About
I am a computational genomics researcher specializing in long-read sequencing technologies and transcriptome analysis. Currently pursuing my PhD at the Institute for Integrative Systems Biology, Spanish National Research Council (CSIC-UV) in Valencia, Spain, under the supervision of Dr. Ana Conesa.
My research focuses on developing computational methods for analyzing long-read RNA sequencing data, with particular expertise in isoform regulatory biology and multiomics integration. I am passionate about advancing our understanding of transcriptome complexity through innovative computational approaches.
As part of the LongTREC (Long-read Transcriptomics Research and Education Consortium) Marie Skłodowska-Curie Actions program, I work on cutting-edge research that bridges computational biology and experimental genomics.
Long-Read Sequencing
Third-generation sequencing technologies and their applications in transcriptomics
Multiomics Integration
Integrating diverse omics data to understand biological systems
Tool Development
Creating computational tools for genomics research
Research Focus
My research centers on "Long reads multiomics methods to understand isoform regulatory biology", where I develop and apply computational methods to analyze transcriptome complexity using third-generation sequencing technologies.
Key Research Areas
- Quality Control Methods: Developing tools like SQANTI3 for comprehensive quality assessment of long-read transcriptomes
- Isoform Detection: Creating algorithms for accurate identification and quantification of transcript isoforms
- Epigenome Profiling: Utilizing long-read sequencing for studying DNA methylation and chromatin modifications
- Transcriptome Assembly: Improving methods for de novo transcriptome reconstruction from long reads
- Differential Analysis: Investigating condition-specific changes in isoform usage and expression
Selected Publications
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms
Nature Methods 21 (5), 793-797, 2024
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Nature Methods 21 (7), 1349-1363, 2024
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
Genome Biology 24 (1), 286, 2023
PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases
Nucleic Acids Research 50 (W1), W551-W559, 2022
Transcriptional differences for COVID-19 disease map genes between males and females indicate a different basal immunophenotype relevant to the disease
Genes 11 (12), 1447, 2020
MirCure: a tool for quality control, filter and curation of microRNAs of animals and plants
Bioinformatics 36 (Supplement_2), i618-i624, 2020
Profiling the epigenome using long-read sequencing
Nature Genetics 57 (1), 27-41, 2025
Transcriptomics in the era of long-read sequencing
Nature Reviews Genetics, 2025
Projects
Major Projects
PaintOmics 4
An advanced web-based platform for integrative analysis of multi-omics datasets with support for multiple pathway databases. Enables comprehensive visualization and analysis of complex biological data.
Technologies: JavaScript, Web-based interface, Multi-omics integration
View on GitHubMirCure
A specialized tool for microRNA quality control, filtering, and curation in both animals and plants. Provides comprehensive analysis capabilities for miRNA research.
Language: R, Bioinformatics pipeline
View on GitHubDeCovid
A tool for conducting wide-spread transcriptional analysis for COVID-19 Disease Map genes. Provides information on gene expression differences between demographic groups using GTEx project data.
Features: Differential expression analysis, GO enrichment, Interactive web interface
View on GitHubParticipating Projects
SQANTI3
A comprehensive quality control and curation pipeline for long-read transcriptomes. SQANTI3 enables accurate identification of known and novel isoforms through extensive annotation and filtering capabilities.
Contribution: Report generation and documentation
View on GitHubSQANTI-SIM
A simulator of controlled transcript novelty for long-read RNA-seq benchmarking. Essential tool for evaluating and comparing different long-read analysis methods.
Contribution: Added PBSIM integration to the simulation framework
View on GitHubExperience
PhD Student & Early Stage Researcher
Institute for Integrative Systems Biology, Spanish National Research Council (CSIC-UV), Valencia, Spain
Conducting research on long-read multiomics methods under the LongTREC Marie Skłodowska-Curie Actions program. Supervised by Dr. Ana Conesa.
- Developing computational methods for isoform regulatory biology
- Contributing to major software projects like SQANTI3
- Collaborating with international research networks
Research Experience
University of Florida, Genetics Institute
Working with Dr. Ana Conesa and Dr. Guillem Ylla in MirCure project, focusing on microRNA quality control and curation methods.
Bachelor of Engineering in Bioengineering
Huazhong Agricultural University (HZAU)
Comprehensive education in bioengineering with focus on computational biology and bioinformatics applications.
Technical Skills
Programming Languages
Tools & Technologies
Data Analysis
Contact
Contact Information
Email: tianyuan.liu@csic.es
Location: Valencia, Spain
Institution: Spanish National Research Council (CSIC)