Author details

Full Name

Ali Mortazavi

Affiliation

ORCID

Career Start Year

1998

Papers

113

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37546854	Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.	bioRxiv	2023
37662399	C5aR1 antagonism suppresses inflammatory glial gene expression and alters cellular signaling in an aggressive Alzheimer's model.		2023
37344645	Signalling by senescent melanocytes hyperactivates hair growth.	Nature	2023
36712559	Single-Cell Transcriptional Changes in Hypothalamic Corticotropin-Releasing Factor-Expressing Neurons After Early-Life Adversity Inform Enduring Alterations in Vulnerabilities to Stress.		2023
37399090	PyWGCNA: a Python package for weighted gene co-expression network analysis.		2023
37066421	The ENCODE Uniform Analysis Pipelines.	bioRxiv	2023
37292896	The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.	bioRxiv	2023
37503119	The ENCODE Uniform Analysis Pipelines.	Res Sq	2023
35348742	Multiple Mechanisms of Photoreceptor Spectral Tuning in Heliconius Butterflies.	Molecular Biology and Evolution	2022
35646075	Heterogeneous Skeletal Muscle Cell and Nucleus Populations Identified by Single-Cell and Single-Nucleus Resolution Transcriptome Assays.	Frontiers in Genetics	2022
35820938	Modulation of C5a-C5aR1 signaling alters the dynamics of AD progression.	Journal of Neuroinflammation	2022
35474001	Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.	Nature	2022
35978440	C5aR1 antagonism alters microglial polarization and mitigates disease progression in a mouse model of Alzheimer's disease.	Acta neuropathologica communications	2022
34799404	Disruption of Î²-Catenin-Dependent Wnt Signaling in Colon Cancer Cells Remodels the Microenvironment to Promote Tumor Invasion.	Mol Cancer Res	2022
35172134	Uncovering the mesendoderm gene regulatory network through multi-omic data integration.	Cell Rep	2022
34949670	Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types.	Genome Res	2022
34634799	Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing.	Nucleic Acids Res	2021
34125087	A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq.	Journal of Visualized Experiments	2021
33849979	An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin.	mBio	2021
34224831	Transcriptome and chromatin landscape changes associated with trastuzumab resistance in HER2+Â breast cancer cells.	Gene	2021
34222260	Linking Chromosomal Silencing With Expression From Autosomal Integrated Transgenes.	Frontiers in Cell and Developmental Biology	2021
33893290	Generation of a humanized AÎ² expressing mouse demonstrating aspects of Alzheimer's disease-like pathology.	Nat Commun	2021
32991665	Swan: a library for the analysis and visualization of long-read transcriptomes.		2021
33359282	Transcatheter aortic valve replacement after chest radiation: A propensity-matched analysis.	International Journal of Cardiology	2021
32797452	A Revised Adaptation of the Smart-Seq2 Protocol for Single-Nematode RNA-Seq.	Methods in Molecular Biology	2021
34579762	Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer.	Breast Cancer Research	2021
34733690	Hemodynamic outcomes after valve-in-valve transcatheter aortic valve replacement: a single-center experience.	Annals of Cardiothoracic Surgery	2021
34620214	Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq.	Genome Biol	2021
34433559	Microglial dyshomeostasis drives perineuronal net and synaptic loss in a CSF1R<sup>+/-</sup> mouse model of ALSP, which can be rescued via CSF1R inhibitors.	Sci Adv	2021
34654824	Systematic phenotyping and characterization of the 5xFAD mouse model of Alzheimer's disease.	Scientific data	2021
34877597	Coordinated Gene Expression and Chromatin Regulation during Hydra Head Regeneration.	Genome Biol Evol	2021
31471558	Intra-individual changes in methylome profiles: an epigenetic 'scar' of early-life adversity?		2020
32365093	Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei.	PLoS Genetics	2020
33283040	Model organism development and evaluation for late-onset Alzheimer's disease: MODEL-AD.	Alzheimers Dement (N Y)	2020
32728249	Expanded encyclopaedias of DNA elements in the human and mouse genomes.	Nature	2020
33326786	Unexpected Transcriptional Programs Contribute to Hippocampal Memory Deficits and Neuronal Stunting after Early-Life Adversity.	Cell Reports	2020
33106502	Slug regulates the Dll4-Notch-VEGFR2 axis to control endothelial cell activation and angiogenesis.	Nat Commun	2020
31042778	A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema.	PLoS Pathogens	2019
31847811	Molecular evolution and expression of opsin genes in Hydra vulgaris.	BMC Genomics	2019
31645363	Dynamics of microRNA expression during mouse prenatal development.	Genome Res	2019
31682608	Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.	PLoS Comput Biol	2019
29912287	TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts.		2019
30978178	Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation.	PLoS Biol	2019
31010097	miR-128 Restriction of LINE-1 (L1) Retrotransposition Is Dependent on Targeting hnRNPA1 mRNA.	International Journal of Molecular Sciences	2019
31355335	The genome of , natural host for Lyme disease and other emerging infections.	Science advances	2019
31113823	Hybrid Assembly of the Genome of the Entomopathogenic Nematode <i>Steinernema carpocapsae</i> Identifies the X-Chromosome.	G3 (Bethesda)	2019
30936186	Intra-individual methylomics detects the impact of early-life adversity.	Life Science Alliance	2019
28070121	NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience.	Molecular Psychiatry	2018
29967126	Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.	Genome Res	2018
30370589	A limited capacity for microglial repopulation in the adult brain.	GLIA	2018