Research output per year
Research output per year
- 1 - 50 out of 212 results
Search results
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2024
Deep Learning Sequence Models for Transcriptional Regulation
Sokolova, K., Chen, K. M., Hao, Y., Zhou, J. & Troyanskaya, O. G., Aug 27 2024, In: Annual Review of Genomics and Human Genetics. 25, 1, p. 105-122 18 p.Research output: Contribution to journal › Review article › peer-review
2 Scopus citations -
Hiding in plain sight: a research parasite's perspective on new lessons in old data
Skinnider, M. A., 2024, In: GigaScience. 13, giae097.Research output: Contribution to journal › Review article › peer-review
Open Access -
Interrogating epigenetic mechanisms with chemically customized chromatin
Hananya, N., Koren, S. & Muir, T. W., Apr 2024, In: Nature Reviews Genetics. 25, 4, p. 255-271 17 p.Research output: Contribution to journal › Review article › peer-review
6 Scopus citations -
Liquid–liquid phase separation in innate immunity
Liu, D., Yang, J. & Cristea, I. M., Jun 2024, In: Trends in Immunology. 45, 6, p. 454-469 16 p.Research output: Contribution to journal › Review article › peer-review
6 Scopus citations -
Mapping protein–protein interactions by mass spectrometry
Liu, X., Abad, L., Chatterjee, L., Cristea, I. M. & Varjosalo, M., 2024, (Accepted/In press) In: Mass Spectrometry Reviews.Research output: Contribution to journal › Review article › peer-review
Open Access4 Scopus citations -
Outstanding Reviewers for Soft Matter in 2023
Baeza, G., Caprini, L., Castaneda-Priego, R., Conrad, J., Demirörs, A., Lintuvuori, J., Noguchi, H., Noya, E., Paoluzzi, M., Shendruk, T., Shibayama, M., Stone, H., Style, R., Thampi, S., Crosby, A. J. & Southall, M., Jul 2 2024, In: Soft matter. 20, 28, p. 5474 1 p.Research output: Contribution to journal › Review article › peer-review
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The 2023 Report on the Proteome from the HUPO Human Proteome Project
Omenn, G. S., Lane, L., Overall, C. M., Lindskog, C., Pineau, C., Packer, N. H., Cristea, I. M., Weintraub, S. T., Orchard, S., Roehrl, M. H. A., Nice, E., Guo, T., Van Eyk, J. E., Liu, S., Bandeira, N., Aebersold, R., Moritz, R. L. & Deutsch, E. W., Feb 2 2024, In: Journal of Proteome Research. 23, 2, p. 532-549 18 p.Research output: Contribution to journal › Review article › peer-review
7 Scopus citations -
2023
Accelerating the development of a sustainable bioenergy portfolio through stable isotopes
Blanc-Betes, E., Gomez-Casanovas, N., Yang, W. H., Chandrasoma, J., Clark, T. J., De Lucia, E. H., Hyde, C. A., Kent, A. D., Pett-Ridge, J., Rabinowitz, J., Raglin, S. S., Schwender, J., Shen, Y., Van Allen, R. & von Haden, A. C., Jul 2023, In: GCB Bioenergy. 15, 7, p. 840-866 27 p.Research output: Contribution to journal › Review article › peer-review
Open Access4 Scopus citations -
Banking on a new understanding: translational opportunities from veterinary biobanks
Dog Aging Project Consortium, Jun 2023, In: GeroScience. 45, 3, p. 1439-1450 12 p.Research output: Contribution to journal › Review article › peer-review
Open Access2 Scopus citations -
Metabolic pathway analysis using stable isotopes in patients with cancer
Bartman, C. R., Faubert, B., Rabinowitz, J. D. & DeBerardinis, R. J., Dec 2023, In: Nature Reviews Cancer. 23, 12, p. 863-878 16 p.Research output: Contribution to journal › Review article › peer-review
Open Access20 Scopus citations -
Orchestration of Mitochondrial Function and Remodeling by Post-Translational Modifications Provide Insight into Mechanisms of Viral Infection
Park, J. W., Tyl, M. D. & Cristea, I. M., May 2023, In: Biomolecules. 13, 5, 869.Research output: Contribution to journal › Review article › peer-review
Open Access1 Scopus citations -
Proliferating active matter
Hallatschek, O., Datta, S. S., Drescher, K., Dunkel, J., Elgeti, J., Waclaw, B. & Wingreen, N. S., Jul 2023, In: Nature Reviews Physics. 5, 7, p. 407-419 13 p.Research output: Contribution to journal › Review article › peer-review
Open Access28 Scopus citations -
Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
Dekker, J., Alber, F., Aufmkolk, S., Beliveau, B. J., Bruneau, B. G., Belmont, A. S., Bintu, L., Boettiger, A., Calandrelli, R., Disteche, C. M., Gilbert, D. M., Gregor, T., Hansen, A. S., Huang, B., Huangfu, D., Kalhor, R., Leslie, C. S., Li, W., Li, Y. & Ma, J. & 15 others, , Aug 3 2023, In: Molecular Cell. 83, 15, p. 2624-2640 17 p.Research output: Contribution to journal › Review article › peer-review
Open Access28 Scopus citations -
The 2022 Report on the Human Proteome from the HUPO Human Proteome Project
Omenn, G. S., Lane, L., Overall, C. M., Pineau, C., Packer, N. H., Cristea, I. M., Lindskog, C., Weintraub, S. T., Orchard, S., Roehrl, M. H. A., Nice, E., Liu, S., Bandeira, N., Chen, Y. J., Guo, T., Aebersold, R., Moritz, R. L. & Deutsch, E. W., Apr 7 2023, In: Journal of Proteome Research. 22, 4, p. 1024-1042 19 p.Research output: Contribution to journal › Review article › peer-review
Open Access37 Scopus citations -
The Logic of Transgenerational Inheritance: Timescales of Adaptation
Sengupta, T., Kaletsky, R. & Murphy, C. T., Oct 16 2023, In: Annual review of cell and developmental biology. 39, p. 45-65 21 p.Research output: Contribution to journal › Review article › peer-review
Open Access2 Scopus citations -
The pentose phosphate pathway in health and disease
TeSlaa, T., Ralser, M., Fan, J. & Rabinowitz, J. D., Aug 2023, In: Nature Metabolism. 5, 8, p. 1275-1289 15 p.Research output: Contribution to journal › Review article › peer-review
Open Access97 Scopus citations -
2022
An open science study of ageing in companion dogs
The Dog Aging Project Consortium, Feb 3 2022, In: Nature. 602, 7895, p. 51-57 7 p.Research output: Contribution to journal › Review article › peer-review
Open Access65 Scopus citations -
Bidirectional communication in oogenesis: a dynamic conversation in mice and Drosophila
Doherty, C. A., Amargant, F., Shvartsman, S. Y., Duncan, F. E. & Gavis, E. R., Apr 2022, In: Trends in Cell Biology. 32, 4, p. 311-323 13 p.Research output: Contribution to journal › Review article › peer-review
Open Access18 Scopus citations -
Eukaryotic gene regulation at equilibrium, or non?
Zoller, B., Gregor, T. & Tkačik, G., Sep 2022, In: Current Opinion in Systems Biology. 31, 100435.Research output: Contribution to journal › Review article › peer-review
Open Access8 Scopus citations -
Evidence gaps and diversity among potential win–win solutions for conservation and human infectious disease control
Hopkins, S. R., Lafferty, K. D., Wood, C. L., Olson, S. H., Buck, J. C., De Leo, G. A., Fiorella, K. J., Fornberg, J. L., Garchitorena, A., Jones, I. J., Kuris, A. M., Kwong, L. H., LeBoa, C., Leon, A. E., Lund, A. J., MacDonald, A. J., Metz, D. C. G., Nova, N., Peel, A. J. & Remais, J. V. & 8 others, , Aug 2022, In: The Lancet Planetary Health. 6, 8, p. e694-e705Research output: Contribution to journal › Review article › peer-review
Open Access16 Scopus citations -
Nuclear antiviral innate responses at the intersection of DNA sensing and DNA repair
Justice, J. L. & Cristea, I. M., Nov 2022, In: Trends in Microbiology. 30, 11, p. 1056-1071 16 p.Research output: Contribution to journal › Review article › peer-review
Open Access15 Scopus citations -
Oncohistones: Exposing the nuances and vulnerabilities of epigenetic regulation
Mitchener, M. M. & Muir, T. W., Aug 18 2022, In: Molecular Cell. 82, 16, p. 2925-2938 14 p.Research output: Contribution to journal › Review article › peer-review
Open Access25 Scopus citations -
Quantitative models for building and growing fated small cell networks
Diegmiller, R., Nunley, H., Shvartsman, S. Y. & Alsous, J. I., 2022, In: Interface Focus. 12, 4, 20210082.Research output: Contribution to journal › Review article › peer-review
Open Access7 Scopus citations -
Signal Transduction Network Principles Underlying Bacterial Collective Behaviors
Bridges, A. A., Prentice, J. A., Wingreen, N. S. & Bassler, B. L., Sep 8 2022, In: Annual Review of Microbiology. 76, p. 235-257 23 p.Research output: Contribution to journal › Review article › peer-review
Open Access22 Scopus citations -
Spatial patterns in ecological systems: from microbial colonies to landscapes
Martinez-Garcia, R., Tarnita, C. E. & Bonachela, J. A., Sep 2022, In: Emerging topics in life sciences. 6, 3, p. 245-258 14 p.Research output: Contribution to journal › Review article › peer-review
13 Scopus citations -
The contribution of Neanderthal introgression to modern human traits
Reilly, P. F., Tjahjadi, A., Miller, S. L., Akey, J. M. & Tucci, S., Sep 26 2022, In: Current Biology. 32, 18, p. R970-R983Research output: Contribution to journal › Review article › peer-review
Open Access24 Scopus citations -
The costs and benefits of primary prevention of zoonotic pandemics
Bernstein, A. S., Ando, A. W., Loch-Temzelides, T., Vale, M. M., Li, B. V., Li, H., Busch, J., Chapman, C. A., Kinnaird, M., Nowak, K., Castro, M. C., Zambrana-Torrelio, C., Ahumada, J. A., Xiao, L., Roehrdanz, P., Kaufman, L., Hannah, L., Daszak, P., Pimm, S. L. & Dobson, A. P., Feb 2022, In: Science Advances. 8, 5, eabl4183.Research output: Contribution to journal › Review article › peer-review
Open Access136 Scopus citations -
The mechanobiology of nuclear phase separation
Lee, D. S. W., Strom, A. R. & Brangwynne, C. P., Jun 1 2022, In: APL Bioengineering. 6, 2, 021503.Research output: Contribution to journal › Review article › peer-review
Open Access15 Scopus citations -
Virus–host protein interactions as footprints of human cytomegalovirus replication
Tyl, M. D., Betsinger, C. N. & Cristea, I. M., Feb 2022, In: Current Opinion in Virology. 52, p. 135-147 13 p.Research output: Contribution to journal › Review article › peer-review
Open Access12 Scopus citations -
2021
Chemical biology approaches to study histone interactors
Burton, A. J., Hamza, G. M., Zhang, A. X. & Muir, T. W., Nov 2021, In: Biochemical Society Transactions. 49, 5, p. 2431-2441 11 p.Research output: Contribution to journal › Review article › peer-review
Open Access3 Scopus citations -
Decoding disease: from genomes to networks to phenotypes
Wong, A. K., Sealfon, R. S. G., Theesfeld, C. L. & Troyanskaya, O. G., Dec 2021, In: Nature Reviews Genetics. 22, 12, p. 774-790 17 p.Research output: Contribution to journal › Review article › peer-review
Open Access55 Scopus citations -
Lamin post-translational modifications: emerging toggles of nuclear organization and function
Murray-Nerger, L. A. & Cristea, I. M., Oct 2021, In: Trends in Biochemical Sciences. 46, 10, p. 832-847 16 p.Research output: Contribution to journal › Review article › peer-review
Open Access20 Scopus citations -
Machine learning methods to model multicellular complexity and tissue specificity
Sealfon, R. S. G., Wong, A. K. & Troyanskaya, O. G., Aug 2021, In: Nature Reviews Materials. 6, 8, p. 717-729 13 p.Research output: Contribution to journal › Review article › peer-review
16 Scopus citations -
Metabolic channeling: predictions, deductions, and evidence
Pareek, V., Sha, Z., He, J., Wingreen, N. S. & Benkovic, S. J., Sep 16 2021, In: Molecular Cell. 81, 18, p. 3775-3785 11 p.Research output: Contribution to journal › Review article › peer-review
Open Access54 Scopus citations -
Molecular Epigenetics: Chemical Biology Tools Come of Age
Bagert, J. D. & Muir, T. W., Jun 20 2021, In: Annual review of biochemistry. 90, p. 287-320 34 p.Research output: Contribution to journal › Review article › peer-review
Open Access12 Scopus citations -
Monitoring mammalian mitochondrial translation with MitoRiboSeq
Li, S. H. J., Nofal, M., Parsons, L. R., Rabinowitz, J. D. & Gitai, Z., Jun 2021, In: Nature Protocols. 16, 6, p. 2802-2825 24 p.Research output: Contribution to journal › Review article › peer-review
Open Access15 Scopus citations -
Plasmodesmata and the problems with size: interpreting the confusion
Peters, W. S., Jensen, K. H., Stone, H. A. & Knoblauch, M., Feb 2021, In: Journal of Plant Physiology. 257, 153341.Research output: Contribution to journal › Review article › peer-review
Open Access29 Scopus citations -
Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project
Omenn, G. S., Lane, L., Overall, C. M., Paik, Y. K., Cristea, I. M., Corrales, F. J., Lindskog, C., Weintraub, S., Roehrl, M. H. A., Liu, S., Bandeira, N., Srivastava, S., Chen, Y. J., Aebersold, R., Moritz, R. L. & Deutsch, E. W., Dec 3 2021, In: Journal of Proteome Research. 20, 12, p. 5227-5240 14 p.Research output: Contribution to journal › Review article › peer-review
Open Access29 Scopus citations -
Quantitative flux analysis in mammals
Bartman, C. R., TeSlaa, T. & Rabinowitz, J. D., Jul 2021, In: Nature Metabolism. 3, 7, p. 896-908 13 p.Research output: Contribution to journal › Review article › peer-review
Open Access39 Scopus citations -
Reactive intermediates for interactome mapping
Seath, C. P., Trowbridge, A. D., Muir, T. W. & Macmillan, D. W. C., Mar 7 2021, In: Chemical Society Reviews. 50, 5, p. 2911-2926 16 p.Research output: Contribution to journal › Review article › peer-review
39 Scopus citations -
Roadmap on emerging concepts in the physical biology of bacterial biofilms: From surface sensing to community formation
Wong, G. C. L., Antani, J. D., Lele, P. P., Chen, J., Nan, B., Kühn, M. J., Persat, A., Bru, J. L., Hoyland-Kroghsbo, N. M., Siryaporn, A., Conrad, J. C., Carrara, F., Yawata, Y., Stocker, R., V Brun, Y., Whitfield, G. B., Lee, C. K., De Anda, J., Schmidt, W. C. & Golestanian, R. & 22 others, , Sep 2021, In: Physical Biology. 18, 5, 051501.Research output: Contribution to journal › Review article › peer-review
Open Access49 Scopus citations -
Subcellular proteomics
Christopher, J. A., Stadler, C., Martin, C. E., Morgenstern, M., Pan, Y., Betsinger, C. N., Rattray, D. G., Mahdessian, D., Gingras, A. C., Warscheid, B., Lehtiö, J., Cristea, I. M., Foster, L. J., Emili, A. & Lilley, K. S., Dec 2021, In: Nature Reviews Methods Primers. 1, 1, 32.Research output: Contribution to journal › Review article › peer-review
Open Access64 Scopus citations -
The Influence of Boundaries on Gravity Currents and Thin Films: Drainage, Confinement, Convergence, and Deformation Effects
Zheng, Z. & Stone, H. A., 2021, In: Annual Review of Fluid Mechanics. 54, p. 27-56 30 p.Research output: Contribution to journal › Review article › peer-review
21 Scopus citations -
The many bits of positional information
Tkačik, G. & Gregor, T., Jan 2021, In: Development (Cambridge). 148, 2, dev176065.Research output: Contribution to journal › Review article › peer-review
Open Access28 Scopus citations -
The nucleolus as a multiphase liquid condensate
Lafontaine, D. L. J., Riback, J. A., Bascetin, R. & Brangwynne, C. P., Mar 2021, In: Nature Reviews Molecular Cell Biology. 22, 3, p. 165-182 18 p.Research output: Contribution to journal › Review article › peer-review
512 Scopus citations -
Towards an ecosystem model of infectious disease
Hassell, J. M., Newbold, T., Dobson, A. P., Linton, Y. M., Franklinos, L. H. V., Zimmerman, D. & Pagenkopp Lohan, K. M., Jul 2021, In: Nature Ecology and Evolution. 5, 7, p. 907-918 12 p.Research output: Contribution to journal › Review article › peer-review
Open Access30 Scopus citations -
2020
A high-stringency blueprint of the human proteome
Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y. K., Overall, C. M., Corrales, F. J., Cristea, I. M., Van Eyk, J. E., Uhlén, M., Lindskog, C., Chan, D. W., Bairoch, A., Waddington, J. C., Justice, J. L., LaBaer, J., Rodriguez, H. & He, F. & 26 others, , Dec 1 2020, In: Nature communications. 11, 1, 5301.Research output: Contribution to journal › Review article › peer-review
Open Access158 Scopus citations -
Can phase separation buffer cellular noise?
Riback, J. A. & Brangwynne, C. P., Jan 24 2020, In: Science. 367, 6476, p. 364-365 2 p.Research output: Contribution to journal › Review article › peer-review
26 Scopus citations -
Chemical Embryology Redux: Metabolic Control of Development
Song, Y. & Shvartsman, S. Y., Aug 2020, In: Trends in Genetics. 36, 8, p. 577-586 10 p.Research output: Contribution to journal › Review article › peer-review
Open Access11 Scopus citations -
Chemoenzymatic Semisynthesis of Proteins
Thompson, R. E. & Muir, T. W., Mar 25 2020, In: Chemical Reviews. 120, 6, p. 3051-3126 76 p.Research output: Contribution to journal › Review article › peer-review
Open Access156 Scopus citations