Gerstein, Mark

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2019) · Nature Communications

Genomic variations and chromosomal abnormalitiesGenomics and Phylogenetic Studies

Cited by 891

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

Li, M., Santpere, G., Imamura Kawasawa, Y., Evgrafov, O. V., Gulden, F. O., Pochareddy, S., Sunkin, S. M., Li, Z., Shin, Y., Zhu, Y., et al. (2018) · Science

Genetics and Neurodevelopmental DisordersGenomics and Chromatin Dynamics

Cited by 810

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science

Genomic variations and chromosomal abnormalitiesGenomics and Phylogenetic Studies

Cited by 702

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation

Polioudakis, D., de la Torre-Ubieta, L., Langerman, J., Elkins, A. G., Shi, X., Stein, J. L., Vuong, C. K., Nichterwitz, S., Gevorgian, M., Opland, C. K., et al. (2019) · Neuron

Single-cell and spatial transcriptomicsNeurogenesis and neuroplasticity mechanisms

Cited by 513

Diverse Cellular Functions of the Hsp90 Molecular Chaperone Uncovered Using Systems Approaches

McClellan, A. J., Xia, Y., Deutschbauer, A. M., Davis, R. W., Gerstein, M., & Frydman, J. (2007) · Cell

Heat shock proteins researchFungal and yeast genetics research

Cited by 474

Annotating non-coding regions of the genome.

Alexander, R. P., Fang, G., Rozowsky, J., Snyder, M., & Gerstein, M. B. (2010) · Nature Reviews Genetics

Genomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

Cited by 464

What is Bioinformatics? A Proposed Definition and Overview of the Field

Luscombe, N. M., Greenbaum, D., & Gerstein, M. (2001) · Methods of Information in Medicine

Genetics, Bioinformatics, and Biomedical ResearchGenomics and Phylogenetic Studies

Cited by 453

The PsychENCODE project

Akbarian, S., Liu, C., Knowles, J. A., Vaccarino, F. M., Farnham, P. J., Crawford, G. E., Jaffe, A. E., Pinto, D., Dracheva, S., Geschwind, D. H., et al. (2015) · Nature Neuroscience

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 451

The genetic architecture of down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies

Korbel, J. O., Tirosh-Wagner, T., Urban, A. E., Chen, X.-N., Kasowski, M., Dai, L., Grubert, F., Erdman, C., Gao, M. C., Lange, K., et al. (2009) · Proceedings of the National Academy of Sciences

Down syndrome and intellectual disability researchGenomic variations and chromosomal abnormalities

Cited by 399

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

Sahraeian, S. M. E., Mohiyuddin, M., Sebra, R., Tilgner, H., Afshar, P. T., Au, K. F., Bani Asadi, N., Gerstein, M. B., Wong, W. H., Snyder, M. P., et al. (2017) · Nature Communications

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 376

MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning

Tang, X., Zou, A., Zhang, Z., Li, Z., Zhao, Y., Zhang, X., Cohan, A., & Gerstein, M. (2024) · Findings of the Association for Computational Linguistics ACL 2024

Artificial Intelligence in Healthcare and EducationMultimodal Machine Learning Applications

Cited by 376

AlleleSeq: analysis of allele-specific expression and binding in a network framework.

Rozowsky, J., Abyzov, A., Wang, J., Alves, P., Raha, D., Harmanci, A., Leng, J., Bjornson, R., Kong, Y., Kitabayashi, N., et al. (2011) · Molecular Systems Biology

Genomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

Cited by 316

Bridging structural biology and genomics: assessing protein interaction data with known complexes

Edwards, A. M., Kus, B., Jansen, R., Greenbaum, D., Greenblatt, J., & Gerstein, M. (2002) · Trends in Genetics

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

Cited by 276

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

Lilue, J., Doran, A. G., Fiddes, I. T., Abrudan, M., Armstrong, J., Bennett, R., Chow, W., Collins, J., Collins, S., Czechanski, A., et al. (2018) · Nature Genetics

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 267

Molecular and cellular reorganization of neural circuits in the human lineage

Sousa, A. M. M., Zhu, Y., Raghanti, M. A., Kitchen, R. R., Onorati, M., Tebbenkamp, A. T. N., Stutz, B., Meyer, K. A., Li, M., Kawasawa, Y. I., et al. (2017) · Science

Single-cell and spatial transcriptomicsNeurogenesis and neuroplasticity mechanisms

Cited by 253

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

Li, X., Gianoulis, T. A., Yip, K. Y., Gerstein, M., & Snyder, M. (2010) · Cell

Fungal and yeast genetics researchAdvanced Proteomics Techniques and Applications

Cited by 237

Diverse human extracellular RNAs are widely detected in human plasma

Freedman, J. E., Gerstein, M., Mick, E., Rozowsky, J., Levy, D., Kitchen, R., Das, S., Shah, R., Danielson, K., Beaulieu, L., et al. (2016) · Nature Communications

MicroRNA in disease regulationExtracellular vesicles in disease

Cited by 202

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

Wu, J. Q., Habegger, L., Noisa, P., Szekely, A., Qiu, C., Hutchison, S., Raha, D., Egholm, M., Lin, H., Weissman, S., et al. (2010) · Proceedings of the National Academy of Sciences

Pluripotent Stem Cells ResearchSingle-cell and spatial transcriptomics

Cited by 189

An integrative ENCODE resource for cancer genomics

Zhang, J., Lee, D., Dhiman, V., Jiang, P., Xu, J., McGillivray, P., Yang, H., Liu, J., Meyerson, W., Clarke, D., et al. (2020) · Nature Communications

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 172

Quantum computing at the frontiers of biological sciences

Emani, P. S., Warrell, J., Anticevic, A., Bekiranov, S., Gandal, M., McConnell, M. J., Sapiro, G., Aspuru-Guzik, A., Baker, J. T., Bastiani, M., et al. (2021) · Nature Methods

Quantum Computing Algorithms and ArchitectureDNA and Biological Computing

Cited by 163

A multiregional proteomic survey of the postnatal human brain

Carlyle, B. C., Kitchen, R. R., Kanyo, J. E., Voss, E. Z., Pletikos, M., Sousa, A. M. M., Lam, T. T., Gerstein, M. B., Sestan, N., & Nairn, A. C. (2017) · Nature Neuroscience

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 143

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

Zhao, X., Collins, R. L., Lee, W.-P., Weber, A. M., Jun, Y., Zhu, Q., Weisburd, B., Huang, Y., Audano, P. A., Wang, H., et al. (2021) · The American Journal of Human Genetics

Genomic variations and chromosomal abnormalitiesGenomics and Rare Diseases

Cited by 132

Robotic cloning and protein production platform of the northeast structural genomics consortium

Acton, T. B., Gunsalus, K. C., Xiao, R., Ma, L. C., Aramini, J., Baran, M. C., Chiang, Y.-W., Climent, T., Cooper, B., Denissova, N. G., et al. (2005) · Methods in Enzymology

Enzyme Structure and FunctionProtein purification and stability

Cited by 129

The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?

Zheng, D., & Gerstein, M. B. (2007) · Trends in Genetics

Chromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Cited by 113