv
. 2024 Nov;
PMID: 39554180
Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference annotations for the human and mouse...
9.
Kudron M, Gevirtzman L, Victorsen A, Lear B, Gao J, Xu J, et al.
Genome Res
. 2024 Oct;
34(12):2319-2334.
PMID: 39438113
A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism...
10.
Liu J, Borsari B, Li Y, Liu S, Gao Y, Xin X, et al.
medRxiv
. 2024 Oct;
PMID: 39399036
Psychiatric disorders are complex and influenced by both genetic and environmental factors. However, studying the full spectrum of these disorders is hindered by practical limitations on measuring human behavior. This...