Miten Jain

The paper uses in vitro transcribed RNA from genomic DNA to benchmark RNA modification detection by Nanopore direct RNA sequencing models.

tRNAZAP is a deep learning toolkit for analyzing nanopore tRNA sequencing data, achieving high accuracy in segmentation and classification tasks.

This paper develops a computational strategy for analyzing nanopore ionic current signals from synthetic proteins, achieving high accuracy in charge-based classification of amino acids.

The paper identifies 21 novel pseudouridine sites in S. cerevisiae tRNAs using DRS and BACS, and maps their modifying enzymes.

SALRR provides a scalable platform for long-read RNA-seq analysis, identifying novel splice variants in human brain tissue.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

This study uses long-read sequencing to map transposable element variation in human brain tissue, revealing regulatory and epigenetic effects across cell types and ancestries.

This paper introduces HS-nano-seq, a method to analyze heparan sulfate using nanopore sequencing, enabling single-molecule detection of sulfation patterns and structural features.

This paper uses long-read sequencing to analyze haplotype-resolved DNA methylation at the APOE locus in brain samples, identifying allele-specific methylation patterns linked to Alzheimer's disease risk.

The paper introduces tRNAZAP, a deep learning method using nanopore ionic current signals to classify tRNA isodecoders, achieving better alignment results than BWA-MEM in E. coli and S. cerevisiae.

The paper profiles RNA modifications in MS2 bacteriophage using LC-MS/MS and Nanopore DRS, finding {Psi} as the predominant modification.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

This paper evaluates updates to Nanopore direct RNA sequencing for detecting RNA modifications, showing improved accuracy in identifying pseudouridine and N6-methyladenosine.

The paper presents the first telomere-to-telomere diploid reference genome of the human embryonic stem cell line H9, revealing genomic features and ancestry.

The paper generates and characterizes a custom genome assembly for the KOLF2.1J iPSC line to improve genomic analysis accuracy compared to standard references.

Clair3-RNA is a deep learning variant caller for long-read RNA sequencing data that achieves high accuracy in SNP detection across different platforms.

The paper identifies FGF14 GAA repeat expansions in Parkinson's disease using long-read sequencing and finds they occur in both patients and controls.

The paper develops epigenetic clocks using long-read DNA methylation data from diverse ancestries, showing improved aging predictions and identifying ancestry-specific aging pathways.

This study shows that PUS7's cytoplasmic localization enhances stress tolerance by increasing pseudouridylation of mRNAs involved in metal and ROS homeostasis.

This study shows that pancreatic injury in axolotl leads to β-cell regeneration without blastema formation, through organ-wide proliferation that recovers β-cell mass.

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

This paper develops machine learning models to quantitatively measure pseudouridine occupancy in human mRNAs using synthetic controls, revealing site-specific requirements for accurate classification.

This paper introduces a local haplotype approximation method to improve variant calling accuracy across long-read sequencing platforms without increasing computational overhead.

The paper generates and characterizes modification-free RNA transcripts from human cell lines for use as controls in nanopore direct RNA sequencing analysis.

The paper maps pseudouridylation sites in human cell lines using nanopore sequencing and shows how psi modifications affect translation through distinct mechanisms.

The paper introduces methods for haplotype-resolved de novo assembly using Shasta and GFAse, showing improved assembly quality with newer Oxford Nanopore reads.

This study uses direct RNA sequencing to examine pseudouridylation dynamics in neurons under healthy and unhealthy conditions, finding changes in psi writer expression and site occupancy.

This study compares 5mC detection accuracy between Nanopore R9 and R10 chemistries using human datasets, finding high concordance and strong correlation with Illumina bisulfite methods.