Publications

Preview image for High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples

Research article

2026

High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples

Yao, L., Shah, S. R., Ozer, A., Zhang, J., Pan, X., Xia, T., Leung, A. K., Wei, M., Lis, J. T., & Yu, H. Nature Biotechnology

Single-cell sequencing methods such as scRNA-seq and scATAC-seq have advanced our understanding of individual cellular functions but experimentally adapting genome-wide assays measuring other genomic features to achieve single-cell resolution remains a technical challenge. Here we introduce Deep-learning-based DEconvolution of Tissue profiles with Accurate Interpretation …

DeepDETAILS

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Preview image for A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers

Research article

2022

A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers

Yao, L., Liang, J., Ozer, A., Leung, A. K.-Y., Lis, J. T.*, & Yu, H.* Nature Biotechnology

Mounting evidence supports the idea that transcriptional patterns serve as more specific identifiers of active enhancers than histone marks; however, the optimal strategy to identify active enhancers both experimentally and computationally has not been determined. Here, we compared 13 genome-wide RNA-seq assays in K562 …

PINTS

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Preview image for Large-scale prediction of ADAR-mediated effective human A-to-I RNA editing

Research article

2019

Large-scale prediction of ADAR-mediated effective human A-to-I RNA editing

Yao, L.=, Wang, H.=, Song, Y.=, Dai, Z., Yu, H., Yin, M., Wang, D., Yang, X., Wang, J., Wang, T., Cao, N., Zhu, J., Shen, X., Song, G., & Zhao, Y. Briefings in Bioinformatics

Adenosine-to-inosine (A-to-I) editing by adenosine deaminase acting on the RNA (ADAR) proteins is one of the most frequent modifications during post- and co-transcription. To facilitate the assignment of biological functions to specific editing sites, we designed an automatic online platform to annotate A-to-I RNA …

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Preview image for BioQueue: a novel pipeline framework to accelerate bioinformatics analysis

Research article

2017

BioQueue: a novel pipeline framework to accelerate bioinformatics analysis

Yao, L.*, Wang, H., Song, Y., & Sui, G.* Bioinformatics

MOTIVATION: With the rapid development of Next-Generation Sequencing, a large amount of data is now available for bioinformatics research. Meanwhile, the presence of many pipeline frameworks makes it possible to analyse these data. However, these tools concentrate mainly on their syntax and design paradigms, …

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Preview image for Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants

Research article

2023

Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants

Chen, Y.=, Paramo, M. I.=, Zhang, Y.=, Yao, L.=, Shah, S. R., Jin, Y., Zhang, J., Pan, X., & Yu, H. Annual Review of Genetics

Despite accumulating evidence implicating noncoding variants in human diseases, unraveling their functionality remains a significant challenge. Systematic annotations of the regulatory landscape and the growth of sequence variant data sets have fueled the development of tools and methods to identify causal noncoding variants and …

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Preview image for Functional genomic assays to annotate enhancer-promoter interactions genome wide

Research article

2022

Functional genomic assays to annotate enhancer-promoter interactions genome wide

Leung, A. K.-Y.=, Yao, L.=, & Yu, H. Human Molecular Genetics

Enhancers are pivotal for regulating gene transcription that occurs at promoters. Identification of the interacting enhancer-promoter pairs and understanding the mechanisms behind how they interact and how enhancers modulate transcription can provide fundamental insight into gene regulatory networks. Recently, advances in high-throughput methods in …

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Preview image for Dual promoter–enhancer activities reflect a unified regulatory logic

Research article

2026

Dual promoter–enhancer activities reflect a unified regulatory logic

Paramo, M. I., Leung, A. K., Shah, S. R., Zhang, J., Tippens, N. D., Liang, J., Yao, L., Jin, Y., Pan, X., Ozer, A., Lis, J. T., & Yu, H. Nature Communications

Growing evidence indicates that transcriptional regulatory elements can exert both promoter and enhancer activity; however, the relationship and determinants of this dual functionality remain poorly understood. We developed a massively parallel dual reporter assay that enables simultaneous assessment of the intrinsic promoter and enhancer …

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Preview image for Comprehensive Evaluation of Diverse Massively Parallel Reporter Assays to Functionally Characterize Human Enhancers Genome-wide

Research article

2025

Comprehensive Evaluation of Diverse Massively Parallel Reporter Assays to Functionally Characterize Human Enhancers Genome-wide

Zhang, J., Leung, A. K., Zhu, Y., Yao, L., Willis, A., Pan, X., Ozer, A., Zhou, Z., Siklenka, K., Barrera, A., Liang, J., Tippens, N. D., Reddy, T. E., Lis, J. T., & Yu, H. Genome Biology

Massively parallel reporter assays (MPRAs) and self-transcribing active regulatory region sequencing (STARR-seq) have revolutionized enhancer characterization by enabling high-throughput functional assessment of regulatory sequences. Here, we systematically evaluated six MPRA and STARR-seq datasets generated in the human K562 cell line and found substantial inconsistencies …

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Preview image for Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A–menin to bivalent promoters

Research article

2025

Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A–menin to bivalent promoters

Wang, N., Pachai, M. R., Li, D., Lee, C. J., Warda, S., Khudoynazarova, M. N., Cho, W. H., Xie, G., Shah, S. R., Yao, L., Qian, C., Wong, E. W. P., Yan, J., Tomas, F. V., Hu, W., Kuo, F., Gao, S. P., Luo, J., Smith, A. E., … & Chen, Y. Nature Genetics

Members of the KMT2C/D–KDM6A complex are recurrently mutated in urothelial carcinoma and in histologically normal urothelium. Here, using genetically engineered mouse models, we demonstrate that Kmt2c/d knockout in the urothelium led to impaired differentiation, augmented responses to growth and inflammatory stimuli and sensitization to …

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Preview image for Capped nascent RNA sequencing reveals novel therapy-responsive enhancers in prostate cancer

Preprint

2022

Capped nascent RNA sequencing reveals novel therapy-responsive enhancers in prostate cancer

Cotter, K. A., Shah, S. R., Paramo, M. I., Lou, S., Yao, L., Rubin, P. D., Chen, Y., Gerstein, M., Rubin, M. A., & Yu, H. bioRxiv

AbstractMounting evidence suggests that enhancer RNA (eRNA) transcription start sites (TSSs) provide higher sensitivity and specificity for enhancer identification than histone modifications and chromatin accessibility. The extent to which changes in eRNA transcription correspond to changes in enhancer activity, however, remains unclear. Here, we …

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Preview image for Survey of the binding preferences of RNA-binding proteins to RNA editing events

Research article

2022

Survey of the binding preferences of RNA-binding proteins to RNA editing events

Hu, X., Zou, Q., Yao, L., & Yang, X. Genome Biology

BACKGROUND: Adenosine-to-inosine (A-to-I) editing is an important RNA posttranscriptional process related to a multitude of cellular and molecular activities. However, systematic characterizations of whether and how the events of RNA editing are associated with the binding preferences of RNA sequences to RNA-binding proteins (RBPs) …

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Preview image for Inhibition of DCLK1 down-regulates PD-L1 expression through Hippo pathway in human pancreatic cancer

Research article

2019

Inhibition of DCLK1 down-regulates PD-L1 expression through Hippo pathway in human pancreatic cancer

Yan, R., Li, J., Zhou, Y., Yao, L., Sun, R., Xu, Y., Ge, Y., & An, G. Life Sciences

Immunotherapy is one of the most promising strategies for cancer, compared with traditional treatments. As one of the key emerging immunotherapies, anti-PD-1/PD-L1 treatment has brought survival benefits to many advanced cancer patients. However, in pancreatic cancer, immunotherapy-based approaches have not achieved a favorable clinical …

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Preview image for Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

Research article

2019

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

Fragoza, R., Das, J., Wierbowski, S. D., Liang, J., Tran, T. N., Liang, S., Beltran, J. F., Rivera-Erick, C. A., Ye, K., Wang, T.-Y., Yao, L., Mort, M., Stenson, P. D., Cooper, D. N., Wei, X., Keinan, A., Schimenti, J. C., Clark, A. G., & Yu, H. Nature Communications

Each human genome carries tens of thousands of coding variants. The extent to which this variation is functional and the mechanisms by which they exert their influence remains largely unexplored. To address this gap, we leverage the ExAC database of 60,706 human exomes to …

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Preview image for bioSyntax: syntax highlighting for computational biology

Research article

2018

bioSyntax: syntax highlighting for computational biology

Babaian, A., Ebou, A., Fegen, A., Kam, H. Y., Novakovsky, G. E., Wong, J., Aïssi D., & Yao, L. BMC Bioinformatics

BACKGROUND: Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information which is obfuscated by the data structure complexity. RESULTS: bioSyntax ( https://biosyntax.org/ ) is a freely available suite …

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Preview image for Circulating microRNAs: Promising Biomarkers Involved in Several Cancers and Other Diseases

Research article

2016

Circulating microRNAs: Promising Biomarkers Involved in Several Cancers and Other Diseases

Zhao, Y.=, Song, Y.=, Yao, L., Song, G., & Teng, C. DNA and Cell Biology

Recently, many studies indicated that microRNAs (miRNAs) stably existed in various body fluids, including serum, plasma, saliva, and urine. Such miRNAs that exist in mammalian body fluids are known as circulating miRNAs, and they can transmit signals between cells and regulate intracellular gene expression. …

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