Xie, Xiaohui

A bivalent chromatin structure marks key developmental genes in embryonic stem cells

Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 5,361

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 4,129

Genome sequence, comparative analysis and haplotype structure of the domestic dog

members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature

Human-Animal Interaction StudiesGenetic and phenotypic traits in livestock

Cited by 2,568

Genome-wide detection and characterization of positive selection in human populations

The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., et al. (2007) · Nature

Forensic and Genetic ResearchGenetic Associations and Epidemiology

Cited by 2,131

Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., & Kellis, M. (2005) · Nature

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 1,872

A high-resolution map of human evolutionary constraint using 29 mammals

Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 1,108

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Broad Institute Genome Sequencing Platform, Mikkelsen, T. S., Broad Institute Whole Genome Assembly Team, Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., Garber, M., Gentles, A. J., et al. (2007) · Nature

Chromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Cited by 711

ERRα and Gabpa/b specify PGC-1α-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle.

Mootha, V. K., Handschin, C., Arlow, D., Xie, X., St. Pierre, J., Sihag, S., Yang, W., Altshuler, D., Puigserver, P., Patterson, N., et al. (2004) · Proceedings of the National Academy of Sciences

Adipose Tissue and MetabolismPeroxisome Proliferator-Activated Receptors

Cited by 688

Distinguishing protein-coding and noncoding genes in the human genome

Clamp, M., Fry, B., Kamal, M., Xie, X., Cuff, J., Lin, M. F., Kellis, M., Lindblad-Toh, K., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 624

Identifying novel constrained elements by exploiting biased substitution patterns

Garber, M., Guttman, M., Clamp, M., Zody, M. C., Friedman, N., & Xie, X. (2009) · Bioinformatics

Genomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

Cited by 370

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

Xie, X., Mikkelsen, T. S., Gnirke, A., Lindblad-Toh, K., Kellis, M., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 305

Comparative sequence analysis reveals an intricate network among REST, CREBand miRNA in mediating neuronal gene expression

Wu, J., & Xie, X. (2006) · Genome Biology

Neurogenesis and neuroplasticity mechanismsMicroRNA in disease regulation

Cited by 260

FactorNet: A deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data

Quang, D., & Xie, X. (2019) · Methods

Genomics and Chromatin DynamicsMachine Learning in Bioinformatics

Cited by 204

Double-ring network model of the head-direction system

Xie, X., Hahnloser, R. H. R., & Seung, H. S. (2002) · Physical Review E

Memory and Neural MechanismsVestibular and auditory disorders

Cited by 124

A family of conserved noncoding elements derived from an ancient transposable element

Xie, X., Kamal, M., & Lander, E. S. (2006) · Proceedings of the National Academy of Sciences

Chromosomal and Genetic VariationsGenomics and Chromatin Dynamics

Cited by 66

Efficient inference, training, and fine-tuning of protein language models

Çelik, M. H., & Xie, X. (2025) · iScience

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 7

Efficient Inference, Training, and Fine-tuning of Protein Language Models

Çelik, M. H., & Xie, X. (2024) · iScience

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 7