Publications

Found 26 results
Filters: Author is Goldberg, Tatyana  [Clear All Filters]
2021
Bernhofer M, Dallago C, Karl T, Satagopam V, Heinzinger M, Littmann M, Olenyi T, Qiu J, Schütze K, Yachdav G, et al. PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Res. 2021 ;49(W1):W535-W540.
Marot-Lassauzaie V, Goldberg T, Armenteros JJuan Almag, Nielsen H, Rost B. Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species. J Mol Evol. 2021 .
2020
Dallago C, Goldberg T, Andrade-Navarro MAngel, Alanis-Lobato G, Rost B. Visualizing Human Protein-Protein Interactions and Subcellular Localizations on Cell Images Through CellMap. Curr Protoc Bioinformatics. 2020 ;69(1):e97.
2019
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MNafiz, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 2019 ;20(1):244.
Littmann M, Goldberg T, Seitz S, Boden M, Rost B. Correction to: Detailed prediction of protein sub-nuclear localization. BMC Bioinformatics. 2019 ;20(1):727.
Littmann M, Goldberg T, Seitz S, Boden M, Rost B. Detailed prediction of protein sub-nuclear localization. BMC Bioinformatics. 2019 ;20(1):205.
2018
Peeken JC, Goldberg T, Pyka T, Bernhofer M, Wiestler B, Kessel KA, Tafti PD, Nüsslin F, Braun AE, Zimmer C, et al. Combining multimodal imaging and treatment features improves machine learning-based prognostic assessment in patients with glioblastoma multiforme. Cancer Med. 2018 .
Cejuela JMiguel, Vinchurkar S, Goldberg T, Shankar MSollepura, Baghudana A, Bojchevski A, Uhlig C, Ofner A, Raharja-Liu P, Jensen LJuhl, et al. LocText: relation extraction of protein localizations to assist database curation. BMC Bioinformatics. 2018 ;19(1):15.
Bernhofer M, Goldberg T, Wolf S, Ahmed M, Zaugg J, Boden M, Rost B. NLSdb-major update for database of nuclear localization signals and nuclear export signals. Nucleic Acids Res. 2018 ;46(D1):D503-D508.
Peeken JC, Bernhofer M, Wiestler B, Goldberg T, Cremers D, Rost B, Wilkens JJ, Combs SE, Nüsslin F. Radiomics in radiooncology - Challenging the medical physicist. Phys Med. 2018 ;48:27-36.
Peeken JC, Goldberg T, Knie C, Komboz B, Bernhofer M, Pasa F, Kessel KA, Tafti PD, Rost B, Nüsslin F, et al. Treatment-related features improve machine learning prediction of prognosis in soft tissue sarcoma patients. Strahlenther Onkol. 2018 ;194(9):824-834.
2017
Dallago C, Goldberg T, Andrade-Navarro MAngel, Alanis-Lobato G, Rost B. CellMap visualizes protein-protein interactions and subcellular localization. F1000Res. 2017 ;6:1824.
Hücker SM, Ardern Z, Goldberg T, Schafferhans A, Bernhofer M, Vestergaard G, Nelson CW, Schloter M, Rost B, Scherer S, et al. Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome. PLoS One. 2017 ;12(9):e0184119.
2016
Goldberg T, Rost B, Bromberg Y. Computational prediction shines light on type III secretion origins. Sci Rep. 2016 ;6:34516.
Ramilowski JA, Goldberg T, Harshbarger J, Kloppmann E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, et al. Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun. 2016 ;7:10706.
Jiang Y, Oron TRonnen, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 2016 ;17(1):184.
Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T. MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics. 2016 .
Neuhaus K, Landstorfer R, Fellner L, Simon S, Schafferhans A, Goldberg T, Marx H, Ozoline ON, Rost B, Kuster B, et al. Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). BMC Genomics. 2016 ;17(1):133.
2015
Yachdav G, Goldberg T, Wilzbach S, Dao D, Shih I, Choudhary S, Crouch S, Franz M, García A, García LJ, et al. Anatomy of BioJS, an open source community for the life sciences. Elife. 2015 ;4.
Ramilowski JA, Goldberg T, Harshbarger J, Kloppman E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, et al. A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun. 2015 ;6:7866.
Vicedo E, Gasik Z, Dong Y-A, Goldberg T, Rost B. Protein disorder reduced in Saccharomyces cerevisiae to survive heat shock. F1000Res. 2015 ;4:1222.
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, et al. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 2015 .
2014
Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, et al. LocTree3 prediction of localization. Nucleic Acids Res. 2014 ;42(Web Server issue):W350-5.
Yachdav G, Kloppmann E, Kaján L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, et al. PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Res. 2014 ;42(Web Server issue):W337-43.
2013
Hamp T, Goldberg T, Rost B. Accelerating the Original Profile Kernel. PLoS One. 2013 ;8(6):e68459.
2012
Goldberg T, Hamp T, Rost B. LocTree2 predicts localization for all domains of life. Bioinformatics. 2012 ;28(18):i458-i465.