Shen, Yufeng

The complete genome of an individual by massively parallel DNA sequencing

Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y.-J., Makhijani, V., Roth, G. T., et al. (2008) · Nature

Genomics and Phylogenetic StudiesGenomics and Rare Diseases

Cited by 1,838

The support of human genetic evidence for approved drug indications

Nelson, M. R., Tipney, H., Painter, J. L., Shen, J., Nicoletti, P., Shen, Y., Floratos, A., Sham, P. C., Li, M. J., Wang, J., et al. (2015) · Nature Genetics

Genetic Associations and EpidemiologyComputational Drug Discovery Methods

Cited by 1,666

Evolutionary and biomedical insights from the rhesus macaque genome.

Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., et al. (2007) · Science

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 1,403

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

The Bovine Genome Sequencing and Analysis Consortium, Elsik, C. G., Tellam, R. L., Worley, K. C., Gibbs, R. A., Muzny, D. M., Weinstock, G. M., Adelson, D. L., Eichler, E. E., Elnitski, L., et al. (2009) · Science

Genetic and phenotypic traits in livestockGenomics and Phylogenetic Studies

Cited by 1,287

The Genome of the Sea Urchin Strongylocentrotus purpuratus

Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., et al. (2006) · Science

Genomics and Phylogenetic StudiesDevelopmental Biology and Gene Regulation

Cited by 1,132

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

Kumar, B. V., Ma, W., Miron, M., Granot, T., Guyer, R. S., Carpenter, D. J., Senda, T., Sun, X., Ho, S.-H., Lerner, H., et al. (2017) · Cell Reports

T-cell and B-cell ImmunologyPsoriasis: Treatment and Pathogenesis

Cited by 1,068

Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands

Jin, S. C., Homsy, J., Zaidi, S., Lu, Q., Morton, S., DePalma, S. R., Zeng, X., Qi, H., Chang, W., Sierant, M. C., et al. (2017) · Nature Genetics

Congenital heart defects researchGenomics and Rare Diseases

Cited by 875

Spatial map of human T cell compartmentalization and maintenance over decades of life

Thome, J. J. C., Yudanin, N., Ohmura, Y., Kubota, M., Grinshpun, B., Sathaliyawala, T., Kato, T., Lerner, H., Shen, Y., & Farber, D. L. (2014) · Cell

T-cell and B-cell ImmunologyPsoriasis: Treatment and Pathogenesis

Cited by 587

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

Zhu, Y., Piehowski, P. D., Zhao, R., Chen, J., Shen, Y., Moore, R. J., Shukla, A. K., Petyuk, V. A., Campbell-Thompson, M., Mathews, C. E., et al. (2018) · Nature Communications

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 587

Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes

Zhou, X., Feliciano, P., Shu, C., Wang, T., Astrovskaya, I., Hall, J. B., Obiajulu, J. U., Wright, J. R., Murali, S. C., Xu, S. X., et al. (2022) · Nature Genetics

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 453

Increased Frequency of De Novo Copy Number Variants in Congenital Heart Disease by Integrative Analysis of Single Nucleotide Polymorphism Array and Exome Sequence Data

Glessner, J. T., Bick, A. G., Ito, K., Homsy, J. G., Rodriguez-Murillo, L., Fromer, M., Mazaika, E., Vardarajan, B., Italia, M., Leipzig, J., et al. (2014) · Circulation Research

Genomic variations and chromosomal abnormalitiesCongenital heart defects research

Cited by 268

Coding mutations in SORL1 and Alzheimer disease

Vardarajan, B. N., Zhang, Y., Lee, J. H., Cheng, R., Bohm, C., Ghani, M., Reitz, C., Reyes‐Dumeyer, D., Shen, Y., Rogaeva, E., et al. (2015) · Annals of Neurology

Alzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

Cited by 191

Long-term maintenance of human naive T cells through in situ homeostasis in lymphoid tissue sites

Thome, J. J. C., Grinshpun, B., Kumar, B. V., Kubota, M., Ohmura, Y., Lerner, H., Sempowski, G. D., Shen, Y., & Farber, D. L. (2016) · Science Immunology

T-cell and B-cell ImmunologyHematopoietic Stem Cell Transplantation

Cited by 162

Protein Identification Using Top-Down Spectra

Liu, X., Sirotkin, Y., Shen, Y., Anderson, G., Tsai, Y. S., Ting, Y. S., Goodlett, D. R., Smith, R. D., Bafna, V., & Pevzner, P. A. (2012) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 153

Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets

Zhu, Y., Dou, M., Piehowski, P. D., Liang, Y., Wang, F., Chu, R. K., Chrisler, W. B., Smith, J. N., Schwarz, K. C., Shen, Y., et al. (2018) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 147

Predicting functional effect of missense variants using graph attention neural networks

Zhang, H., Xu, M. S., Fan, X., Chung, W. K., & Shen, Y. (2022) · Nature Machine Intelligence

Genomics and Rare DiseasesMachine Learning in Bioinformatics

Cited by 98

Role of common and rare APP DNA sequence variants in Alzheimer disease

Hooli, B. V., Mohapatra, G., Mattheisen, M., Parrado, A. R., Roehr, J. T., Shen, Y., Gusella, J. F., Moir, R., Saunders, A. J., Lange, C., et al. (2012) · Neurology

Alzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

Cited by 87

High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics

Shen, Y., Tolić, N., Piehowski, P. D., Shukla, A. K., Kim, S., Zhao, R., Qu, Y., Robinson, E., Smith, R. D., & Paša-Tolić, L. (2017) · Journal of Chromatography A

Advanced Proteomics Techniques and ApplicationsAnalytical Chemistry and Chromatography

Cited by 63

Association of Damaging Variants in Genes With Increased Cancer Risk Among Patients With Congenital Heart Disease

Morton, S. U., Shimamura, A., Newburger, P. E., Opotowsky, A. R., Quiat, D., Pereira, A. C., Jin, S. C., Gurvitz, M., Brueckner, M., Chung, W. K., et al. (2021) · JAMA Cardiology

Congenital Heart Disease StudiesGenomics and Rare Diseases

Cited by 62

A homozygous splice variant in ATP5PO , disrupts mitochondrial complex V function and causes Leigh syndrome in two unrelated families

Ganapathi, M., Friocourt, G., Gueguen, N., Friederich, M. W., Le Gac, G., Okur, V., Loaëc, N., Ludwig, T., Ka, C., Tanji, K., et al. (2022) · Journal of Inherited Metabolic Disease

Mitochondrial Function and PathologyMetabolism and Genetic Disorders

Cited by 18

PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context

Zhong, G., Zhao, Y., Zhuang, D., Chung, W. K., & Shen, Y. (2025) · Nature Communications

Genomics and Rare DiseasesMachine Learning in Bioinformatics

Cited by 15

PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context

Zhong, G., Zhao, Y., Zhuang, D., Chung, W. K., & Shen, Y. (2024) · Nature Communications

Genomics and Rare DiseasesMachine Learning in Bioinformatics

Cited by 15

SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants

Fan, X., Pan, H., Tian, A., Chung, W. K., & Shen, Y. (2023) · Briefings in Bioinformatics

Genomics and Rare DiseasesMachine Learning in Bioinformatics

Cited by 11