Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F. (2022). To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. BMC Biol. 2022 Jun 16;20(1):146. doi: 10.1186/s12915-022-01347-7.
Alfatah M, Eisenhaber F. (2022). The PICLS high-throughput screening method for agents extending cellular longevity identifies 2,5-anhydro-D-mannitol as novel anti-aging compound. Geroscience. 2022 Jun 15. doi: 10.1007/s11357-022-00598-0. Online ahead of print.
Szenker-Ravi E, Ott T, Khatoo M, Moreau de Bellaing A, Goh WX, Chong YL, Beckers A, Kannesan D, Louvel G, Anujan P, Ravi V, Bonnard C, Moutton S, Schoen P, Fradin M, Colin E, Megarbane A, Daou L, Chehab G, Di Filippo S, Rooryck C, Deleuze JF, Boland A, Arribard N, Eker R, Tohari S, Ng AY, Rio M, Lim CT, Eisenhaber B, Eisenhaber F, Venkatesh B, Amiel J, Crollius HR, Gordon CT, Gossler A, Roy S, Attie-Bitach T, Blum M, Bouvagnet P, Reversade B. (2022). Publisher Correction: Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates. Nat Genet. 2022 Jun;54(6):906. doi: 10.1038/s41588-022-01053-8.
Tantoso E, Eisenhaber B, Eisenhaber F. (2022). Optimizing the Parametrization of Homologue Classification in the Pan-Genome Computation for a Bacterial Species: Case Study Streptococcus pyogenes. Methods Mol Biol. 2022;2449:299-324. doi: 10.1007/978-1-0716-2095-3_13.
Jing JL, Ning TCY, Natali F, Eisenhaber F, Alfatah M. (2022). Iron Supplementation Delays Aging and Extends Cellular Lifespan through Potentiation of Mitochondrial Function. Cells. 2022 Mar 2;11(5):862. doi: 10.3390/cells11050862.
Eisenhaber F, Thakar J, Ponte-Sucre A, Dandekar T. (2022). Editorial: Innovative Strategies From Synthetic Biology and Bacterial Pathways to Master Biochemical Environmental Challenges. Front Bioeng Biotechnol. 2022 Jan 11;9:828632. doi: 10.3389/fbioe.2021.828632. eCollection 2021.
Szenker-Ravi E, Ott T, Khatoo M, Moreau de Bellaing A, Goh WX, Chong YL, Beckers A, Kannesan D, Louvel G, Anujan P, Ravi V, Bonnard C, Moutton S, Schoen P, Fradin M, Colin E, Megarbane A, Daou L, Chehab G, Di Filippo S, Rooryck C, Deleuze JF, Boland A, Arribard N, Eker R, Tohari S, Ng AY, Rio M, Lim CT, Eisenhaber B, Eisenhaber F, Venkatesh B, Amiel J, Crollius HR, Gordon CT, Gossler A, Roy S, Attie-Bitach T, Blum M, Bouvagnet P, Reversade B. (2022). Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates. Nat Genet. 2022 Jan;54(1):62-72. doi: 10.1038/s41588-021-00970-4. Epub 2021 Dec 13.
Tromp J, Seekings PJ, Hung CL, Iversen MB, Frost MJ, Ouwerkerk W, Jiang Z, Eisenhaber F, Goh RSM, Zhao H, Huang W, Ling LH, Sim D, Cozzone P, Richards AM, Lee HK, Solomon SD, Lam CSP, Ezekowitz JA. (2022). Automated interpretation of systolic and diastolic function on the echocardiogram: a multicohort study. Lancet Digit Health. 2022 Jan;4(1):e46-e54. doi: 10.1016/S2589-7500(21)00235-1. Epub 2021 Dec 1.
Zhang Z, Yu J, Eisenhaber F, Gao X, Gojobori T. (2021). WITHDRAWN: In Memory of Vladimir B. Bajic (1952-2019). Genomics Proteomics Bioinformatics. 2021 Mar 17:S1672-0229(21)00070-X. doi: 10.1016/j.gpb.2019.12.003. Online ahead of print.
Sirota FL, Maurer-Stroh S, Li Z, Eisenhaber F, Eisenhaber B. (2021). Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. Front Bioeng Biotechnol. 2021 Aug 2;9:701120. doi: 10.3389/fbioe.2021.701120. eCollection 2021.
Eisenhaber B, Sinha S, Jadalanki CK, Shitov VA, Tan QW, Sirota FL, Eisenhaber F. (2021). Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites. Biol Direct. 2021 Jan 12;16(1):4. doi: 10.1186/s13062-021-00291-w.
Su CT, Sinha S, Eisenhaber B, Eisenhaber F. (2020). Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site. Biol Direct. 2020 Sep 29;15(1):14. doi: 10.1186/s13062-020-00266-3.
Niska-Blakie J, Gopinathan L, Low KN, Kien YL, Goh CMF, Caldez MJ, Pfeiffenberger E, Jones OS, Ong CB, Kurochkin IV, Coppola V, Tessarollo L, Choi H, Kanagasundaram Y, Eisenhaber F, Maurer-Stroh S, Kaldis P. (2020). Knockout of the non-essential gene SUGCT creates diet-linked, age-related microbiome disbalance with a diabetes-like metabolic syndrome phenotype. Cell Mol Life Sci. 2020 Sep;77(17):3423-3439. doi: 10.1007/s00018-019-03359-z. Epub 2019 Nov 13.
Goh F, Zhang MM, Lim TR, Low KN, Nge CE, Heng E, Yeo WL, Sirota FL, Crasta S, Tan Z, Ng V, Leong CY, Zhang H, Lezhava A, Chen SL, Hoon SS, Eisenhaber F, Eisenhaber B, Kanagasundaram Y, Wong FT, Ng SB. (2020). Identification and engineering of 32 membered antifungal macrolactone notonesomycins. Microb Cell Fact. 2020 Mar 19;19(1):71. doi: 10.1186/s12934-020-01328-x.
Tantoso E, Wong WC, Tay WH, Lee J, Sinha S, Eisenhaber B, Eisenhaber F. (2019). Hypocrisy Around Medical Patient Data: Issues of Access for Biomedical Research, Data Quality, Usefulness for the Purpose and Omics Data as Game Changer. Asian Bioeth Rev. 2019 Jun 1;11(2):189-207. doi: 10.1007/s41649-019-00085-3. eCollection 2019 Jun.
Sinha S, Nge CE, Leong CY, Ng V, Crasta S, Alfatah M, Goh F, Low KN, Zhang H, Arumugam P, Lezhava A, Chen SL, Kanagasundaram Y, Ng SB, Eisenhaber F, Eisenhaber B. (2019). Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723. BMC Genomics. 2019 May 14;20(1):374. doi: 10.1186/s12864-019-5762-6.
Toh YK, Shin J, Balakrishna AM, Kamariah N, Grüber A, Eisenhaber F, Eisenhaber B, Grüber G. (2019). Effect of the additional cysteine 503 of vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F (AhpF) and the mechanism of AhpF and subunit C assembling. Free Radic Biol Med. 2019 Jul;138:10-22. doi: 10.1016/j.freeradbiomed.2019.04.036. Epub 2019 Apr 30.
Maurer-Stroh S, Krutz NL, Kern PS, Gunalan V, Nguyen MN, Limviphuvadh V, Eisenhaber F, Gerberick GF. (2019). AllerCatPro-prediction of protein allergenicity potential from the protein sequence. Bioinformatics. 2019 Sep 1;35(17):3020-3027. doi: 10.1093/bioinformatics/btz029.
Berger KA, Pigott DM, Tomlinson F, Godding D, Maurer-Stroh S, Taye B, Sirota FL, Han A, Lee RTC, Gunalan V, Eisenhaber F, Hay SI, Russell CA. (2018). The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine. Open Forum Infect Dis. 2018 Nov 27;5(12):ofy318. doi: 10.1093/ofid/ofy318. eCollection 2018 Dec.
Ng SB, Kanagasundaram Y, Fan H, Arumugam P, Eisenhaber B, Eisenhaber F. (2018). The 160K Natural Organism Library, a unique resource for natural products research. Nat Biotechnol. 2018 Jul 6;36(7):570-573. doi: 10.1038/nbt.4187.
Kamariah N, Eisenhaber B, Eisenhaber F, Grüber G. (2018). Molecular mechanism of the Escherichia coli AhpC in the function of a chaperone under heat-shock conditions. Sci Rep. 2018 Sep 20;8(1):14151. doi: 10.1038/s41598-018-32527-7.
Sirota FL, Goh F, Low KN, Yang LK, Crasta SC, Eisenhaber B, Eisenhaber F, Kanagasundaram Y, Ng SB. (2018). Isolation and Identification of an Anthracimycin Analogue from Nocardiopsis kunsanensis, a Halophile from a Saltern, by Genomic Mining Strategy. J Genomics. 2018 May 21;6:63-73. doi: 10.7150/jgen.24368. eCollection 2018.
Eisenhaber B, Sinha S, Wong WC, Eisenhaber F. (2018). Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z. Cell Cycle. 2018;17(7):874-880. doi: 10.1080/15384101.2018.1456294. Epub 2018 May 15.
Wong WC, Ng HK, Tantoso E, Soong R, Eisenhaber F. (2018). Finite-size effects in transcript sequencing count distribution: its power-law correction necessarily precedes downstream normalization and comparative analysis. Biol Direct. 2018 Feb 12;13(1):2. doi: 10.1186/s13062-018-0204-y.
Limviphuvadh V, Tan CS, Konishi F, Jenjaroenpun P, Xiang JS, Kremenska Y, Mu YS, Syn N, Lee SC, Soo RA, Eisenhaber F, Maurer-Stroh S, Yong WP. (2018). Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. BMC Cancer. 2018 May 11;18(1):555. doi: 10.1186/s12885-018-4471-x.
Sinha S, Eisenhaber B, Jensen LJ, Kalbuaji B, Eisenhaber F. (2018). Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. Proteomics. 2018 Nov;18(21-22):e1800093. doi: 10.1002/pmic.201800093. Epub 2018 Oct 30.
Kamariah N, Eisenhaber B, Eisenhaber F, Grüber G. (2018). Active site C(P)-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins. Free Radic Biol Med. 2018 Apr;118:59-70. doi: 10.1016/j.freeradbiomed.2018.02.027. Epub 2018 Feb 21.
Kurochkin IV, Guarnera E, Wong JH, Eisenhaber F, Berezovsky IN. (2017). Toward Allosterically Increased Catalytic Activity of Insulin-Degrading Enzyme against Amyloid Peptides. Biochemistry. 2017 Jan 10;56(1):228-239. doi: 10.1021/acs.biochem.6b00783. Epub 2016 Dec 16.
Berezovsky IN, Guarnera E, Zheng Z, Eisenhaber B, Eisenhaber F. (2017). Protein function machinery: from basic structural units to modulation of activity. Curr Opin Struct Biol. 2017 Feb;42:67-74. doi: 10.1016/j.sbi.2016.10.021. Epub 2016 Nov 16.
Marakasova ES, Eisenhaber B, Maurer-Stroh S, Eisenhaber F, Baranova A. (2017). Prenylation of viral proteins by enzymes of the host: Virus-driven rationale for therapy with statins and FT/GGT1 inhibitors. Bioessays. 2017 Oct;39(10). doi: 10.1002/bies.201700014. Epub 2017 Sep 8.
Amit M, Na’ara S, Francis D, Matanis W, Zolotov S, Eisenhaber B, Eisenhaber F, Weiler Sagie M, Malkin L, Billan S, Charas T, Gil Z. (2017). Post-translational Regulation of Radioactive Iodine Therapy Response in Papillary Thyroid Carcinoma. J Natl Cancer Inst. 2017 Dec 1;109(12). doi: 10.1093/jnci/djx092.
Toh YK, Balakrishna AM, Manimekalai MSS, Chionh BB, Seetharaman RRC, Eisenhaber F, Eisenhaber B, Grüber G. (2017). Novel insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F. Biochim Biophys Acta Gen Subj. 2017 Dec;1861(12):3201-3214. doi: 10.1016/j.bbagen.2017.09.011. Epub 2017 Sep 19.
Kamariah N, Eisenhaber B, Eisenhaber F, Grüber G. (2017). Essential role of the flexible linker on the conformational equilibrium of bacterial peroxiredoxin reductase for effective regeneration of peroxiredoxin. J Biol Chem. 2017 Apr 21;292(16):6667-6679. doi: 10.1074/jbc.M117.775858. Epub 2017 Mar 7.
Baker JA, Wong WC, Eisenhaber B, Warwicker J, Eisenhaber F. (2017). Erratum to: Charged residues next to transmembrane regions revisited: “Positive-inside rule” is complemented by the “negative inside depletion/outside enrichment rule”. BMC Biol. 2017 Aug 18;15(1):72. doi: 10.1186/s12915-017-0410-6.
Lua WH, Ling WL, Su CT, Yeo JY, Verma CS, Eisenhaber B, Eisenhaber F, Gan SK. (2017). Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: A story of bad signal peptides and good ones that nevertheless do not make it. Cell Cycle. 2017 Mar 4;16(5):457-467. doi: 10.1080/15384101.2017.1281480. Epub 2017 Jan 19.
Baker JA, Wong WC, Eisenhaber B, Warwicker J, Eisenhaber F. (2017). Charged residues next to transmembrane regions revisited: “Positive-inside rule” is complemented by the “negative inside depletion/outside enrichment rule”. BMC Biol. 2017 Jul 24;15(1):66. doi: 10.1186/s12915-017-0404-4.
Taye B, Vaz C, Tanavde V, Kuznetsov VA, Eisenhaber F, Sugrue RJ, Maurer-Stroh S. (2017). Benchmarking selected computational gene network growing tools in context of virus-host interactions. Sci Rep. 2017 Jul 19;7(1):5805. doi: 10.1038/s41598-017-06020-6.
Yap CK, Eisenhaber B, Eisenhaber F, Wong WC. (2016). xHMMER3x2: Utilizing HMMER3’s speed and HMMER2’s sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation. Biol Direct. 2016 Nov 29;11(1):63. doi: 10.1186/s13062-016-0163-0.
Kamariah N, Sek MF, Eisenhaber B, Eisenhaber F, Grüber G. (2016). Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins. Sci Rep. 2016 Nov 28;6:37610. doi: 10.1038/srep37610.
Eisenhaber B, Kuchibhatla D, Sherman W, Sirota FL, Berezovsky IN, Wong WC, Eisenhaber F. (2016). The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment. Methods Mol Biol. 2016;1415:477-506. doi: 10.1007/978-1-4939-3572-7_25.
Kamariah N, Nartey W, Eisenhaber B, Eisenhaber F, Grüber G. (2016). Low resolution solution structure of an enzymatic active AhpC10:AhpF2 ensemble of the Escherichia coli Alkyl hydroperoxide Reductase. J Struct Biol. 2016 Jan;193(1):13-22. doi: 10.1016/j.jsb.2015.11.004. Epub 2015 Nov 14.
Kulemzina I, Ang K, Zhao X, Teh JT, Verma V, Suranthran S, Chavda AP, Huber RG, Eisenhaber B, Eisenhaber F, Yan J, Ivanov D. (2016). A Reversible Association between Smc Coiled Coils Is Regulated by Lysine Acetylation and Is Required for Cohesin Association with the DNA. Mol Cell. 2016 Sep 15;63(6):1044-54. doi: 10.1016/j.molcel.2016.08.008. Epub 2016 Sep 8.
Van TD, Tran N, Le L, Eisenhaber F. (2016). A Perspective on Rational Designs of a Hemagglutinin Based Universal Influenza Vaccine. Curr Pharm Des. 2016 Apr 19. Online ahead of print.
Wong WC, Yap CK, Eisenhaber B, Eisenhaber F. (2015). dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity. Biol Direct. 2015 Aug 1;10:39. doi: 10.1186/s13062-015-0068-3.
Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. (2015). Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access. Proteomics. 2015 Jul;15(14):2525-46. doi: 10.1002/pmic.201400633.
Nartey W, Basak S, Kamariah N, Manimekalai MS, Robson S, Wagner G, Eisenhaber B, Eisenhaber F, Grüber G. (2015). NMR studies reveal a novel grab and release mechanism for efficient catalysis of the bacterial 2-Cys peroxiredoxin machinery. FEBS J. 2015 Dec;282(23):4620-38. doi: 10.1111/febs.13522. Epub 2015 Oct 16.
Sherman WA, Kuchibhatla DB, Limviphuvadh V, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. (2015). HPMV: human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes. J Bioinform Comput Biol. 2015 Oct;13(5):1550028. doi: 10.1142/S0219720015500286. Epub 2015 Oct 27.
Kamariah N, Manimekalai MS, Nartey W, Eisenhaber F, Eisenhaber B, Grüber G. (2015). Crystallographic and solution studies of NAD(+)- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps. Biochim Biophys Acta. 2015 Oct;1847(10):1139-52. doi: 10.1016/j.bbabio.2015.06.011. Epub 2015 Jun 17.
Eisenhaber F. (2014). Unix interfaces, Kleisli, bucandin structure, etc. – the heroic beginning of bioinformatics in Singapore. J Bioinform Comput Biol. 2014 Jun;12(3):1471002. doi: 10.1142/S0219720014710024. Epub 2014 Jun 5.
Eisenhaber B, Eisenhaber S, Kwang TY, Grüber G, Eisenhaber F. (2014). Transamidase subunit GAA1/GPAA1 is a M28 family metallo-peptide-synthetase that catalyzes the peptide bond formation between the substrate protein’s omega-site and the GPI lipid anchor’s phosphoethanolamine. Cell Cycle. 2014;13(12):1912-7. doi: 10.4161/cc.28761. Epub 2014 Apr 17.
Dip PV, Kamariah N, Subramanian Manimekalai MS, Nartey W, Balakrishna AM, Eisenhaber F, Eisenhaber B, Grüber G. (2014). Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli. Acta Crystallogr D Biol Crystallogr. 2014 Nov;70(Pt 11):2848-62. doi: 10.1107/S1399004714019233. Epub 2014 Oct 16.
Kuchibhatla DB, Sherman WA, Chung BY, Cook S, Schneider G, Eisenhaber B, Karlin DG. (2014). Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently “orphan” viral proteins. J Virol. 2014 Jan;88(1):10-20. doi: 10.1128/JVI.02595-13. Epub 2013 Oct 23.
Maurer-Stroh S, Li Y, Bastien N, Gunalan V, Lee RT, Eisenhaber F, Booth TF. (2014). Potential human adaptation mutation of influenza A(H5N1) virus, Canada. Emerg Infect Dis. 2014 Sep;20(9):1580-2. doi: 10.3201/eid2009.140240.
Wong WC, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. (2014). On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation. BMC Bioinformatics. 2014 Jun 2;15:166. doi: 10.1186/1471-2105-15-166.
Mah TL, Yap XN, Limviphuvadh V, Li N, Sridharan S, Kuralmani V, Feng M, Liem N, Adhikari S, Yong WP, Soo RA, Maurer-Stroh S, Eisenhaber F, Tong JC. (2014). Novel SNP improves differential survivability and mortality in non-small cell lung cancer patients. BMC Genomics. 2014;15 Suppl 9(Suppl 9):S20. doi: 10.1186/1471-2164-15-S9-S20. Epub 2014 Dec 8.
Dip PV, Kamariah N, Nartey W, Beushausen C, Kostyuchenko VA, Ng TS, Lok SM, Saw WG, Eisenhaber F, Eisenhaber B, Grüber G. (2014). Key roles of the Escherichia coli AhpC C-terminus in assembly and catalysis of alkylhydroperoxide reductase, an enzyme essential for the alleviation of oxidative stress. Biochim Biophys Acta. 2014 Dec;1837(12):1932-1943. doi: 10.1016/j.bbabio.2014.08.007.
Eisenhaber F, Sung WK, Wong L. (2014). Guest Editorial for the International Conference on Genome Informatics (GIW 2013). IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):5-6. doi: 10.1109/tcbb.2014.2299751.
Eisenhaber F, Sherman WA. (2014). 10 years for the Journal of Bioinformatics and Computational Biology (2003-2013) – a retrospective. J Bioinform Comput Biol. 2014 Jun;12(3):1471001. doi: 10.1142/S0219720014710012. Epub 2014 May 21.
Marakasova ES, Akhmatova NK, Amaya M, Eisenhaber B, Eisenhaber F, van Hoek ML, Baranova AV. (2013). [Prenylation: from bacteria to eukaryotes]. Mol Biol (Mosk). 2013 Sep-Oct;47(5):717-30.
Maurer-Stroh S, Lee RT, Gunalan V, Eisenhaber F. (2013). The highly pathogenic H7N3 avian influenza strain from July 2012 in Mexico acquired an extended cleavage site through recombination with host 28S rRNA. Virol J. 2013 May 1;10:139. doi: 10.1186/1743-422X-10-139.
Goncearenco A, Mitternacht S, Yong T, Eisenhaber B, Eisenhaber F, Berezovsky IN. (2013). SPACER: Server for predicting allosteric communication and effects of regulation. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W266-72. doi: 10.1093/nar/gkt460. Epub 2013 Jun 3.
Maurer-Stroh S, Gao H, Han H, Baeten L, Schymkowitz J, Rousseau F, Zhang L, Eisenhaber F. (2013). Motif discovery with data mining in 3D protein structure databases: discovery, validation and prediction of the U-shape zinc binding (“Huf-Zinc”) motif. J Bioinform Comput Biol. 2013 Feb;11(1):1340008. doi: 10.1142/S0219720013400088. Epub 2013 Jan 16.
Saw WG, Eisenhaber B, Eisenhaber F, Grüber G. (2013). Low-resolution structure of the soluble domain GPAA1 (yGPAA170-247) of the glycosylphosphatidylinositol transamidase subunit GPAA1 from Saccharomyces cerevisiae. Biosci Rep. 2013 Mar 28;33(2):e00033. doi: 10.1042/BSR20120107.
Eisenhaber F, Sung WK, Wong L. (2013). International Conference on Genome Informatics (GIW 2013) in Singapore: Introduction to the systems biology contributions. BMC Syst Biol. 2013;7 Suppl 6(Suppl 6):I1. doi: 10.1186/1752-0509-7-S6-I1. Epub 2013 Dec 13.
Kuznetsov V, Lee HK, Maurer-Stroh S, Molnár MJ, Pongor S, Eisenhaber B, Eisenhaber F. (2013). How bioinformatics influences health informatics: usage of biomolecular sequences, expression profiles and automated microscopic image analyses for clinical needs and public health. Health Inf Sci Syst. 2013 Jan 10;1:2. doi: 10.1186/2047-2501-1-2. eCollection 2013.
Ma J, Eisenhaber F, Maurer-Stroh S. (2013). Automatic phylogenetic classification of bacterial beta-lactamase sequences including structural and antibiotic substrate preference information. J Bioinform Comput Biol. 2013 Dec;11(6):1343011. doi: 10.1142/S0219720013430117. Epub 2013 Dec 11.
Maurer-Stroh S, Gunalan V, Wong WC, Eisenhaber F. (2013). A simple shortcut to unsupervised alignment-free phylogenetic genome groupings, even from unassembled sequencing reads. J Bioinform Comput Biol. 2013 Dec;11(6):1343005. doi: 10.1142/S0219720013430051. Epub 2013 Dec 2.
Lee RT, Gunalan V, Van TD, Le LT, Eisenhaber F, Maurer-Stroh S. (2013). A new piece in the puzzle of the novel avian-origin influenza A (H7N9) virus. Biol Direct. 2013 Oct 26;8:26. doi: 10.1186/1745-6150-8-26.
Wong WC, Maurer-Stroh S, Schneider G, Eisenhaber F. (2012). Transmembrane helix: simple or complex. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W370-5. doi: 10.1093/nar/gks379. Epub 2012 May 7.
Romeo A, Sonnleitner E, Sorger-Domenigg T, Nakano M, Eisenhaber B, Bläsi U. (2012). Transcriptional regulation of nitrate assimilation in Pseudomonas aeruginosa occurs via transcriptional antitermination within the nirBD-PA1779-cobA operon. Microbiology (Reading). 2012 Jun;158(Pt 6):1543-1552. doi: 10.1099/mic.0.053850-0. Epub 2012 Apr 5.
Tan J, Kuchibhatla D, Sirota FL, Sherman WA, Gattermayer T, Kwoh CY, Eisenhaber F, Schneider G, Maurer-Stroh S. (2012). Tachyon search speeds up retrieval of similar sequences by several orders of magnitude. Bioinformatics. 2012 Jun 15;28(12):1645-6. doi: 10.1093/bioinformatics/bts197. Epub 2012 Apr 23.
Sirota FL, Batagov A, Schneider G, Eisenhaber B, Eisenhaber F, Maurer-Stroh S. (2012). Beware of moving targets: reference proteome content fluctuates substantially over the years. J Bioinform Comput Biol. 2012 Dec;10(6):1250020. doi: 10.1142/S0219720012500205. Epub 2012 Aug 7.
Eisenhaber F. (2012). A decade after the first full human genome sequencing: when will we understand our own genome?. J Bioinform Comput Biol. 2012 Oct;10(5):1271001. doi: 10.1142/S0219720012710011. Epub 2012 Jun 22.
Wong WC, Maurer-Stroh S, Eisenhaber F. (2011). The Janus-faced E-values of HMMER2: extreme value distribution or logistic function?. J Bioinform Comput Biol. 2011 Feb;9(1):179-206.
Kunze M, Neuberger G, Maurer-Stroh S, Ma J, Eck T, Braverman N, Schmid JA, Eisenhaber F, Berger J. (2011). Structural requirements for interaction of peroxisomal targeting signal 2 and its receptor PEX7. J Biol Chem. 2011 Dec 30;286(52):45048-62. doi: 10.1074/jbc.M111.301853. Epub 2011 Nov 5.
Toh YK, Kamariah N, Maurer-Stroh S, Roessle M, Eisenhaber F, Adhikari S, Eisenhaber B, Grüber G. (2011). Structural insight into the glycosylphosphatidylinositol transamidase subunits PIG-K and PIG-S from yeast. J Struct Biol. 2011 Feb;173(2):271-81. doi: 10.1016/j.jsb.2010.11.026. Epub 2010 Dec 4.
Kamariah N, Eisenhaber F, Adhikari S, Eisenhaber B, Grüber G. (2011). Purification and crystallization of yeast glycosylphosphatidylinositol transamidase subunit PIG-S (PIG-S(71-467)). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Aug 1;67(Pt 8):896-9. doi: 10.1107/S1744309111024080. Epub 2011 Jul 19.
Eisenhaber B, Sammer M, Lua WH, Benetka W, Liew LL, Yu W, Lee HK, Koranda M, Eisenhaber F, Adhikari S. (2011). Nuclear import of a lipid-modified transcription factor: mobilization of NFAT5 isoform a by osmotic stress. Cell Cycle. 2011 Nov 15;10(22):3897-911. doi: 10.4161/cc.10.22.18043. Epub 2011 Nov 15.
Wong WC, Maurer-Stroh S, Eisenhaber F. (2011). Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins. Biol Direct. 2011 Oct 25;6:57. doi: 10.1186/1745-6150-6-57.
Lee VJ, Yap J, Maurer-Stroh S, Lee RT, Eisenhaber F, Tay JK, Ting PJ, Loh JP, Wong CW, Tan BH, Koay ES, Kelly PM, Hibberd ML. (2011). Investigation of causes of oseltamivir chemoprophylaxis failures during influenza A (H1N1-2009) outbreaks. J Clin Virol. 2011 Feb;50(2):104-8. doi: 10.1016/j.jcv.2010.10.004. Epub 2010 Nov 19.
Dellago H, Löscher M, Ajuh P, Ryder U, Kaisermayer C, Grillari-Voglauer R, Fortschegger K, Gross S, Gstraunthaler A, Borth N, Eisenhaber F, Lamond AI, Grillari J. (2011). Exo70, a subunit of the exocyst complex, interacts with SNEV(hPrp19/hPso4) and is involved in pre-mRNA splicing. Biochem J. 2011 Aug 15;438(1):81-91. doi: 10.1042/BJ20110183.
Prokesch A, Bogner-Strauss JG, Hackl H, Rieder D, Neuhold C, Walenta E, Krogsdam A, Scheideler M, Papak C, Wong WC, Vinson C, Eisenhaber F, Trajanoski Z. (2011). Arxes: retrotransposed genes required for adipogenesis. Nucleic Acids Res. 2011 Apr;39(8):3224-39. doi: 10.1093/nar/gkq1289. Epub 2010 Dec 21.
Van Damme P, Maurer-Stroh S, Hao H, Colaert N, Timmerman E, Eisenhaber F, Vandekerckhove J, Gevaert K. (2010). The substrate specificity profile of human granzyme A. Biol Chem. 2010 Aug;391(8):983-97. doi: 10.1515/BC.2010.096.
Maurer-Stroh S, Paing SS, Lee RT, Eisenhaber F. (2010). Sporadic human cases of swine-origin influenza before 2009 share the Sa epitope. Cell Cycle. 2010 Sep 15;9(18):3826-8. doi: 10.4161/cc.9.18.13166. Epub 2010 Sep 26.
Limviphuvadh V, Chua LL, Rahim RA, Eisenhaber F, Maurer-Stroh S, Adhikari S. (2010). Similarity of molecular phenotype between known epilepsy gene LGI1 and disease candidate gene LGI2. BMC Biochem. 2010 Sep 24;11:39. doi: 10.1186/1471-2091-11-39.
Mujezinovic N, Schneider G, Wildpaner M, Mechtler K, Eisenhaber F. (2010). Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction. BMC Genomics. 2010 Feb 10;11 Suppl 1(Suppl 1):S13. doi: 10.1186/1471-2164-11-S1-S13.
Bogner-Strauss JG, Prokesch A, Sanchez-Cabo F, Rieder D, Hackl H, Duszka K, Krogsdam A, Di Camillo B, Walenta E, Klatzer A, Lass A, Pinent M, Wong WC, Eisenhaber F, Trajanoski Z. (2010). Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ. Cell Mol Life Sci. 2010 Dec;67(23):4049-64. doi: 10.1007/s00018-010-0424-5. Epub 2010 Jun 15.
Kawase-Koga Y, Low R, Otaegi G, Pollock A, Deng H, Eisenhaber F, Maurer-Stroh S, Sun T. (2010). RNAase-III enzyme Dicer maintains signaling pathways for differentiation and survival in mouse cortical neural stem cells. J Cell Sci. 2010 Feb 15;123(Pt 4):586-94. doi: 10.1242/jcs.059659. Epub 2010 Jan 26.
Eisenhaber B, Eisenhaber F. (2010). Prediction of posttranslational modification of proteins from their amino acid sequence. Methods Mol Biol. 2010;609:365-84. doi: 10.1007/978-1-60327-241-4_21.
Sirota FL, Ooi HS, Gattermayer T, Schneider G, Eisenhaber F, Maurer-Stroh S. (2010). Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset. BMC Genomics. 2010 Feb 10;11 Suppl 1(Suppl 1):S15. doi: 10.1186/1471-2164-11-S1-S15.
Wong WC, Maurer-Stroh S, Eisenhaber F. (2010). More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PLoS Comput Biol. 2010 Jul 29;6(7):e1000867. doi: 10.1371/journal.pcbi.1000867.
Limviphuvadh V, Chua LL, Eisenhaber F, Adhikari S, Maurer-Stroh S. (2010). Is LGI2 the candidate gene for partial epilepsy with pericentral spikes?. J Bioinform Comput Biol. 2010 Feb;8(1):117-27. doi: 10.1142/s0219720010004550.
Schneider G, Wildpaner M, Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. (2010). Integrated tools for biomolecular sequence-based function prediction as exemplified by the ANNOTATOR software environment. Methods Mol Biol. 2010;609:257-67. doi: 10.1007/978-1-60327-241-4_15.
Dhir S, Pacurar M, Franklin D, Gáspári Z, Kertész-Farkas A, Kocsor A, Eisenhaber F, Pongor S. (2010). Detecting atypical examples of known domain types by sequence similarity searching: the SBASE domain library approach. Curr Protein Pept Sci. 2010 Nov;11(7):538-49. doi: 10.2174/138920310794109148.
Ooi HS, Schneider G, Chan YL, Lim TT, Eisenhaber B, Eisenhaber F. (2010). Databases of protein-protein interactions and complexes. Methods Mol Biol. 2010;609:145-59. doi: 10.1007/978-1-60327-241-4_9.
Ooi HS, Schneider G, Lim TT, Chan YL, Eisenhaber B, Eisenhaber F. (2010). Biomolecular pathway databases. Methods Mol Biol. 2010;609:129-44. doi: 10.1007/978-1-60327-241-4_8.
Lee RT, Santos CL, de Paiva TM, Cui L, Sirota FL, Eisenhaber F, Maurer-Stroh S. (2010). All that glitters is not gold–founder effects complicate associations of flu mutations to disease severity. Virol J. 2010 Nov 1;7:297. doi: 10.1186/1743-422X-7-297.
Maurer-Stroh S, Lee RT, Eisenhaber F, Cui L, Phuah SP, Lin RT. (2010). A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. PLoS Curr. 2010 Jun 1;2:RRN1162. doi: 10.1371/currents.rrn1162.
Dhar PK, Thwin CS, Tun K, Tsumoto Y, Maurer-Stroh S, Eisenhaber F, Surana U. (2009). Synthesizing non-natural parts from natural genomic template. J Biol Eng. 2009 Feb 3;3:2. doi: 10.1186/1754-1611-3-2.
Maurer-Stroh S, Ma J, Lee RT, Sirota FL, Eisenhaber F. (2009). Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites. Biol Direct. 2009 May 20;4:18; discussion 18. doi: 10.1186/1745-6150-4-18.
Roser M, Eibl N, Eisenhaber B, Seringer J, Nagel M, Nagorka S, Luft FC, Frei U, Gollasch M. (2009). Gitelman syndrome. Hypertension. 2009 Jun;53(6):893-7. doi: 10.1161/HYPERTENSIONAHA.108.127993. Epub 2009 Apr 6.
Tse WK, Eisenhaber B, Ho SH, Ng Q, Eisenhaber F, Jiang YJ. (2009). Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development. BMC Genomics. 2009 Dec 30;10:637. doi: 10.1186/1471-2164-10-637.
Ranganathan S, Eisenhaber F, Tong JC, Tan TW. (2009). Extending Asia Pacific bioinformatics into new realms in the “-omics” era. BMC Genomics. 2009 Dec 3;10 Suppl 3(Suppl 3):S1. doi: 10.1186/1471-2164-10-S3-S1.
Eisenhaber F, Kwoh CK, Ng SK, Sung WK, Wong L. (2009). Brief overview of bioinformatics activities in Singapore. PLoS Comput Biol. 2009 Sep;5(9):e1000508. doi: 10.1371/journal.pcbi.1000508. Epub 2009 Sep 25.
Grillari J, Löscher M, Denegri M, Lee K, Fortschegger K, Eisenhaber F, Ajuh P, Lamond AI, Katinger H, Grillari-Voglauer R. (2009). Blom7alpha is a novel heterogeneous nuclear ribonucleoprotein K homology domain protein involved in pre-mRNA splicing that interacts with SNEVPrp19-Pso4. J Biol Chem. 2009 Oct 16;284(42):29193-204. doi: 10.1074/jbc.M109.036632. Epub 2009 Jul 29.
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G. (2009). ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W435-40. doi: 10.1093/nar/gkp254. Epub 2009 Apr 23.
Wong WC, Loh M, Eisenhaber F. (2008). On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation. Biol Direct. 2008 Jun 3;3:23. doi: 10.1186/1745-6150-3-23.
Benetka W, Mehlmer N, Maurer-Stroh S, Sammer M, Koranda M, Neumüller R, Betschinger J, Knoblich JA, Teige M, Eisenhaber F. (2008). Experimental testing of predicted myristoylation targets involved in asymmetric cell division and calcium-dependent signalling. Cell Cycle. 2008 Dec;7(23):3709-19. doi: 10.4161/cc.7.23.7176. Epub 2008 Dec 13.
Neuberger G, Schneider G, Eisenhaber F. (2007). pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. Biol Direct. 2007 Jan 12;2:1. doi: 10.1186/1745-6150-2-1.
Maurer-Stroh S, Koranda M, Benetka W, Schneider G, Sirota FL, Eisenhaber F. (2007). Towards complete sets of farnesylated and geranylgeranylated proteins. PLoS Comput Biol. 2007 Apr 6;3(4):e66. doi: 10.1371/journal.pcbi.0030066. Epub 2007 Feb 23.
Eisenhaber B, Chumak N, Eisenhaber F, Hauser MT. (2007). The ring between ring fingers (RBR) protein family. Genome Biol. 2007;8(3):209. doi: 10.1186/gb-2007-8-3-209.
Eisenhaber B, Eisenhaber F. (2007). Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure?. Curr Protein Pept Sci. 2007 Apr;8(2):197-203. doi: 10.2174/138920307780363424.
Watrin E, Schleiffer A, Tanaka K, Eisenhaber F, Nasmyth K, Peters JM. (2006). Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression. Curr Biol. 2006 May 9;16(9):863-74. doi: 10.1016/j.cub.2006.03.049.
Benetka W, Koranda M, Maurer-Stroh S, Pittner F, Eisenhaber F. (2006). Farnesylation or geranylgeranylation? Efficient assays for testing protein prenylation in vitro and in vivo. BMC Biochem. 2006 Feb 28;7:6. doi: 10.1186/1471-2091-7-6.
Novatchkova M, Schneider G, Fritz R, Eisenhaber F, Schleiffer A. (2006). DOUTfinder–identification of distant domain outliers using subsignificant sequence similarity. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W214-8. doi: 10.1093/nar/gkl332.
Mujezinovic N, Raidl G, Hutchins JR, Peters JM, Mechtler K, Eisenhaber F. (2006). Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise. Proteomics. 2006 Oct;6(19):5117-31. doi: 10.1002/pmic.200500928.
Schneider G, Neuberger G, Wildpaner M, Tian S, Berezovsky I, Eisenhaber F. (2006). Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. BMC Bioinformatics. 2006 Mar 21;7:164. doi: 10.1186/1471-2105-7-164.
Kraft C, Vodermaier HC, Maurer-Stroh S, Eisenhaber F, Peters JM. (2005). The WD40 propeller domain of Cdh1 functions as a destruction box receptor for APC/C substrates. Mol Cell. 2005 May 27;18(5):543-53. doi: 10.1016/j.molcel.2005.04.023.
O’Connor E, Eisenhaber B, Dalley J, Wang T, Missen C, Bulleid N, Bishop PN, Trump D. (2005). Species specific membrane anchoring of nyctalopin, a small leucine-rich repeat protein. Hum Mol Genet. 2005 Jul 1;14(13):1877-87. doi: 10.1093/hmg/ddi194. Epub 2005 May 19.
Grillari J, Ajuh P, Stadler G, Löscher M, Voglauer R, Ernst W, Chusainow J, Eisenhaber F, Pokar M, Fortschegger K, Grey M, Lamond AI, Katinger H. (2005). SNEV is an evolutionarily conserved splicing factor whose oligomerization is necessary for spliceosome assembly. Nucleic Acids Res. 2005 Dec 6;33(21):6868-83. doi: 10.1093/nar/gki986. Print 2005.
Maurer-Stroh S, Eisenhaber F. (2005). Refinement and prediction of protein prenylation motifs. Genome Biol. 2005;6(6):R55. doi: 10.1186/gb-2005-6-6-r55. Epub 2005 May 27.
Novatchkova M, Bachmair A, Eisenhaber B, Eisenhaber F. (2005). Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family. BMC Bioinformatics. 2005 Feb 7;6:22. doi: 10.1186/1471-2105-6-22.
Novatchkova M, Wildpaner M, Schweizer D, Eisenhaber F. (2005). PhyloDome–visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W121-5. doi: 10.1093/nar/gki373.
Betschinger J, Eisenhaber F, Knoblich JA. (2005). Phosphorylation-induced autoinhibition regulates the cytoskeletal protein Lethal (2) giant larvae. Curr Biol. 2005 Feb 8;15(3):276-82. doi: 10.1016/j.cub.2005.01.012.
Hackl H, Burkard TR, Sturn A, Rubio R, Schleiffer A, Tian S, Quackenbush J, Eisenhaber F, Trajanoski Z. (2005). Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. Genome Biol. 2005;6(13):R108. doi: 10.1186/gb-2005-6-13-r108. Epub 2005 Dec 19.
Rabitsch KP, Gregan J, Schleiffer A, Javerzat JP, Eisenhaber F, Nasmyth K. (2004). Two fission yeast homologs of Drosophila Mei-S332 are required for chromosome segregation during meiosis I and II. Curr Biol. 2004 Feb 17;14(4):287-301. doi: 10.1016/j.cub.2004.01.051.
Cserzo M, Eisenhaber F, Eisenhaber B, Simon I. (2004). TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics. 2004 Jan 1;20(1):136-7. doi: 10.1093/bioinformatics/btg394.
Novatchkova M, Budhiraja R, Coupland G, Eisenhaber F, Bachmair A. (2004). SUMO conjugation in plants. Planta. 2004 Nov;220(1):1-8. doi: 10.1007/s00425-004-1370-y. Epub 2004 Sep 23.
Lorenz A, Wells JL, Pryce DW, Novatchkova M, Eisenhaber F, McFarlane RJ, Loidl J. (2004). S. pombe meiotic linear elements contain proteins related to synaptonemal complex components. J Cell Sci. 2004 Jul 1;117(Pt 15):3343-51. doi: 10.1242/jcs.01203.
Eisenhaber B, Eisenhaber F, Maurer-Stroh S, Neuberger G. (2004). Prediction of sequence signals for lipid post-translational modifications: insights from case studies. Proteomics. 2004 Jun;4(6):1614-25. doi: 10.1002/pmic.200300781.
Maurer-Stroh S, Eisenhaber F. (2004). Myristoylation of viral and bacterial proteins. Trends Microbiol. 2004 Apr;12(4):178-85. doi: 10.1016/j.tim.2004.02.006.
Maurer-Stroh S, Gouda M, Novatchkova M, Schleiffer A, Schneider G, Sirota FL, Wildpaner M, Hayashi N, Eisenhaber F. (2004). MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins. Genome Biol. 2004;5(3):R21. doi: 10.1186/gb-2004-5-3-r21. Epub 2004 Feb 13.
Novatchkova M, Eisenhaber F. (2004). Linking transcriptional mediators via the GACKIX domain super family. Curr Biol. 2004 Jan 20;14(2):R54-5. doi: 10.1016/j.cub.2003.12.042.
Silverman J, Takai H, Buonomo SB, Eisenhaber F, de Lange T. (2004). Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint. Genes Dev. 2004 Sep 1;18(17):2108-19. doi: 10.1101/gad.1216004.
Neuberger G, Kunze M, Eisenhaber F, Berger J, Hartig A, Brocard C. (2004). Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins. Genome Biol. 2004;5(12):R97. doi: 10.1186/gb-2004-5-12-r97. Epub 2004 Nov 30.
Zimmermann R, Strauss JG, Haemmerle G, Schoiswohl G, Birner-Gruenberger R, Riederer M, Lass A, Neuberger G, Eisenhaber F, Hermetter A, Zechner R. (2004). Fat mobilization in adipose tissue is promoted by adipose triglyceride lipase. Science. 2004 Nov 19;306(5700):1383-6. doi: 10.1126/science.1100747.
Kurzbauer R, Teis D, de Araujo ME, Maurer-Stroh S, Eisenhaber F, Bourenkov GP, Bartunik HD, Hekman M, Rapp UR, Huber LA, Clausen T. (2004). Crystal structure of the p14/MP1 scaffolding complex: how a twin couple attaches mitogen-activated protein kinase signaling to late endosomes. Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10984-9. doi: 10.1073/pnas.0403435101. Epub 2004 Jul 19.
Eisenhaber B, Schneider G, Wildpaner M, Eisenhaber F. (2004). A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe. J Mol Biol. 2004 Mar 19;337(2):243-53. doi: 10.1016/j.jmb.2004.01.025.
Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP. (2003). The Tudor domain ‘Royal Family’: Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem Sci. 2003 Feb;28(2):69-74. doi: 10.1016/S0968-0004(03)00004-5.
Novatchkova M, Leibbrandt A, Werzowa J, Neubüser A, Eisenhaber F. (2003). The STIR-domain superfamily in signal transduction, development and immunity. Trends Biochem Sci. 2003 May;28(5):226-9. doi: 10.1016/S0968-0004(03)00067-7.
Vodermaier HC, Gieffers C, Maurer-Stroh S, Eisenhaber F, Peters JM. (2003). TPR subunits of the anaphase-promoting complex mediate binding to the activator protein CDH1. Curr Biol. 2003 Sep 2;13(17):1459-68. doi: 10.1016/s0960-9822(03)00581-5.
Washietl S, Eisenhaber F. (2003). Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses. BMC Bioinformatics. 2003 Nov 7;4:55. doi: 10.1186/1471-2105-4-55.
Maurer-Stroh S, Washietl S, Eisenhaber F. (2003). Protein prenyltransferases: anchor size, pseudogenes and parasites. Biol Chem. 2003 Jul;384(7):977-89. doi: 10.1515/BC.2003.110.
Maurer-Stroh S, Washietl S, Eisenhaber F. (2003). Protein prenyltransferases. Genome Biol. 2003;4(4):212. doi: 10.1186/gb-2003-4-4-212. Epub 2003 Apr 1.
Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. (2003). Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence. J Mol Biol. 2003 May 2;328(3):581-92. doi: 10.1016/s0022-2836(03)00319-x.
Eisenhaber F, Eisenhaber B, Kubina W, Maurer-Stroh S, Neuberger G, Schneider G, Wildpaner M. (2003). Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1. Nucleic Acids Res. 2003 Jul 1;31(13):3631-4. doi: 10.1093/nar/gkg537.
Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. (2003). Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences. J Mol Biol. 2003 May 2;328(3):567-79. doi: 10.1016/s0022-2836(03)00318-8.
Schleiffer A, Kaitna S, Maurer-Stroh S, Glotzer M, Nasmyth K, Eisenhaber F. (2003). Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners. Mol Cell. 2003 Mar;11(3):571-5. doi: 10.1016/s1097-2765(03)00108-4.
Wick N, Luedemann S, Vietor I, Cotten M, Wildpaner M, Schneider G, Eisenhaber F, Huber LA. (2003). Induction of short interspersed nuclear repeat-containing transcripts in epithelial cells upon infection with a chicken adenovirus. J Mol Biol. 2003 May 9;328(4):779-90. doi: 10.1016/s0022-2836(03)00363-2.
Eisenhaber B, Wildpaner M, Schultz CJ, Borner GH, Dupree P, Eisenhaber F. (2003). Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice. Plant Physiol. 2003 Dec;133(4):1691-701. doi: 10.1104/pp.103.023580.
Eisenhaber B, Maurer-Stroh S, Novatchkova M, Schneider G, Eisenhaber F. (2003). Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins. Bioessays. 2003 Apr;25(4):367-85. doi: 10.1002/bies.10254.
Cserzö M, Eisenhaber F, Eisenhaber B, Simon I. (2002). On filtering false positive transmembrane protein predictions. Protein Eng. 2002 Sep;15(9):745-52. doi: 10.1093/protein/15.9.745.
Maurer-Stroh S, Eisenhaber B, Eisenhaber F. (2002). N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. J Mol Biol. 2002 Apr 5;317(4):523-40. doi: 10.1006/jmbi.2002.5425.
Maurer-Stroh S, Eisenhaber B, Eisenhaber F. (2002). N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J Mol Biol. 2002 Apr 5;317(4):541-57. doi: 10.1006/jmbi.2002.5426.
Ivanov D, Schleiffer A, Eisenhaber F, Mechtler K, Haering CH, Nasmyth K. (2002). Eco1 is a novel acetyltransferase that can acetylate proteins involved in cohesion. Curr Biol. 2002 Feb 19;12(4):323-8. doi: 10.1016/s0960-9822(02)00681-4.
Novatchkova M, Eisenhaber F. (2002). A CH domain-containing N terminus in NuMA?. Protein Sci. 2002 Oct;11(10):2281-4. doi: 10.1110/ps.0221002.
Bachmair A, Novatchkova M, Potuschak T, Eisenhaber F. (2001). Ubiquitylation in plants: a post-genomic look at a post-translational modification. Trends Plant Sci. 2001 Oct;6(10):463-70. doi: 10.1016/s1360-1385(01)02080-5.
Eisenhaber F, Wechselberger C, Kreil G. (2001). The Brix domain protein family – a key to the ribosomal biogenesis pathway?. Trends Biochem Sci. 2001 Jun;26(6):345-7. doi: 10.1016/s0968-0004(01)01851-5.
Wildpaner M, Schneider G, Schleiffer A, Eisenhaber F. (2001). Taxonomy workbench. Bioinformatics. 2001 Dec;17(12):1179-82. doi: 10.1093/bioinformatics/17.12.1179.
Eisenhaber B, Bork P, Eisenhaber F. (2001). Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes. Protein Eng. 2001 Jan;14(1):17-25. doi: 10.1093/protein/14.1.17.
Christian S, Ahorn H, Koehler A, Eisenhaber F, Rodi HP, Garin-Chesa P, Park JE, Rettig WJ, Lenter MC. (2001). Molecular cloning and characterization of endosialin, a C-type lectin-like cell surface receptor of tumor endothelium. J Biol Chem. 2001 Mar 9;276(10):7408-14. doi: 10.1074/jbc.M009604200. Epub 2000 Nov 17.
Christian S, Ahorn H, Novatchkova M, Garin-Chesa P, Park JE, Weber G, Eisenhaber F, Rettig WJ, Lenter MC. (2001). Molecular cloning and characterization of EndoGlyx-1, an EMILIN-like multisubunit glycoprotein of vascular endothelium. J Biol Chem. 2001 Dec 21;276(51):48588-95. doi: 10.1074/jbc.M106152200. Epub 2001 Sep 14.
Novatchkova M, Eisenhaber F. (2001). Can molecular mechanisms of biological processes be extracted from expression profiles? Case study: endothelial contribution to tumor-induced angiogenesis. Bioessays. 2001 Dec;23(12):1159-75. doi: 10.1002/bies.10013.
Senti K, Keleman K, Eisenhaber F, Dickson BJ. (2000). brakeless is required for lamina targeting of R1-R6 axons in the Drosophila visual system. Development. 2000 Jun;127(11):2291-301. doi: 10.1242/dev.127.11.2291.
Rea S, Eisenhaber F, O’Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CD, Jenuwein T. (2000). Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature. 2000 Aug 10;406(6796):593-9. doi: 10.1038/35020506.
Panizza S, Tanaka T, Hochwagen A, Eisenhaber F, Nasmyth K. (2000). Pds5 cooperates with cohesin in maintaining sister chromatid cohesion. Curr Biol. 2000 Dec 14-28;10(24):1557-64. doi: 10.1016/s0960-9822(00)00854-x.
Eisenhaber B, Bork P, Yuan Y, Löffler G, Eisenhaber F. (2000). Automated annotation of GPI anchor sites: case study C. elegans. Trends Biochem Sci. 2000 Jul;25(7):340-1. doi: 10.1016/s0968-0004(00)01601-7.
Eisenhaber B, Bork P, Eisenhaber F. (1999). Prediction of potential GPI-modification sites in proprotein sequences. J Mol Biol. 1999 Sep 24;292(3):741-58. doi: 10.1006/jmbi.1999.3069.
Sunyaev SR, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, Kuznetsov EN. (1999). PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng. 1999 May;12(5):387-94. doi: 10.1093/protein/12.5.387.
Eisenhaber F, Bork P. (1999). Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries. Bioinformatics. 1999 Jul-Aug;15(7-8):528-35. doi: 10.1093/bioinformatics/15.7.528.
Eisenhaber F, Bork P. (1998). Wanted: subcellular localization of proteins based on sequence. Trends Cell Biol. 1998 Apr;8(4):169-70. doi: 10.1016/s0962-8924(98)01226-4.
Eisenhaber B, Bork P, Eisenhaber F. (1998). Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase. Protein Eng. 1998 Dec;11(12):1155-61. doi: 10.1093/protein/11.12.1155.
Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y. (1998). Predicting function: from genes to genomes and back. J Mol Biol. 1998 Nov 6;283(4):707-25. doi: 10.1006/jmbi.1998.2144.
Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P. (1998). Homology-based fold predictions for Mycoplasma genitalium proteins. J Mol Biol. 1998 Jul 17;280(3):323-6. doi: 10.1006/jmbi.1998.1884.
Bork P, Dandekar T, Eisenhaber F, Huynen M. (1998). Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases. J Mol Med (Berl). 1998 Feb;76(2):77-9. doi: 10.1007/s001090050194.
Sunyaev SR, Eisenhaber F, Argos P, Kuznetsov EN, Tumanyan VG. (1998). Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?. Proteins. 1998 May 15;31(3):225-46.
Walther D, Eisenhaber F, Argos P. (1996). Principles of helix-helix packing in proteins: the helical lattice superposition model. J Mol Biol. 1996 Jan 26;255(3):536-53. doi: 10.1006/jmbi.1996.0044.
Eisenhaber F, Frömmel C, Argos P. (1996). Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class. Proteins. 1996 Jun;25(2):169-79. doi: 10.1002/(SICI)1097-0134(199606)25:2<169::AID-PROT3>3.0.CO;2-D.
Eisenhaber F, Imperiale F, Argos P, Frömmel C. (1996). Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods. Proteins. 1996 Jun;25(2):157-68. doi: 10.1002/(SICI)1097-0134(199606)25:2<157::AID-PROT2>3.0.CO;2-F.
Eisenhaber F, Argos P. (1996). Hydrophobic regions on protein surfaces: definition based on hydration shell structure and a quick method for their computation. Protein Eng. 1996 Dec;9(12):1121-33. doi: 10.1093/protein/9.12.1121.
Eisenhaber F. (1996). Hydrophobic regions on protein surfaces. Derivation of the solvation energy from their area distribution in crystallographic protein structures. Protein Sci. 1996 Aug;5(8):1676-86. doi: 10.1002/pro.5560050821.
Eisenhaber F, Persson B, Argos P. (1995). Protein structure prediction: recognition of primary, secondary, and tertiary structural features from amino acid sequence. Crit Rev Biochem Mol Biol. 1995;30(1):1-94. doi: 10.3109/10409239509085139.
Juffer AH, Eisenhaber F, Hubbard SJ, Walther D, Argos P. (1995). Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding. Protein Sci. 1995 Dec;4(12):2499-509. doi: 10.1002/pro.5560041206.
Schrauber H, Eisenhaber F, Argos P. (1993). Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol. 1993 Mar 20;230(2):592-612. doi: 10.1006/jmbi.1993.1172.
Gusev AG, Antsiferova LI, Eisenhaber B. (1993). Prolonged postsynaptic changes in the sensorimotor cortex of the awake rabbit in response to stimulation of fibers of the white matter of the new cortex and the corpus callosum. Neurosci Behav Physiol. 1993 May-Jun;23(3):240-7. doi: 10.1007/BF01182922.
Eisenhaber F, Tumanyan VG, Abagyan RA. (1990). Structure of the hydration shells of oligo(dA-dT).oligo(dA-dT) and oligo(dA).oligo(dT) tracts in B-type conformation on the basis of Monte Carlo calculations. Biopolymers. 1990;30(5-6):563-81. doi: 10.1002/bip.360300509.
Eisenhaber F, Mannik JH, Tumanyan VG. (1990). Structural principles of B-DNA grooves hydration in fibers as revealed by Monte Carlo simulations and X-ray diffraction. Biopolymers. 1990 Aug 15-Sep;29(10-11):1453-64. doi: 10.1002/bip.360291012.
Gusev AG, Zhavoronkova LA, Antsiferova LI, Eisenhaber B. (1989). [Prolonged post-tetanic potentiation in the sensorimotor cortex of the alert rabbit]. Zh Vyssh Nerv Deiat Im I P Pavlova. 1989 Jul-Aug;39(4):752-3.
Eisenhaber F, Tumanyan VG, Eisenmenger F, Gunia W. (1989). Hydration of B-DNA: comparison between the water network around poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) on the basis of Monte Carlo computations. Biopolymers. 1989 Mar;28(3):741-61. doi: 10.1002/bip.360280305.
Eisenhaber F, Tumanian VG. (1988). [Structure of the hydration envelope of the B-form of polydeoxyribonucleotides poly(dA-dC).poly(dG-dT) and poly(dA-dG).poly(dTs-dT) from the data of Monte-Carlo simulation]. Biofizika. 1988 May-Jun;33(3):422-9.
