Publications

2019

Rolland SG, Schneid S, Schwarz M, Rackles E, Fischer C, Haeussler S, Regmi SG, Yeroslaviz A, Habermann B, Mokranjac D, Lambie E, Conradt B. Compromised Mitochondrial Protein Import Acts as a Signal for UPR(mt). Cell Rep. 2019 Aug 13;28(7):1659-1669.e5. doi: 10.1016/j.celrep.2019.07.049. PubMed PMID: 31412237.

Pfeiffer F, Marchfelder A, Habermann B, Dyall-Smith ML. The Genome Sequence of the Halobacterium salinarum Type Strain Is Closely Related to That of Laboratory Strains NRC-1 and R1. Microbiol Resour Announc. 2019 Jul 11;8(28). pii: e00429-19. doi: 10.1128/MRA.00429-19. PubMed PMID: 31296677.

Silva Ramos E, Motori E, Brüser C, Kühl I, Yeroslaviz A, Ruzzenente B, Kauppila JHK, Busch JD, Hultenby K, Habermann BH, Jakobs S, Larsson NG, Mourier A. Mitochondrial fusion is required for regulation of mitochondrial DNA replication. PLoS Genet. 2019 Jun 6;15(6):e1008085. doi:10.1371/journal.pgen.1008085. eCollection 2019 Jun. PubMed PMID: 31170154.

Chabbert D, Caubit X, Roubertoux PL, Carlier M, Habermann B, Jacq B, Salin P, Metwaly M, Frahm C, Fatmi A, Garratt AN, Severac D, Dubois E, Kerkerian-Le Goff L, Fasano L, Gubellini P. Postnatal Tshz3 Deletion Drives Altered Corticostriatal Function and Autism Spectrum Disorder-like Behavior. Biol Psychiatry. 2019 Mar 28. pii: S0006-3223(19)31144-8. doi: 10.1016/j.biopsych.2019.03.974. PubMed PMID: 31060802.

Höpfler M, Kern MJ, Straub T, Prytuliak R, Habermann BH, Pfander B, Jentsch S. Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance. EMBO J. 2019 Apr 23. pii: e100368. doi: 10.15252/embj.2018100368. PubMed PMID: 31015336.

Fan Y, Bazai SK, Daian F, Arechederra M, Richelme S, Temiz NA, Yim A, Habermann BH, Dono R, Largaespada DA, Maina F. Evaluating the landscape of gene cooperativity with receptor tyrosine kinases in liver tumorigenesis using transposon-mediated mutagenesis. J Hepatol. 2019 Mar;70(3):470-482. doi:10.1016/j.jhep.2018.11.027


2018

Zamora-Lagos MA^, Eckstein S^, Langer A, Gazanis A, Pfeiffer F, Habermann B*, Heermann R.* Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain. BMC Genomics. 2018 Nov 29;19(1):854. doi:10.1186/s12864-018-5121-z. PubMed PMID: 30497380. ^ co-first authors; * co-corresponding authors.

Arechederra M, Daian F, Yim A, Bazai SK, Richelme S, Dono R, Saurin AJ, Habermann BH, Maina F. Hypermethylation of gene body CpG islands predicts high dosage of functional oncogenes in liver cancer. Nat Commun. 2018 Aug 8;9(1):3164. doi: 10.1038/s41467-018-05550-5. Erratum in: Nat Commun. 2018 Sep 25;9(1):3976. PubMed PMID: 30089774; PubMed Central PMCID: PMC6082886. (Publisher correction)

Spletter ML, Barz C, Yeroslaviz A, Zhang X, Lemke SB, Bonnard A, Brunner E, Cardone G, Basler K, Habermann BH, Schnorrer F. A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle. Elife. 2018 May 30;7. pii: e34058. doi: 10.7554/eLife.34058. PubMed PMID: 29846170; PubMed Central PMCID: PMC6005683.

Krempel R, Kulkarni P, Yim A, Lang U, Habermann B, Frommolt P. Integrative analysis and machine learning on cancer genomics data using the Cancer Systems Biology Database (CancerSysDB). BMC Bioinformatics. 2018 Apr 24;19(1):156. doi: 10.1186/s12859-018-2157-7. PubMed PMID: 29699486; PubMed Central PMCID: PMC5921751.

Schmähling S, Meiler A, Lee Y, Mohammed A, Finkl K, Tauscher K, Israel L, Wirth M, Philippou-Massier J, Blum H, Habermann B, Imhof A, Song JJ, Müller J. Regulation and function of H3K36 di-methylation by the trithorax-group protein complex AMC. Development. 2018 Apr 5;145(7). pii: dev163808. doi: 10.1242/dev.163808. PubMed PMID: 29540501; PubMed Central PMCID: PMC5963871.

Dürrbaum M, Kruse C, Nieken KJ, Habermann B, Storchová Z. The deregulated microRNAome contributes to the cellular response to aneuploidy. BMC Genomics. 2018 Mar 14;19(1):197. doi: 10.1186/s12864-018-4556-6. PubMed PMID: 29703144.

Donohoe CD, Csordás G, Correia A, Jindra M, Klein C, Habermann B, Uhlirova M. Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture. PLoS Genet. 2018 Mar 1;14(3):e1007241. doi: 10.1371/journal.pgen.1007241. eCollection 2018 Mar. PubMed PMID: 29494583; PubMed Central PMCID: PMC5849342.

Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW. The axolotl genome and the evolution of key tissue formation regulators. Nature. 2018 Feb 1;554(7690):50-55. doi: 10.1038/nature25458. Epub 2018 Jan 24. Erratum in: Nature. 2018 Jul;559(7712):E2. PubMed PMID: 29364872. (Author correction)

Prytuliak R, Pfeiffer F, Habermann BH. SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data. BMC Bioinformatics. 2018 Jan 26;19(1):24. doi: 10.1186/s12859-018-2020-x. PubMed PMID: 29373955; PubMed Central PMCID: PMC5787307.

Ramírez F, Bhardwaj V, Arrigoni L, Lam KC, Grüning BA, Villaveces J, Habermann B, Akhtar A, Manke T. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat Commun. 2018 Jan 15;9(1):189. doi: 10.1038/s41467-017-02525-w. PubMed PMID: 29335486; PubMed Central PMCID: PMC5768762.

Pfeiffer F^, Zamora-Lagos MA^, Blettinger M, Yeroslaviz A, Dahl A, Gruber S*, Habermann BH.* The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains. BMC Genomics. 2018 Jan 5;19(1):20. doi: 10.1186/s12864-017-4301-6. PubMed PMID: 29304740; PubMed Central PMCID: PMC5756416. ^ co-first authors; * co-corresponding authors.


2017

Pfeiffer F, Bagyan I, Alfaro-Espinoza G, Zamora-Lagos MA, Habermann B, Marin-Sanguino A, Oesterhelt D, Kunte HJ. Revision and reannotation of the Halomonas elongata DSM 2581(T) genome. Microbiologyopen. 2017 Aug;6(4). doi: 10.1002/mbo3.465. Epub 2017 Mar 27. PubMed PMID: 28349658; PubMed Central PMCID: PMC5552945.

Prytuliak R, Volkmer M, Meier M, Habermann BH. HH-MOTiF: de novo detection of short linear motifs in proteins by Hidden Markov Model comparisons. Nucleic Acids Res. 2017 Jul 3;45(W1):W470-W477. doi: 10.1093/nar/gkx341. PubMed PMID: 28460141; PubMed Central PMCID: PMC5570144. (Author correction)

Papanikos F, Daniel K, Goercharn-Ramlal A, Fei JF, Kurth T, Wojtasz L, Dereli I, Fu J, Penninger J, Habermann B, Surani A, Stewart AF, Toth A. The enigmatic meiotic dense body and its newly discovered component, SCML1, are dispensable for fertility and gametogenesis in mice. Chromosoma. 2017 Jun;126(3):399-415. doi: 10.1007/s00412-016-0598-1. Epub 2016 May 10. PubMed PMID: 27165042.

Sun S, Habermann BH. A Guide to Computational Methods for Predicting Mitochondrial Localization. Methods Mol Biol. 2017;1567:1-14. doi: 10.1007/978-1-4939-6824-4_1. PubMed PMID: 28276009.


2016

Book Chapter: Habermann, BH. 2016. Evolutionary Biology pp 393-419: Oh Brother, Where Art Thou? Finding Orthologs in the Twilight and Midnight Zones of Sequence Similarity (Springer link).

Roth S, Bergmann H, Jaeger M, Yeroslaviz A, Neumann K, Koenig PA, Prazeres da Costa C, Vanes L, Kumar V, Johnson M, Menacho-Márquez M, Habermann B, Tybulewicz VL, Netea M, Bustelo XR, Ruland J. Vav Proteins Are Key Regulators of Card9 Signaling for Innate Antifungal Immunity. Cell Rep. 2016 Dec 6;17(10):2572-2583. doi: 10.1016/j.celrep.2016.11.018. PubMed PMID: 27926862; PubMed Central PMCID: PMC5177621.

Le HQ, Ghatak S, Yeung CY, Tellkamp F, Günschmann C, Dieterich C, Yeroslaviz A, Habermann B, Pombo A, Niessen CM, Wickström SA. Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment. Nat Cell Biol. 2016 Aug;18(8):864-75. doi: 10.1038/ncb3387. Epub 2016 Jul 11. PubMed PMID: 27398909.

Nakel K, Bonneau F, Basquin C, Habermann B, Eckmann CR, Conti E. Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity. RNA. 2016 Aug;22(8):1139-45. doi: 10.1261/rna.056598.116. Epub 2016 Jun 10. PubMed PMID: 27288313; PubMed Central PMCID: PMC4931106.

Kowalinski E, Kögel A, Ebert J, Reichelt P, Stegmann E, Habermann B, Conti E. Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex. Mol Cell. 2016 Jul 7;63(1):125-34. doi: 10.1016/j.molcel.2016.05.028. Epub 2016 Jun 23. PubMed PMID: 27345150; PubMed Central PMCID: PMC4942675.

Crevenna AH, Blank B, Maiser A, Emin D, Prescher J, Beck G, Kienzle C, Bartnik K, Habermann B, Pakdel M, Leonhardt H, Lamb DC, von Blume J. Secretory cargo sorting by Ca2+-dependent Cab45 oligomerization at the trans-Golgi network. J Cell Biol. 2016 May 9;213(3):305-14. doi: 10.1083/jcb.201601089. Epub 2016 May 2. PubMed PMID: 27138253; PubMed Central PMCID: PMC4862333.

Braun F, Rinschen MM, Bartels V, Frommolt P, Habermann B, Hoeijmakers JH, Schumacher B, Dollé ME, Müller RU, Benzing T, Schermer B, Kurschat CE. Altered lipid metabolism in the aging kidney identified by three layered omic analysis. Aging (Albany NY). 2016 Mar;8(3):441-57. PubMed PMID: 26886165; PubMed Central PMCID: PMC4833139.


2015

Lee SH, Princz LN, Klügel MF, Habermann B, Pfander B, Biertümpfel C. Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage. Elife. 2015 Dec 18;4. pii: e12256. doi: 10.7554/eLife.12256. PubMed PMID: 26682650; PubMed Central PMCID: PMC5039027.

Garmhausen M, Hofmann F, Senderov V, Thomas M, Kandel BA, Habermann BH. Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways. BMC Genomics. 2015 Oct 14;16:790. doi: 10.1186/s12864-015-2017-z. PubMed PMID: 26467653; PubMed Central PMCID: PMC4606501.

Gebhardt A, Habjan M, Benda C, Meiler A, Haas DA, Hein MY, Mann A, Mann M, Habermann B, Pichlmair A. mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3. Nat Commun. 2015 Sep 18;6:8192. doi: 10.1038/ncomms9192. PubMed PMID: 26382858; PubMed Central PMCID: PMC4595607.

Villaveces JM, Koti P, Habermann BH. Tools for visualization and analysis of molecular networks, pathways, and -omics data. Adv Appl Bioinform Chem. 2015 Jun 4;8:11-22. doi: 10.2147/AABC.S63534. eCollection 2015. Review. PubMed PMID: 26082651; PubMed Central PMCID: PMC4461095.

Villaveces JM, Jiménez RC, Porras P, Del-Toro N, Duesbury M, Dumousseau M, Orchard S, Choi H, Ping P, Zong NC, Askenazi M, Habermann BH, Hermjakob H. Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. Database (Oxford). 2015 Feb 4;2015. pii: bau131. doi: 10.1093/database/bau131. Print 2015. PubMed PMID: 25652942; PubMed Central PMCID: PMC4316181.

Spletter ML, Barz C, Yeroslaviz A, Schönbauer C, Ferreira IR, Sarov M, Gerlach D, Stark A, Habermann BH, Schnorrer F. The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle. EMBO Rep. 2015 Feb;16(2):178-91. doi: 10.15252/embr.201439791. Epub 2014 Dec 22. PubMed PMID: 25532219; PubMed Central PMCID: PMC4328745.

Stingele J, Habermann B, Jentsch S. DNA-protein crosslink repair: proteases as DNA repair enzymes. Trends Biochem Sci. 2015 Feb;40(2):67-71. doi: 10.1016/j.tibs.2014.10.012. Epub 2014 Dec 9. PubMed PMID: 25496645.


2014

Baggio F, Bratic A, Mourier A, Kauppila TE, Tain LS, Kukat C, Habermann B, Partridge L, Larsson NG. Drosophila melanogaster LRPPRC2 is involved in coordination of mitochondrial translation. Nucleic Acids Res. 2014 Dec 16;42(22):13920-38. doi: 10.1093/nar/gku1132. Epub 2014 Nov 26. PubMed PMID: 25428350; PubMed Central PMCID: PMC4267620.

Nousch M, Yeroslaviz A, Habermann B, Eckmann CR. The cytoplasmic poly(A) polymerases GLD-2 and GLD-4 promote general gene expression via distinct mechanisms. Nucleic Acids Res. 2014 Oct;42(18):11622-33. doi: 10.1093/nar/gku838. Epub 2014 Sep 12. PubMed PMID: 25217583; PubMed Central PMCID: PMC4191412.

Kienzle C, Basnet N, Crevenna AH, Beck G, Habermann B, Mizuno N, von Blume J. Cofilin recruits F-actin to SPCA1 and promotes Ca2+-mediated secretory cargo sorting. J Cell Biol. 2014 Sep 1;206(5):635-54. doi: 10.1083/jcb.201311052. PubMed PMID: 25179631; PubMed Central PMCID: PMC4151145.

Wagner I, Volkmer M, Sharan M, Villaveces JM, Oswald F, Surendranath V, Habermann BH. morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring. BMC Bioinformatics. 2014 Aug 6;15:263. doi: 10.1186/1471-2105-15-263. PubMed PMID: 25096057; PubMed Central PMCID: PMC4137093.

Gritenaite D, Princz LN, Szakal B, Bantele SC, Wendeler L, Schilbach S, Habermann BH, Matos J, Lisby M, Branzei D, Pfander B. A cell cycle-regulated Slx4-Dpb11 complex promotes the resolution of DNA repair intermediates linked to stalled replication. Genes Dev. 2014 Jul 15;28(14):1604-19. doi: 10.1101/gad.240515.114. PubMed PMID: 25030699; PubMed Central PMCID: PMC4102767.

Villaveces JM, Jimenez RC, Habermann BH. PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers. F1000Res. 2014 Feb 13;3:44. doi: 10.12688/f1000research.3-44.v1. eCollection 2014. PubMed PMID: 25075287; PubMed Central PMCID: PMC4097353.

Villaveces JM, Jimenez RC, Habermann BH. KEGGViewer, a BioJS component to visualize KEGG Pathways. F1000Res. 2014 Feb 13;3:43. doi: 10.12688/f1000research.3-43.v1. eCollection 2014. PubMed PMID: 24715980; PubMed Central PMCID: PMC3954160.

Metodiev MD, Spåhr H, Loguercio Polosa P, Meharg C, Becker C, Altmueller J, Habermann B, Larsson NG, Ruzzenente B. NSUN4 is a dual function mitochondrial protein required for both methylation of 12S rRNA and coordination of mitoribosomal assembly. PLoS Genet. 2014 Feb 6;10(2):e1004110. doi: 10.1371/journal.pgen.1004110. eCollection 2014 Feb. PubMed PMID: 24516400; PubMed Central PMCID: PMC3916286.

Deceglie S, Lionetti C, Stewart JB, Habermann B, Roberti M, Cantatore P, Loguercio Polosa P. Characterization of the sea urchin mitochondrial transcription factor A reveals unusual features. Mitochondrion. 2014 Jan;14(1):34-41. doi: 10.1016/j.mito.2013.10.003. Epub 2013 Nov 1. PubMed PMID: 24184823.


2013

Erkut C, Vasilj A, Boland S, Habermann B, Shevchenko A, Kurzchalia TV. Molecular strategies of the Caenorhabditis elegans dauer larva to survive extreme desiccation. PLoS One. 2013 Dec 4;8(12):e82473. doi: 10.1371/journal.pone.0082473. eCollection 2013. PubMed PMID: 24324795; PubMed Central PMCID: PMC3853187.

Oortveld MA, Keerthikumar S, Oti M, Nijhof B, Fernandes AC, Kochinke K, Castells-Nobau A, van Engelen E, Ellenkamp T, Eshuis L, Galy A, van Bokhoven H, Habermann B, Brunner HG, Zweier C, Verstreken P, Huynen MA, Schenck A. Human intellectual disability genes form conserved functional modules in Drosophila. PLoS Genet. 2013 Oct;9(10):e1003911. doi: 10.1371/journal.pgen.1003911. Epub 2013 Oct 31. PubMed PMID: 24204314; PubMed Central PMCID: PMC3814316.

Schermer B, Bartels V, Frommolt P, Habermann B, Braun F, Schultze JL, Roodbergen M, Hoeijmakers JH, Schumacher B, Nürnberg P, Dollé ME, Benzing T, Müller RU, Kurschat CE. Transcriptional profiling reveals progeroid Ercc1(-/Δ) mice as a model system for glomerular aging. BMC Genomics. 2013 Aug 16;14:559. doi: 10.1186/1471-2164-14-559. PubMed PMID: 23947592; PubMed Central PMCID: PMC3751413.

Knapp D, Schulz H, Rascon CA, Volkmer M, Scholz J, Nacu E, Le M, Novozhilov S, Tazaki A, Protze S, Jacob T, Hubner N, Habermann B, Tanaka EM. Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program. PLoS One. 2013 May 1;8(5):e61352. doi: 10.1371/journal.pone.0061352. Print 2013. PubMed PMID: 23658691; PubMed Central PMCID: PMC3641036.

Terzioglu M, Ruzzenente B, Harmel J, Mourier A, Jemt E, López MD, Kukat C, Stewart JB, Wibom R, Meharg C, Habermann B, Falkenberg M, Gustafsson CM, Park CB, Larsson NG. MTERF1 binds mtDNA to prevent transcriptional interference at the light-strand promoter but is dispensable for rRNA gene transcription regulation. Cell Metab. 2013 Apr 2;17(4):618-26. doi: 10.1016/j.cmet.2013.03.006. PubMed PMID: 23562081.

Book Chapter: Surendranath V, Theis M, Habermann BH, Buchholz F. Designing efficient and specific endoribonuclease-prepared siRNAs. Methods Mol Biol. 2013;942:193-204. doi: 10.1007/978-1-62703-119-6_11. PubMed PMID: 23027053.

Stewart R, Rascón CA, Tian S, Nie J, Barry C, Chu LF, Ardalani H, Wagner RJ, Probasco MD, Bolin JM, Leng N, Sengupta S, Volkmer M, Habermann B, Tanaka EM, Thomson JA, Dewey CN. Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. PLoS Comput Biol. 2013;9(3):e1002936. doi: 10.1371/journal.pcbi.1002936. Epub 2013 Mar 7. PubMed PMID: 23505351; PubMed Central PMCID: PMC3591270.

Heestand BN, Shen Y, Liu W, Magner DB, Storm N, Meharg C, Habermann B, Antebi A. Dietary restriction induced longevity is mediated by nuclear receptor NHR-62 in Caenorhabditis elegans. PLoS Genet. 2013;9(7):e1003651. doi: 10.1371/journal.pgen.1003651. Epub 2013 Jul 25. PubMed PMID: 23935515; PubMed Central PMCID: PMC3723528.

Wredenberg A, Lagouge M, Bratic A, Metodiev MD, Spåhr H, Mourier A, Freyer C, Ruzzenente B, Tain L, Grönke S, Baggio F, Kukat C, Kremmer E, Wibom R, Polosa PL, Habermann B, Partridge L, Park CB, Larsson NG. MTERF3 regulates mitochondrial ribosome biogenesis in invertebrates and mammals. PLoS Genet. 2013;9(1):e1003178. doi: 10.1371/journal.pgen.1003178. Epub 2013 Jan 3. PubMed PMID: 23300484; PubMed Central PMCID: PMC3536695.


2012

Spåhr H, Habermann B, Gustafsson CM, Larsson NG, Hallberg BM. Structure of the human MTERF4-NSUN4 protein complex that regulates mitochondrial ribosome biogenesis. Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15253-8. Epub 2012 Sep 4. PubMed PMID: 22949673; PubMed Central PMCID: PMC3458362.

Winter JF, Höpfner S, Korn K, Farnung BO, Bradshaw CR, Marsico G, Volkmer M, Habermann B, Zerial M. Caenorhabditis elegans screen reveals role of PAR-5 in RAB-11-recycling endosome positioning and apicobasal cell polarity. Nat Cell Biol. 2012 May 27;14(7):666-76. doi: 10.1038/ncb2508. PubMed PMID: 22634595.

Stein M, Pilli M, Bernauer S, Habermann BH, Zerial M, Wade RC. The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity. PLoS One. 2012;7(4):e34870. doi: 10.1371/journal.pone.0034870. Epub 2012 Apr 16. PubMed PMID: 22523562; PubMed Central PMCID: PMC3327705.


2011

Bratic A, Wredenberg A, Grönke S, Stewart JB, Mourier A, Ruzzenente B, Kukat C, Wibom R, Habermann B, Partridge L, Larsson NG. The bicoid stability factor controls polyadenylation and expression of specific mitochondrial mRNAs in Drosophila melanogaster. PLoS Genet. 2011 Oct;7(10):e1002324. doi: 10.1371/journal.pgen.1002324. Epub 2011 Oct 13. PubMed PMID: 22022283; PubMed Central PMCID: PMC3192837.

Cámara Y, Asin-Cayuela J, Park CB, Metodiev MD, Shi Y, Ruzzenente B, Kukat C, Habermann B, Wibom R, Hultenby K, Franz T, Erdjument-Bromage H, Tempst P, Hallberg BM, Gustafsson CM, Larsson NG. MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome. Cell Metab. 2011 May 4;13(5):527-39. doi: 10.1016/j.cmet.2011.04.002. PubMed PMID: 21531335.

Bradshaw CR, Surendranath V, Henschel R, Mueller MS, Habermann BH. HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. PLoS One. 2011 Mar 10;6(3):e17568. doi: 10.1371/journal.pone.0017568. PubMed PMID: 21423752; PubMed Central PMCID: PMC3053371.


2010

O'Donnell L, Panier S, Wildenhain J, Tkach JM, Al-Hakim A, Landry MC, Escribano-Diaz C, Szilard RK, Young JT, Munro M, Canny MD, Kolas NK, Zhang W, Harding SM, Ylanko J, Mendez M, Mullin M, Sun T, Habermann B, Datti A, Bristow RG, Gingras AC, Tyers MD, Brown GW, Durocher D. The MMS22L-TONSL complex mediates recovery from replication stress and homologous recombination. Mol Cell. 2010 Nov 24;40(4):619-31. doi: 10.1016/j.molcel.2010.10.024. Epub 2010 Nov 4. PubMed PMID: 21055983; PubMed Central PMCID: PMC3031522.

Pulvers JN, Bryk J, Fish JL, Wilsch-Bräuninger M, Arai Y, Schreier D, Naumann R, Helppi J, Habermann B, Vogt J, Nitsch R, Tóth A, Enard W, Pääbo S, Huttner WB. Mutations in mouse Aspm (abnormal spindle-like microcephaly associated) cause not only microcephaly but also major defects in the germline. Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16595-600. doi: 10.1073/pnas.1010494107. Epub 2010 Sep 7. PubMed PMID: 20823249; PubMed Central PMCID: PMC2944708.

Gloor Y, Schöne M, Habermann B, Ercan E, Beck M, Weselek G, Müller-Reichert T, Walch-Solimena C. Interaction between Sec7p and Pik1p: the first clue for the regulation of a coincidence detection signal. Eur J Cell Biol. 2010 Aug;89(8):575-83. doi: 10.1016/j.ejcb.2010.02.004. PubMed PMID: 20434792.

Surendranath V, Chusainow J, Hauber J, Buchholz F, Habermann BH. SeLOX--a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W293-8. doi: 10.1093/nar/gkq523. Epub 2010 Jun 6. PubMed PMID: 20529878; PubMed Central PMCID: PMC2896191.

Katis VL, Lipp JJ, Imre R, Bogdanova A, Okaz E, Habermann B, Mechtler K, Nasmyth K, Zachariae W. Rec8 phosphorylation by casein kinase 1 and Cdc7-Dbf4 kinase regulates cohesin cleavage by separase during meiosis. Dev Cell. 2010 Mar 16;18(3):397-409. doi: 10.1016/j.devcel.2010.01.014. PubMed PMID: 20230747; PubMed Central PMCID: PMC2994640.

Collinet C, Stöter M, Bradshaw CR, Samusik N, Rink JC, Kenski D, Habermann B, Buchholz F, Henschel R, Mueller MS, Nagel WE, Fava E, Kalaidzidis Y, Zerial M. Systems survey of endocytosis by multiparametric image analysis. Nature. 2010 Mar 11;464(7286):243-9. doi: 10.1038/nature08779. Epub 2010 Feb 28. Erratum in: Nature. 2014 Sep 18;513(7518):444. PubMed PMID: 20190736.


2009

Oliver H, Diallo G, de Quincey E, Alexopoulou D, Habermann B, Kostkova P, Schroeder M, Jupp S, Khelif K, Stevens R, Jawaheer G, Madle G. A user-centred evaluation framework for the Sealife semantic web browsers. BMC Bioinformatics. 2009 Oct 1;10 Suppl 10:S14. doi: 10.1186/1471-2105-10-S10-S14. PubMed PMID: 19796398; PubMed Central PMCID: PMC2755822.

Erler A, Wegmann S, Elie-Caille C, Bradshaw CR, Maresca M, Seidel R, Habermann B, Muller DJ, Stewart AF. Conformational adaptability of Redbeta during DNA annealing and implications for its structural relationship with Rad52. J Mol Biol. 2009 Aug 21;391(3):586-98. doi: 10.1016/j.jmb.2009.06.030. Epub 2009 Jun 13. PubMed PMID: 19527729.

Lawo S, Bashkurov M, Mullin M, Ferreria MG, Kittler R, Habermann B, Tagliaferro A, Poser I, Hutchins JR, Hegemann B, Pinchev D, Buchholz F, Peters JM, Hyman AA, Gingras AC, Pelletier L. HAUS, the 8-subunit human Augmin complex, regulates centrosome and spindle integrity. Curr Biol. 2009 May 26;19(10):816-26. doi: 10.1016/j.cub.2009.04.033. Epub 2009 May 7. PubMed PMID: 19427217.


2008

Entchev EV, Schwudke D, Zagoriy V, Matyash V, Bogdanova A, Habermann B, Zhu L, Shevchenko A, Kurzchalia TV. LET-767 is required for the production of branched chain and long chain fatty acids in Caenorhabditis elegans. J Biol Chem. 2008 Jun 20;283(25):17550-60. doi: 10.1074/jbc.M800965200. Epub 2008 Apr 4. PubMed PMID: 18390550.

Schenck A, Goto-Silva L, Collinet C, Rhinn M, Giner A, Habermann B, Brand M, Zerial M. The endosomal protein Appl1 mediates Akt substrate specificity and cell survival in vertebrate development. Cell. 2008 May 2;133(3):486-97. doi: 10.1016/j.cell.2008.02.044. PubMed PMID: 18455989.

Demmel L, Gravert M, Ercan E, Habermann B, Müller-Reichert T, Kukhtina V, Haucke V, Baust T, Sohrmann M, Kalaidzidis Y, Klose C, Beck M, Peter M, Walch-Solimena C. The clathrin adaptor Gga2p is a phosphatidylinositol 4-phosphate effector at the Golgi exit. Mol Biol Cell. 2008 May;19(5):1991-2002. doi: 10.1091/mbc.E06-10-0937. Epub 2008 Feb 20. PubMed PMID: 18287542; PubMed Central PMCID: PMC2366843.

Shevchenko A, Roguev A, Schaft D, Buchanan L, Habermann B, Sakalar C, Thomas H, Krogan NJ, Shevchenko A, Stewart AF. Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol. 2008;9(11):R167. doi: 10.1186/gb-2008-9-11-r167. Epub 2008 Nov 28. PubMed PMID: 19040720; PubMed Central PMCID: PMC2614481.


2007

Kittler R, Pelletier L, Heninger AK, Slabicki M, Theis M, Miroslaw L, Poser I, Lawo S, Grabner H, Kozak K, Wagner J, Surendranath V, Richter C, Bowen W, Jackson AL, Habermann B, Hyman AA, Buchholz F. Genome-scale RNAi profiling of cell division in human tissue culture cells. Nat Cell Biol. 2007 Dec;9(12):1401-12. Epub 2007 Nov 11. PubMed PMID: 17994010.

Kittler R^, Surendranath V^, Heninger AK, Slabicki M, Theis M, Putz G, Franke K, Caldarelli A, Grabner H, Kozak K, Wagner J, Rees E, Korn B, Frenzel C, Sachse C, Sönnichsen B, Guo J, Schelter J, Burchard J, Linsley PS, Jackson AL, Habermann B*, Buchholz F.* Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies. Nat Methods. 2007 Apr;4(4):337-44. Epub 2007 Mar 11. PubMed PMID: 17351622. ^co-first authors; * co-corresponding authors.

Dong Y, Bogdanova A, Habermann B, Zachariae W, Ahringer J. Identification of the C. elegans anaphase promoting complex subunit Cdc26 by phenotypic profiling and functional rescue in yeast. BMC Dev Biol. 2007 Mar 20;7:19. PubMed PMID: 17374146; PubMed Central PMCID: PMC1847674.


2006

Demontis F, Habermann B, Dahmann C. PDZ-domain-binding sites are common among cadherins. Dev Genes Evol. 2006 Nov;216(11):737-41. Epub 2006 Oct 5. PubMed PMID: 17021864.

Bradshaw CR, Surendranath V, Habermann B. ProFAT: a web-based tool for the functional annotation of protein sequences. BMC Bioinformatics. 2006 Oct 23;7:466. PubMed PMID: 17059594; PubMed Central PMCID: PMC1636073. doi: 10.1186/1471-2105-7-466

Dolznig H, Grebien F, Deiner EM, Stangl K, Kolbus A, Habermann B, Kerenyi MA, Kieslinger M, Moriggl R, Beug H, Müllner EW. Erythroid progenitor renewal versus differentiation: genetic evidence for cell autonomous, essential functions of EpoR, Stat5 and the GR. Oncogene. 2006 May 11;25(20):2890-900. PubMed PMID: 16407844; PubMed Central PMCID: PMC3035873.

Schroeder M, Burger A, Kostkova P, Stevens R, Habermann B, Dieng-Kuntz R. Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases. Stud Health Technol Inform. 2006;120:167-78. PubMed PMID: 16823135.


2005

Zayas RM, Hernández A, Habermann B, Wang Y, Stary JM, Newmark PA. The planarian Schmidtea mediterranea as a model for epigenetic germ cell specification: analysis of ESTs from the hermaphroditic strain. Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18491-6. Epub 2005 Dec 12. Erratum in: Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):19033. PubMed PMID: 16344473; PubMed Central PMCID: PMC1317986.

Itoh T, Erdmann KS, Roux A, Habermann B, Werner H, De Camilli P. Dynamin and the actin cytoskeleton cooperatively regulate plasma membrane invagination by BAR and F-BAR proteins. Dev Cell. 2005 Dec;9(6):791-804. PubMed PMID: 16326391.

Kittler R, Heninger AK, Franke K, Habermann B, Buchholz F. Production of endoribonuclease-prepared short interfering RNAs for gene silencing in mammalian cells. Nat Methods. 2005 Oct;2(10):779-84. PubMed PMID: 16179925.

Ozlü N, Srayko M, Kinoshita K, Habermann B, O'toole ET, Müller-Reichert T, Schmalz N, Desai A, Hyman AA. An essential function of the C. elegans ortholog of TPX2 is to localize activated aurora A kinase to mitotic spindles. Dev Cell. 2005 Aug;9(2):237-48. PubMed PMID: 16054030.

Pelkmans L, Fava E, Grabner H, Hannus M, Habermann B, Krausz E, Zerial M. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature. 2005 Jul 7;436(7047):78-86. Epub 2005 May 11. PubMed PMID: 15889048.

Maddox AS, Habermann B, Desai A, Oegema K. Distinct roles for two C. elegans anillins in the gonad and early embryo. Development. 2005 Jun;132(12):2837-48. PubMed PMID: 15930113.


2004

Kittler R, Putz G, Pelletier L, Poser I, Heninger AK, Drechsel D, Fischer S, Konstantinova I, Habermann B, Grabner H, Yaspo ML, Himmelbauer H, Korn B, Neugebauer K, Pisabarro MT, Buchholz F. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature. 2004 Dec 23;432(7020):1036-40. PubMed PMID: 15616564.

Dammermann A, Müller-Reichert T, Pelletier L, Habermann B, Desai A, Oegema K. Centriole assembly requires both centriolar and pericentriolar material proteins. Dev Cell. 2004 Dec;7(6):815-29. PubMed PMID: 15572125.

Joosten M, Blázquez-Domingo M, Lindeboom F, Boulmé F, Van Hoven-Beijen A, Habermann B, Löwenberg B, Beug H, Müllner EW, Delwel R, Von Lindern M. Translational control of putative protooncogene Nm23-M2 by cytokines via phosphoinositide 3-kinase signaling. J Biol Chem. 2004 Sep 10;279(37):38169-76. Epub 2004 Jul 7. PubMed PMID: 15247270.

Liska AJ, Popov AV, Sunyaev S, Coughlin P, Habermann B, Shevchenko A, Bork P, Karsenti E, Shevchenko A. Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome. Proteomics. 2004 Sep;4(9):2707-21. PubMed PMID: 15352245.

Putta S, Smith JJ, Walker JA, Rondet M, Weisrock DW, Monaghan J, Samuels AK, Kump K, King DC, Maness NJ, Habermann B, Tanaka E, Bryant SV, Gardiner DM, Parichy DM, Voss SR. From biomedicine to natural history research: EST resources for ambystomatid salamanders. BMC Genomics. 2004 Aug 13;5(1):54. PubMed PMID: 15310388; PubMed Central PMCID: PMC509418.

Henschel A, Buchholz F, Habermann B. DEQOR: a web-based tool for the design and quality control of siRNAs. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W113-20. PubMed PMID: 15215362; PubMed Central PMCID: PMC441546. doi: 10.1093/nar/gkh408.

Pelletier L, Ozlü N, Hannak E, Cowan C, Habermann B, Ruer M, Müller-Reichert T, Hyman AA. The Caenorhabditis elegans centrosomal protein SPD-2 is required for both pericentriolar material recruitment and centriole duplication. Curr Biol. 2004 May 25;14(10):863-73. Erratum in: Curr Biol. 2006 Jun 20;16(12):1255. PubMed PMID: 15186742.

Schwickart M, Havlis J, Habermann B, Bogdanova A, Camasses A, Oelschlaegel T, Shevchenko A, Zachariae W. Swm1/Apc13 is an evolutionarily conserved subunit of the anaphase-promoting complex stabilizing the association of Cdc16 and Cdc27. Mol Cell Biol. 2004 Apr;24(8):3562-76. PubMed PMID: 15060174; PubMed Central PMCID: PMC381669.

Habermann B. The BAR-domain family of proteins: a case of bending and binding? EMBO Rep. 2004 Mar;5(3):250-5. Review. PubMed PMID: 14993925; PubMed Central PMCID: PMC1299016. DOI 10.1038/sj.embor.7400105.

Habermann B, Oegema J, Sunyaev S, Shevchenko A. The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches. Mol Cell Proteomics. 2004 Mar;3(3):238-49. Epub 2003 Dec 26. PubMed PMID: 14695901. doi: 10.1074/mcp.M300073-MCP200.

Miaczynska M, Christoforidis S, Giner A, Shevchenko A, Uttenweiler-Joseph S, Habermann B, Wilm M, Parton RG, Zerial M. APPL proteins link Rab5 to nuclear signal transduction via an endosomal compartment. Cell. 2004 Feb 6;116(3):445-56. PubMed PMID: 15016378.

Habermann B*, Bebin AG, Herklotz S, Volkmer M, Eckelt K, Pehlke K, Epperlein HH, Schackert HK, Wiebe G, Tanaka EM*. An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries. Genome Biol. 2004;5(9):R67. Epub 2004 Aug 13. PubMed PMID: 15345051; PubMed Central PMCID: PMC522874. doi: 10.1186/gb-2004-5-9-r67. * co-corresponding authors.


1993 - 2003

Spitzenberger F, Pietropaolo S, Verkade P, Habermann B, Lacas-Gervais S, Mziaut H, Pietropaolo M, Solimena M. Islet cell autoantigen of 69 kDa is an arfaptin-related protein associated with the Golgi complex of insulinoma INS-1 cells. J Biol Chem. 2003 Jul 11;278(28):26166-73. Epub 2003 Apr 7. PubMed PMID: 12682071.

Dolznig H^, Habermann B^, Stangl K^, Deiner EM, Moriggl R, Beug H, Müllner EW. Apoptosis protection by the Epo target Bcl-X(L) allows factor-independent differentiation of primary erythroblasts. Curr Biol. 2002 Jul 9;12(13):1076-85. PubMed PMID: 12121614. ^co-first authors.

Kinoshita K, Habermann B, Hyman AA. XMAP215: a key component of the dynamic microtubule cytoskeleton. Trends Cell Biol. 2002 Jun;12(6):267-73. Review. PubMed PMID: 12074886.

Hannak E, Oegema K, Kirkham M, Gönczy P, Habermann B, Hyman AA. The kinetically dominant assembly pathway for centrosomal asters in Caenorhabditis elegans is gamma-tubulin dependent. J Cell Biol. 2002 May 13;157(4):591-602. Epub 2002 May 13. PubMed PMID: 12011109; PubMed Central PMCID: PMC2173857.

Severin F, Habermann B, Huffaker T, Hyman T. Stu2 promotes mitotic spindle elongation in anaphase. J Cell Biol. 2001 Apr 16;153(2):435-42. PubMed PMID: 11309422; PubMed Central PMCID: PMC2169465.

Mikulits W, Pradet-Balade B, Habermann B, Beug H, Garcia-Sanz JA, Müllner EW. Isolation of translationally controlled mRNAs by differential screening. FASEB J. 2000 Aug;14(11):1641-52. PubMed PMID: 10928999.

Jank B, Doblhoff-Dier O, van der Plas J, Habermann B. Sequence motifs in a flagellin of Pseudomonas putida. Microbiology. 1995 Jul;141 ( Pt 7):1491-2. PubMed PMID: 7551017.

Mühlhahn P, Czisch M, Morenweiser R, Habermann B, Engh RA, Sommerhoff CP, Auerswald EA, Holak TA. Structure of leech derived tryptase inhibitor (LDTI-C) in solution. FEBS Lett. 1994 Dec 5;355(3):290-6. PubMed PMID: 7988692.

Jank B, Habermann B, Schweyen RJ, Link TA. PMP47, a peroxisomal homologue of mitochondrial solute carrier proteins. Trends Biochem Sci. 1993 Nov;18(11):427-8. Review. PubMed PMID: 8291088.