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Items: 1 to 50 of 321

1.

funtrp: identifying protein positions for variation driven functional tuning.

Miller M, Vitale D, Kahn PC, Rost B, Bromberg Y.

Nucleic Acids Res. 2019 Oct 4. pii: gkz818. doi: 10.1093/nar/gkz818. [Epub ahead of print]

PMID:
31584091
2.

FunFam protein families improve residue level molecular function prediction.

Scheibenreif L, Littmann M, Orengo C, Rost B.

BMC Bioinformatics. 2019 Jul 18;20(1):400. doi: 10.1186/s12859-019-2988-x.

3.

Ocean acidification has little effect on the biochemical composition of the coccolithophore Emiliania huxleyi.

Heidenreich E, Wördenweber R, Kirschhöfer F, Nusser M, Friedrich F, Fahl K, Kruse O, Rost B, Franzreb M, Brenner-Weiß G, Rokitta S.

PLoS One. 2019 Jul 10;14(7):e0218564. doi: 10.1371/journal.pone.0218564. eCollection 2019.

4.

Company matters: The presence of other genotypes alters traits and intraspecific selection in an Arctic diatom under climate change.

Wolf KKE, Romanelli E, Rost B, John U, Collins S, Weigand H, Hoppe CJM.

Glob Chang Biol. 2019 Sep;25(9):2869-2884. doi: 10.1111/gcb.14675. Epub 2019 Jul 2.

PMID:
31058393
5.

Detailed prediction of protein sub-nuclear localization.

Littmann M, Goldberg T, Seitz S, Bodén M, Rost B.

BMC Bioinformatics. 2019 Apr 23;20(1):205. doi: 10.1186/s12859-019-2790-9.

6.

CT-based radiomic features predict tumor grading and have prognostic value in patients with soft tissue sarcomas treated with neoadjuvant radiation therapy.

Peeken JC, Bernhofer M, Spraker MB, Pfeiffer D, Devecka M, Thamer A, Shouman MA, Ott A, Nüsslin F, Mayr NA, Rost B, Nyflot MJ, Combs SE.

Radiother Oncol. 2019 Jun;135:187-196. doi: 10.1016/j.radonc.2019.01.004. Epub 2019 Apr 5.

PMID:
30961895
7.

Combining multimodal imaging and treatment features improves machine learning-based prognostic assessment in patients with glioblastoma multiforme.

Peeken JC, Goldberg T, Pyka T, Bernhofer M, Wiestler B, Kessel KA, Tafti PD, Nüsslin F, Braun AE, Zimmer C, Rost B, Combs SE.

Cancer Med. 2019 Jan;8(1):128-136. doi: 10.1002/cam4.1908. Epub 2018 Dec 18.

8.

N2 fixation in free-floating filaments of Trichodesmium is higher than in transiently suboxic colony microenvironments.

Eichner M, Thoms S, Rost B, Mohr W, Ahmerkamp S, Ploug H, Kuypers MMM, de Beer D.

New Phytol. 2019 Apr;222(2):852-863. doi: 10.1111/nph.15621. Epub 2018 Dec 29.

9.

Potassium channel-based optogenetic silencing.

Bernal Sierra YA, Rost BR, Pofahl M, Fernandes AM, Kopton RA, Moser S, Holtkamp D, Masala N, Beed P, Tukker JJ, Oldani S, Bönigk W, Kohl P, Baier H, Schneider-Warme F, Hegemann P, Beck H, Seifert R, Schmitz D.

Nat Commun. 2018 Nov 5;9(1):4611. doi: 10.1038/s41467-018-07038-8.

10.

VGLUT2 Functions as a Differential Marker for Hippocampal Output Neurons.

Wozny C, Beed P, Nitzan N, Pössnecker Y, Rost BR, Schmitz D.

Front Cell Neurosci. 2018 Oct 2;12:337. doi: 10.3389/fncel.2018.00337. eCollection 2018.

11.

Dark Proteins Important for Cellular Function.

Schafferhans A, O'Donoghue SI, Heinzinger M, Rost B.

Proteomics. 2018 Nov;18(21-22):e1800227. doi: 10.1002/pmic.201800227.

PMID:
30318701
12.

Cannabinoid type 2 receptors mediate a cell type-specific self-inhibition in cortical neurons.

Stumpf A, Parthier D, Sammons RP, Stempel AV, Breustedt J, Rost BR, Schmitz D.

Neuropharmacology. 2018 Sep 1;139:217-225. doi: 10.1016/j.neuropharm.2018.07.020. Epub 2018 Jul 17.

PMID:
30025920
13.

ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes.

Tran L, Hamp T, Rost B.

PLoS One. 2018 Jul 18;13(7):e0199988. doi: 10.1371/journal.pone.0199988. eCollection 2018.

14.

Evolutionary couplings and sequence variation effect predict protein binding sites.

Schelling M, Hopf TA, Rost B.

Proteins. 2018 Oct;86(10):1064-1074. doi: 10.1002/prot.25585. Epub 2018 Oct 22.

PMID:
30020551
15.

HFSP: high speed homology-driven function annotation of proteins.

Mahlich Y, Steinegger M, Rost B, Bromberg Y.

Bioinformatics. 2018 Jul 1;34(13):i304-i312. doi: 10.1093/bioinformatics/bty262.

16.

Structure-based analysis of CysZ-mediated cellular uptake of sulfate.

Assur Sanghai Z, Liu Q, Clarke OB, Belcher-Dufrisne M, Wiriyasermkul P, Giese MH, Leal-Pinto E, Kloss B, Tabuso S, Love J, Punta M, Banerjee S, Rajashankar KR, Rost B, Logothetis D, Quick M, Hendrickson WA, Mancia F.

Elife. 2018 May 24;7. pii: e27829. doi: 10.7554/eLife.27829.

17.

Correcting mistakes in predicting distributions.

Marot-Lassauzaie V, Bernhofer M, Rost B.

Bioinformatics. 2018 Oct 1;34(19):3385-3386. doi: 10.1093/bioinformatics/bty346.

18.

Radiomics in radiooncology - Challenging the medical physicist.

Peeken JC, Bernhofer M, Wiestler B, Goldberg T, Cremers D, Rost B, Wilkens JJ, Combs SE, Nüsslin F.

Phys Med. 2018 Apr;48:27-36. doi: 10.1016/j.ejmp.2018.03.012. Epub 2018 Mar 27. Review.

PMID:
29728226
19.

Treatment-related features improve machine learning prediction of prognosis in soft tissue sarcoma patients.

Peeken JC, Goldberg T, Knie C, Komboz B, Bernhofer M, Pasa F, Kessel KA, Tafti PD, Rost B, Nüsslin F, Braun AE, Combs SE.

Strahlenther Onkol. 2018 Sep;194(9):824-834. doi: 10.1007/s00066-018-1294-2. Epub 2018 Mar 20.

PMID:
29557486
20.

CellMap visualizes protein-protein interactions and subcellular localization.

Dallago C, Goldberg T, Andrade-Navarro MA, Alanis-Lobato G, Rost B.

Version 2. F1000Res. 2017 Oct 11 [revised 2018 Jan 1];6:1824. doi: 10.12688/f1000research.12707.2. eCollection 2017.

21.

ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes.

Cevost J, Vaillant C, Meyer S, Rost B.

Bioinformatics. 2018 Feb 15;34(4):609-616. doi: 10.1093/bioinformatics/btx634.

PMID:
29444234
22.

LocText: relation extraction of protein localizations to assist database curation.

Cejuela JM, Vinchurkar S, Goldberg T, Prabhu Shankar MS, Baghudana A, Bojchevski A, Uhlig C, Ofner A, Raharja-Liu P, Jensen LJ, Rost B.

BMC Bioinformatics. 2018 Jan 17;19(1):15. doi: 10.1186/s12859-018-2021-9.

23.

NLSdb-major update for database of nuclear localization signals and nuclear export signals.

Bernhofer M, Goldberg T, Wolf S, Ahmed M, Zaugg J, Boden M, Rost B.

Nucleic Acids Res. 2018 Jan 4;46(D1):D503-D508. doi: 10.1093/nar/gkx1021.

24.

Optogenetic Tools for Subcellular Applications in Neuroscience.

Rost BR, Schneider-Warme F, Schmitz D, Hegemann P.

Neuron. 2017 Nov 1;96(3):572-603. doi: 10.1016/j.neuron.2017.09.047. Review.

25.

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome.

Hücker SM, Ardern Z, Goldberg T, Schafferhans A, Bernhofer M, Vestergaard G, Nelson CW, Schloter M, Rost B, Scherer S, Neuhaus K.

PLoS One. 2017 Sep 13;12(9):e0184119. doi: 10.1371/journal.pone.0184119. eCollection 2017.

26.

Controls of primary production in two phytoplankton blooms in the Antarctic Circumpolar Current.

Hoppe CJM, Klaas C, Ossebaar S, Soppa MA, Cheah W, Laglera LM, Santos-Echeandia J, Rost B, Wolf-Gladrow DA, Bracher A, Hoppema M, Strass V, Trimborn S.

Deep Sea Res Part 2 Top Stud Oceanogr. 2017 Apr;138:63-73. doi: 10.1016/j.dsr2.2015.10.005.

27.

Common sequence variants affect molecular function more than rare variants?

Mahlich Y, Reeb J, Hecht M, Schelling M, De Beer TAP, Bromberg Y, Rost B.

Sci Rep. 2017 May 9;7(1):1608. doi: 10.1038/s41598-017-01054-2.

28.

Effects of ocean acidification on primary production in a coastal North Sea phytoplankton community.

Eberlein T, Wohlrab S, Rost B, John U, Bach LT, Riebesell U, Van de Waal DB.

PLoS One. 2017 Mar 8;12(3):e0172594. doi: 10.1371/journal.pone.0172594. eCollection 2017.

29.

nala: text mining natural language mutation mentions.

Cejuela JM, Bojchevski A, Uhlig C, Bekmukhametov R, Kumar Karn S, Mahmuti S, Baghudana A, Dubey A, Satagopam VP, Rost B.

Bioinformatics. 2017 Jun 15;33(12):1852-1858. doi: 10.1093/bioinformatics/btx083.

30.

CO2-dependent carbon isotope fractionation in dinoflagellates relates to their inorganic carbon fluxes.

Hoins M, Eberlein T, Van de Waal DB, Sluijs A, Reichart GJ, Rost B.

J Exp Mar Bio Ecol. 2016 Aug;481:9-14. doi: 10.1016/j.jembe.2016.04.001.

31.

TMSEG: Novel prediction of transmembrane helices.

Bernhofer M, Kloppmann E, Reeb J, Rost B.

Proteins. 2016 Nov;84(11):1706-1716. doi: 10.1002/prot.25155. Epub 2016 Sep 16.

32.

Computational prediction shines light on type III secretion origins.

Goldberg T, Rost B, Bromberg Y.

Sci Rep. 2016 Oct 7;6:34516. doi: 10.1038/srep34516.

33.

RIM-binding protein 2 regulates release probability by fine-tuning calcium channel localization at murine hippocampal synapses.

Grauel MK, Maglione M, Reddy-Alla S, Willmes CG, Brockmann MM, Trimbuch T, Rosenmund T, Pangalos M, Vardar G, Stumpf A, Walter AM, Rost BR, Eickholt BJ, Haucke V, Schmitz D, Sigrist SJ, Rosenmund C.

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):11615-11620. Epub 2016 Sep 26.

34.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

35.

Human cerebrospinal fluid monoclonal N-methyl-D-aspartate receptor autoantibodies are sufficient for encephalitis pathogenesis.

Kreye J, Wenke NK, Chayka M, Leubner J, Murugan R, Maier N, Jurek B, Ly LT, Brandl D, Rost BR, Stumpf A, Schulz P, Radbruch H, Hauser AE, Pache F, Meisel A, Harms L, Paul F, Dirnagl U, Garner C, Schmitz D, Wardemann H, Prüss H.

Brain. 2016 Oct;139(Pt 10):2641-2652. Epub 2016 Aug 20.

PMID:
27543972
36.

Predicted Molecular Effects of Sequence Variants Link to System Level of Disease.

Reeb J, Hecht M, Mahlich Y, Bromberg Y, Rost B.

PLoS Comput Biol. 2016 Aug 18;12(8):e1005047. doi: 10.1371/journal.pcbi.1005047. eCollection 2016 Aug.

37.

Protein function in precision medicine: deep understanding with machine learning.

Rost B, Radivojac P, Bromberg Y.

FEBS Lett. 2016 Aug;590(15):2327-41. doi: 10.1002/1873-3468.12307. Epub 2016 Aug 6. Review.

38.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T.

Bioinformatics. 2016 Nov 15;32(22):3501-3503. Epub 2016 Jul 13.

39.

Combined Effects of Ocean Acidification and Light or Nitrogen Availabilities on 13C Fractionation in Marine Dinoflagellates.

Hoins M, Eberlein T, Groβmann CH, Brandenburg K, Reichart GJ, Rost B, Sluijs A, Van de Waal DB.

PLoS One. 2016 May 6;11(5):e0154370. doi: 10.1371/journal.pone.0154370. eCollection 2016.

40.

Acidification, not carbonation, is the major regulator of carbon fluxes in the coccolithophore Emiliania huxleyi.

Kottmeier DM, Rokitta SD, Rost B.

New Phytol. 2016 Jul;211(1):126-37. doi: 10.1111/nph.13885. Epub 2016 Feb 25.

41.

Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation.

Petrou VI, Herrera CM, Schultz KM, Clarke OB, Vendome J, Tomasek D, Banerjee S, Rajashankar KR, Belcher Dufrisne M, Kloss B, Kloppmann E, Rost B, Klug CS, Trent MS, Shapiro L, Mancia F.

Science. 2016 Feb 5;351(6273):608-12. doi: 10.1126/science.aad1172.

42.

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC).

Neuhaus K, Landstorfer R, Fellner L, Simon S, Schafferhans A, Goldberg T, Marx H, Ozoline ON, Rost B, Kuster B, Keim DA, Scherer S.

BMC Genomics. 2016 Feb 24;17:133. doi: 10.1186/s12864-016-2456-1.

43.

Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human.

Ramilowski JA, Goldberg T, Harshbarger J, Kloppmann E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, Forrest ARR.

Nat Commun. 2016 Feb 10;7:10706. doi: 10.1038/ncomms10706. No abstract available.

44.

Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis.

Ardiccioni C, Clarke OB, Tomasek D, Issa HA, von Alpen DC, Pond HL, Banerjee S, Rajashankar KR, Liu Q, Guan Z, Li C, Kloss B, Bruni R, Kloppmann E, Rost B, Manzini MC, Shapiro L, Mancia F.

Nat Commun. 2016 Jan 5;7:10175. doi: 10.1038/ncomms10175.

45.

Protein disorder reduced in Saccharomyces cerevisiae to survive heat shock.

Vicedo E, Gasik Z, Dong YA, Goldberg T, Rost B.

F1000Res. 2015 Nov 6;4:1222. doi: 10.12688/f1000research.7178.1. eCollection 2015.

46.

Unexpected features of the dark proteome.

Perdigão N, Heinrich J, Stolte C, Sabir KS, Buckley MJ, Tabor B, Signal B, Gloss BS, Hammang CJ, Rost B, Schafferhans A, O'Donoghue SI.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15898-903. doi: 10.1073/pnas.1508380112. Epub 2015 Nov 17.

47.

Optogenetic acidification of synaptic vesicles and lysosomes.

Rost BR, Schneider F, Grauel MK, Wozny C, Bentz C, Blessing A, Rosenmund T, Jentsch TJ, Schmitz D, Hegemann P, Rosenmund C.

Nat Neurosci. 2015 Dec;18(12):1845-1852. doi: 10.1038/nn.4161. Epub 2015 Nov 9.

48.

Tools and data services registry: a community effort to document bioinformatics resources.

Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.

Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3.

49.

Vesicular Synaptobrevin/VAMP2 Levels Guarded by AP180 Control Efficient Neurotransmission.

Koo SJ, Kochlamazashvili G, Rost B, Puchkov D, Gimber N, Lehmann M, Tadeus G, Schmoranzer J, Rosenmund C, Haucke V, Maritzen T.

Neuron. 2015 Oct 21;88(2):330-44. doi: 10.1016/j.neuron.2015.08.034. Epub 2015 Sep 24.

50.

Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes.

Vicedo E, Schlessinger A, Rost B.

PLoS One. 2015 Aug 7;10(8):e0133990. doi: 10.1371/journal.pone.0133990. eCollection 2015.

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