Anthony Cesnik

Proteoform Systems Biology

Overview

  • Total peer-reviewed publications: 25
  • Total preprints: 1
  • Total citations: 1148
  • h-index: 17
  • Updated publication list and metrics
  • Published in Nature (lead author) and Science (coauthor)

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Lead Author Publications

(1) Cesnik, A.*; Schaffer, L. V.*; Gaur, I.; Jain, M.; Ideker, T.; Lundberg, E. “Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes.” Annual Review of Biomedical Data Science 2024 27, 369­389. *Contributed equally

(2) Mahdessian, D.*; Cesnik, A. J.*; Gnann, C.; Danielsson, F.; Stenström, L.; Arif, M.; Zhang, C.; Le, T.; Johansson, F.; Shutten, R.; Bäckström, A.; Axelsson, U.; Thul, P.; Cho, N. H.; Carja, O.; Uhlén, M.; Mardinoglu, A.; Stadler, C.; Lindskog, C.; Ayoglu, B.; Leonetti, M. D.; Pontén, F.; Sullivan, D. P.; Lundberg, E. “Spatiotemporal dissection of the cell cycle with single­cell proteogenomics.” Nature 2021, 590, 649–654. *Contributed equally

(3) Gnann, C.*; Cesnik, A. J.*; Lundberg, E. “Illuminating non­genetic cellular heterogeneity with spatial proteomics.” Trends in Cancer 2021, 7, 4, 278–282. *Contributed equally

(4) Cesnik, A. J.; Miller, R. M.; Ibrahim, K.; Lu, L.; Shortreed, M. R.; Frey, B. L.; Smith, L. M. “Spritz: A Proteogenomic Database Engine.” Journal of Proteome Research 2021, 20, 4, 1826–1834.

(5) Cesnik, A. J.; Yang, B.; Truong, A.; Spiniello, M.; Steinbrink, M.; Shortreed, M. R.; Frey, B. L.; Jarrard, D. F.; Smith, L. M. “Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers.” Translational Oncology 2018, 11, 3, 808–814.

(6) LeDuc, R.*; Schwämmle, V.*; Shortreed, M. R.*; Cesnik, A. J.*; Solntsev, S. K.*; Shaw, J.*; Martin, M. J.; Vizcaíno, J. A.; Alpi, E.; Danis, P.; Kelleher, N. L.; Smith, L. M.; Ge, Y.; Agar, J. N.; Chamot­Rooke, J.; Loo, J.; Paša­Tolić, L.; Tsybin, Y. O. “ProForma: a Standard Proteoform Notation.” Journal of Proteome Research, 2018, 17, 3, 1321–1325. *Contributed equally

(7) Cesnik, A. J.; Shortreed, M. R.; Schaffer, L. V.; Knoener, R. A.; Frey, B. L.; Scalf, M.; Solntsev, S. K.; Dai, Y. Gasch, A. P.; Smith, L. M. “Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.” Journal of Proteome Research 2018, 17, 1, 568–578.

(8) Cesnik, A. J.; Shortreed, M. R.; Sheynkman, G. M.; Frey, B. L.; Smith, L. M. “Human Proteomic Variation Revealed by Combining RNA­Seq Proteogenomics and Global Post­Translational Modification (G­PTM) Search Strategy.” Journal of Proteome Research 2016, 15, 3, 800–808. **American Chemical Society Editor’s Choice

Contributing Author Publications

(9) Gnann, C.; Cesnik, A.; Sigaeva, A.; Le, T.; Sariyar, S.; Mahdessian, D.; Schutten, R.; Raghavan, P.; Leonetti, M. D.; Lindskog, C.; Uhlén, M.; Axelsson, U.; Lundberg, E. “Dissecting autonomous enzyme variability in single cells” bioRxiv 2024, 2024.10.03.616530.

(10) Mah,C.K.*; Ahmed,N.*; Lopez,N.A.; Lam,D.C.; Pong,A.; Monell,A.; Kern,C.; Han,Y.; Prasad,G.; Cesnik,A.J.; Lundberg, E.; Zhu, Q.; Carter, H.; Yeo, G. W. “Bento: a toolkit for subcellular analysis of spatial transcriptomics data” Genome Biology 2024, 25, 82, 1–25.

(11) LeDuc, R. D.; Deutsch, E. W.; Binz, P. A.; Fellers, R. T.; Cesnik, A. J.; Klein, J. A.; Van Den Bossche, T.; Gabriels, R.; Yalavarthi, A.; Perez-­Riverol, Y.; Carver, J.; Bittremieux, W.; Kawano, S.; Pullman, B.; Bandeira, N.; Kelleher, N. L.; Thomas, P. M.; Vizcaíno, J. A. “Proteomics Standards Initiative’s ProForma 2.0: Unifying the encoding of Proteoforms and Peptidoforms.” Journal of Proteome Research 2022, in press.

(12) Melani, R. D.*; Gerbasi, V. R.*; Anderson, L. C.*; Sikora, J. W.; Toby, T. K.; Hutton, J. E.; Butcher, D. S.; Negrão, F.; Seckler, H. S.; Srzentić, K.; Fornelli, L; Camarillo, J. M.; LeDuc, R. D.; Cesnik, A. J.; Lundberg, E., Greer, J. B.; Fellers, R. T.; Robey, M. T.; DeHart, C. J.; Forte, E.; Hendrickson, C. L.; Abbatiello, S. E.; Thomas, P. M.; Kokaji, A. I.; Levitsky, J.; Kelleher, N. L. “The Blood Proteoform Atlas: A compositional map of proteoforms in human haematopoietic cells.” Science 2022, 375, 6579, 411–418. *Contributed equally

(13) Carr, A. V.; Frey, B. L.; Scalf, M.; Cesnik, A. J.; Rolfs, Z.; Pike, K. A.; Yang, B.; Jarrard, D. F.; Shortreed, M. R.; Smith, L. M. “MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses.” Journal of Proteome Research 2022, 21, 2, 410–419.

(14) Stenström, L.; Mahdessian, D.; Gnann, C.; Cesnik, A. J.; Ouyang, W.; Leonetti, M. D.; Uhlén, M.; Cuylen­Haering, C.; Thul, P. J.; Lundberg, E. “Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder.” Molecular Systems Biology 2020, 16, e9469.

(15) Tan, Z.; Zhu, J.; Stemmer, P. M.; Sun, L.; Yang, Z.; Schultz, K.; Gaffrey, M. J.; Cesnik, A. J.; Yi, X.; Hao, X.; Shortreed, M. R.; Shi, T.; Lubman, D. M. “Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC­1 Cell Line.” Journal of Proteome Research, 2020, 19, 4, 1635–1646.

(16) Ouyang, W.; Winsnes, C. F.; Hjelmare, M.; Cesnik, A. J.; Åkesson, L.; Xu, H.; Sullivan, D. P.; Dai, S.; Lan, J.; Jinmo, P.; Galib, S. M.; Henkel, C.; Hwang, K.; Poplavskiy, D.; Tunguz, B.; Wolfinger, R. D.; Gu, Y.; Li, C.; Xie, J.; Buslov, D.; Fironov, S.; Kiselev, A.; Panchenko, D.; Cao, X.; Wei, R.; Wu, Y.; Zhu, X.; Tseng, K. L.; Gao, Z.; Ju, C.; Yi, X.; Zheng, H.; Kappel, C.; Lundberg, E. “Analysis of the Human Protein Atlas Image Classification competition.” Nature Methods 2019, 16, 1254–1261.

(17) Spiniello, M.; Steinbrink, M. I.; Cesnik, A. J.; Miller, R. M.; Scalf, M.; Shortreed, M. R.; Smith, L. M. “Comprehensive in vivo identification of the c­Myc mRNA protein interactome using HyPR­MS.” RNA 2019, 25, 1337–1352.

(18) Schaffer, L. V.; Rensvold, J. W..; Shortreed, M. R.; Cesnik, A. J.; Jochem, A.; Scalf, M.; Frey, B. L; Pagliarini, D. J.; Smith, L. M. “Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top­Down and Intact­Mass Strategy.” Journal of Proteome Research 2018, 17, 10, 3526–3536.

(19) Spiniello, M.; Knoener, R. A.; Steinbrink, M. I.; Yang, B.; Cesnik, A. J.; Buxton, K. E.; Scalf, M.; Jarrard, D. F.; Smith, L. M. “HyPR­MS for multiplexed discovery of the MALAT1, NEAT1, and NORAD lncRNA protein interactomes.” Journal of Proteome Research 2018, 17, 9, 3022–3038.

(20) Schaffer, L. V.; Shortreed, M. R.; Cesnik, A. J.; Frey, B. L.; Scalf, M.; Solntsev, S. K.; Dai, Y.; Gasch, A. P.; Smith, L. M. “Expanding Proteoform Identifications in Top­Down Proteomic Analyses by Constructing Proteoform Families.” Analytical Chemistry 2018, 90, 2, 1325–1333.

(21) Proffitt, J. M.; Glenn, J.; Cesnik, A. J.; Jadhav, A.; Shortreed, M. R.; Smith, L. M.; Kavanagh, K.; Cox, L. A.; Olivier, M. “Proteomics in non­human primates: Utilizing RNA­seq data to improve protein identification by mass spectrometry in vervet monkeys.” BMC Genomics 2017, 18, 887.

(22) Dai, Y.; Shortreed, M. R.; Scalf, M.; Frey, B. L.; Cesnik, A. J.; Solntsev, S. K.; Schaffer, L. V.; Smith, L. M. “Elucidating E. coli Proteoform Families Using Intact­Mass Proteomics and a Global PTM Discovery Database.” Journal of Proteome Research 2017, 16, 11, 4156–4165.

(23) Guillen-­Ahlers, H.; Rao, P. K.; Levenstein, M. E.; Kennedy­Darling, J.; Perumalla, D. S.; Jadhav, A. Y. L.; Glenn, J. P.; Ludwig­Kubinski, A.; Drigalenko, E.; Montoya, M. J.; Göring, H. H.; Anderson, C. D.; Scalf, M.; Gildersleeve, H. I.S.; Cole, R.; Greene, A. M. Oduro, A. K.; Lazarova, K.; Cesnik, A. J.; Barfknecht, J.; Cirillo, L. A.; Gasch, A. P.; Shortreed, M. R.; Smith, L. M.; Olivier, M. “HyCCAPP as a tool to characterize promoter DNA­protein interactions in Saccharomyces cerevisiae.” Genomics 2016, 107, 6, 267–273.

(24) Sheynkman, G. M.; Shortreed, M. R.; Cesnik, A. J.; Smith, L. M. “Proteogenomics: Integrating Next­Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.” Annual Review of Analytical Chemistry 2016, 9, 512–545.

(25) Shortreed, M. R.; Frey, B. L.; Scalf, M.; Knoener, R. A.; Cesnik, A. J.; Smith, L. M. “Elucidating Proteoform Families from Proteoform Intact Mass and Lysine Count Measurements.” Journal of Proteome Research 2016, 15, 4, 1213–1221.

(26) Papa, C. M.; Cesnik, A. J.; Evans, T. C.; Choi, K. S. “Electrochemical Synthesis of Binary and Ternary Niobium­Containing Oxide Electrodes Using the p­Benzoquinone/Hydroquinone Redox Couple.” Langmuir 2015, 31, 34, 9502–9510.