2017

Mircetic J, Dietrich A, Paszkowski-Rogacz M, Krause M, Buchholz F (2017)
Development of a genetic sensor that eliminates p53 deficient cells.
Nat Commun. 2017 Nov 13;8(1):1463. doi: 10.1038/s41467-017-01688-w. PubMed

Toyoda Y, Cattin CJ, Stewart MP, Poser I, Buchholz F, Müller DJ, Hyman AA (2017)
Genome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding.
Nat Commun., 2017 Nov 2;8(1):1266. doi: 10.1038/s41467-017-01147-6. PubMed

Meinke G, Karpinski J, Buchholz F, Bohm A (2017)
Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA.
Nucleic Acids Res., 2017 Sep 19;45(16):9726-9740. doi: 10.1093/nar/gkx603. PubMed

Korotkevich E, Niwayama R, Courtois A, Friese S, Berger N, Buchholz F, Hiiragi T. (2017)
The Apical Domain Is Required and Sufficient for the First Lineage Segregation in the Mouse Embryo.
Dev Cell. 2017 Feb 6;40(3):235-247.e7. doi: 10.1016/j.devcel.2017.01.006. PubMed

Jahn A, Rane G, Paszkowski-Rogacz M, Sayols S, Bluhm A, Han CT, Draškovič I, Londoño-Vallejo JA, Kumar AP, Buchholz F, Butter F, Kappei D (2017)
ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator.
EMBO Rep. Jun;18(6):929-946. doi: 10.15252/embr.201744095. PubMed

Mircetic J, Steinebrunner I, Ding L, Fei JF, Bogdanova A, Drechsel D, and Buchholz F (2017)
Purified Cas9 Fusion Proteins for Advanced Genome Manipulation.
Small Methods.160052. DOI: 10.1002/smtd.201600052 PubMed

Kappei D, Scheibe M, Paszkowski-Rogacz M, Bluhm A, Gossmann TI, Dietz S, Dejung M, Herlyn H, Buchholz F, Mann M, Butter F (2017)
Phylointeractomics reconstructs functional evolution of protein binding.
Nat Commun. Feb 8;8:14334. doi: 10.1038/ncomms14334. PubMed

2016

Karpinski J., Hauber I., Chemnitz J., Schäfer C., Paszkowski-Rogacz M., Chakraborty D., Beschorner N., Hofmann-Sieber H., Lange U.C., Grundhoff A., Hackmann K., Schrock E., Abi-Ghanem J., Pisabarro M.T., Surendranath V., Schambach A., Lindner C., van Lunzen J., Hauber J. Buchholz, F. (2016)
Directed evolution of a recombinase that excises the provirus of most HIV-1 primary isolates with high specificity.
Nature Biotechnology. On-line Feb 22. doi: 10.1038/nbt.3467. PubMed

Gebler C., Lohoff, T., Paszkowski-Rogacz M., Mircetic J., Chakraborty D., Camgoz A., Hamann M.V., Theis M., Thiede C., Buchholz F. (2016)
Inactivations of cancer mutations utilizing CRISPR/Cas9.
JNCI. doi: 10.1093/jnci/djw183. PubMed

Karimova M, Splith V, Karpinski J, Pisabarro MT, Buchholz F.
Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering. (2016)
Sci Rep. 2016 Jul 22;6:30130. doi: 10.1038/srep30130. PubMed

Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F.
Cre Recombinase and Other Tyrosine Recombinases. (2016)
Chem Rev. May 10. PubMed

Herberg M, Glauche I, Zerjatke T, Winzi M, Buchholz F, Roeder I.
Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics. (2016)
J R Soc Interface. Apr;13(117). pii: 20160167. doi: 10.1098/rsif.2016.0167. PubMed

Linge A, Lohaus F, Löck S, Nowak A, Gudziol V, Valentini C, von Neubeck C, Jütz M, Tinhofer I, Budach V, Sak A, Stuschke M, Balermpas P, Rödel C, Grosu AL, Abdollahi A, Debus J, Ganswindt U, Belka C, Pigorsch S, Combs SE, Mönnich D, Zips D, Buchholz F, Aust DE, Baretton GB, Thames HD, Dubrovska A, Alsner J, Overgaard J, Krause M, Baumann M; DKTK-ROG.
HPV status, cancer stem cell marker expression, hypoxia gene signatures and tumour volume identify good prognosis subgroups in patients with HNSCC after primary radiochemotherapy: A multicentre retrospective study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG). (2016)
Radiother Oncol. Dec;121(3):364-373. doi: 10.1016/j.radonc.2016.11.008. PubMed

Linge A, Löck S, Gudziol V, Nowak A, Lohaus F, von Neubeck C, Jütz M, Abdollahi A, Debus J, Tinhofer I, Budach V, Sak A, Stuschke M, Balermpas P, Rödel C, Avlar M, Grosu AL, Bayer C, Belka C, Pigorsch S, Combs SE, Welz S, Zips D, Buchholz F, Aust DE, Baretton GB, Thames HD, Dubrovska A, Alsner J, Overgaard J, Baumann M, Krause M; DKTK-ROG.
Low Cancer Stem Cell Marker Expression and Low Hypoxia Identify Good Prognosis Subgroups in HPV(-) HNSCC after Postoperative Radiochemotherapy: A Multicenter Study of the DKTK-ROG. (2016)
Clin Cancer Res. Jun 1;22(11):2639-49. doi: 10.1158/1078-0432.CCR-15-1990. PubMed

Bäumer N, Appel N, Terheyden L, Buchholz F, Rossig C, Müller-Tidow C, Berdel WE, Bäumer S.
Antibody-coupled siRNA as an efficient method for in vivo mRNA knockdown. (2016)
Nat Protoc. Jan;11(1):22-36. doi: 10.1038/nprot.2015.137. PubMed

Buchholz F, HauberJ (2016)
Antiviral therapy of persistent viral infection using genome editing
Curr Opin Viro. Oct 7;20:85-91. doi: 10.1016/j.coviro.2016.09.012. PubMed

2015

Schmitt-Engel C, Schultheis D, Schwirz J, Ströhlein N, Troelenberg N, Majumdar U, Anh Dao V, Grossmann D, Richter T, Tech M, Dönitz J, Gerischer L, Theis M, Schild I, Trauner J, Koniszewski NDB, Küster E, Kittelmann S, Hu Y, Lehmann S, Siemanowski J, Ulrich J, Panfilio KA, Schröder R, Morgenstern B, Stanke M, Buchholz F., Frasch M, Roth S, Wimmer EA, Schoppmeier M, Klingler M, Bucher G (2015)
The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology.
Nature Communications Jul 28 PubMed

Bäumer S, Bäumer N, Appel N, Terheyden L, Fremerey J, Schelhaas S, Wardelmann E, Buchholz F., Berdel WE, Müller-Tidow C. (2015)
Antibody-mediated delivery of anti-KRAS-siRNA in vivo overcomes therapy resistance in colon cancer.
Clinical Cancer Research Mar 15 PubMed

Theis M, Paszkowski-Rogacz M, Weisswange I, Chakraborty D, Buchholz F. (2015)
Targeting Human Long Noncoding Transcripts by Endoribonuclease-Prepared siRNAs.
J Biomol Screen Mar 15;21(6):1383-94 PubMed

Wermke M, Camgoz A, Paszkowski-Rogacz M, Thieme S, von Bonin M, Dahl A, Platzbecker U, Theis M, Ehninger G, Brenner S, Bornhäuser M, Buchholz F. (2015)
RNAi profiling of primary human AML cells identifies ROCK1 as a therapeutic target and nominates fasudil as an antileukemic drug.
Blood Jun 11;125(24):3760-8 PubMed

Karimova M, Beschorner N, Dammermann W, Chemnitz J, Indenbirken D, Bockmann JH, Grundhoff A, Lüth S, Buchholz F., Schulze zur Wiesch J, Hauber J. (2015)
CRISPR/Cas9 nickase-mediated disruption of hepatitis B virus open reading frame S and X.
Science Reports Sep 3;5:13734 PubMed

Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F., Hyman AA, Mann M. (2015)
A human interactome in three quantitative dimensions organized by stoichiometries and abundances.
Cell Oct 22; 163(3):712-23 PubMed

Bäumer N, Appel N, Terheyden L, Buchholz F., Rossig C, Müller-Tidow C, Berdel WE, Bäumer S. (2015)
Antibody-coupled siRNA as an efficient method for in vivo mRNA knockdown.
Nature Protocols Dec 3; (1):22-36 PubMed

Ding L, Paszkowski-Rogacz M, Winzi M, Chakraborty D, Theis M, Singh S, Ciotta G, Poser I, Roguev A, Chu WK, Choudhary C, Mann M, Stewart AF, Krogan N, Buchholz F. (2015)
Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells.
Cell Systems Aug 26 Cell Systems

Appel N, Bäumer N, Wardelmann E, Buchholz F., Müller-Tidow C, Berdel WE, Bäumer S. (2015)
Molecular targeting of EGFR-downstream effectors in colorectal cancer cells by antibody-mediated siRNA treatment.
Oncol Res. Treat Aug 26;38(suppl 5):1-288 Oncol Res Treat

2014

Machyna M, Kehr S, Straube K, Kappai D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM (2014)
The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies.
Molecular Cell Nov. 6, Vol 56, Issue 3, p389-399. PubMed

Karpinski J, Chemnitz J, Hauber I, Abi-Ghanem J, Paszkowski-Rogacz M, Surendranath V, Chakrabort D, Hackmann K, Schröck E, Pisabarro MT, Hauber J, Buchholz F. (2014) Universal Tre (uTre) recombinase specifically targets the majority of HIV-1 isolates.
J Int AIDS Soc. Nov 2, 17(Suppl 3):19706 PubMed

Günal-Sadık G, Paszkowski-Rogacz M, Singaravelu K, Beyer A, Buchholz F, Jessberger R. (2014)
Stage-specific binding profiles of cohesin in resting and activated B lymphocytes suggest a role for cohesin in immunoglobulin class switching and maturation.
PLoS One Nov 6;9(11):e111748. PubMed

Liakhovitskaia A, Rybtsov S, Smith T, Batsivari A, Rybtsova N, Rode C, de Bruijn M, Buchholz F, Gordon-Keylock S, Zhao S, Medvinsky A. (2014)
Runx1 is required for progression of CD41+ embryonic precursors into HSCs but not prior to this.
Development. Sep;141(17):3319-23. PubMed

Winzi M, Paszkowski-Rogacz M, Buchholz F. (2014)
Another brick in the wall: RNAi Screens identify new barriers in iPSC reprogramming.
Cell Stem Cell. Aug 7;15(2):116-8. PubMed

Raychaudhuri S., Loew C., Körner R., Pinkert S., Theis M., Hayer-Hartl M., Buchholz F., Hartl F.U. (2014)
Interplay of Acetyltransferase EP300 and the Proteasome System in Regulating Heat Shock Transcription Factor 1.
Cell. Feb 27;156(5):975-85. doi: 10.1016/j.cell.2014.01.055. PubMed

2013

Hauber I., Hofmann-Sieber H., Chemnitz J., Dubrau D., Chusainow J., Stucka R., Hartjen P., Schambach A., Ziegler P., Hackmann K., Schröck E., Schumacher U., Lindner C., Grundhoff A., Baum C., Manz M.G., Buchholz F., Hauber J. (2013).
Highly significant antiviral activity of HIV-1 LTR-specific tre-recombinase in humanized mice.
PLoS Pathogens, Sep;9(9):e1003587. PubMed

Scheibe M., Arnoult N., Kappei D., Buchholz F., Decottignies A., Butter F., Mann M. (2013)
Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators.
Genome Res. Dec;23(12):2149-57. PubMed

Hirst J., Borner G.H., Edgar J., Hein M.Y., Mann M., Buchholz F., Antrobus R., Robinson M.S. (2013)
Interaction Between AP-5 and the Hereditary Spastic Paraplegia Proteins SPG11 and SPG15.
Mol Biol Cell. Aug;24(16):2558-69. PubMed

Kappei, D., Butter, F., Scheibe, M., Draskovic, I., Krastev, D.B., Kittler, R., Londono-Vallejo, J.A., Mann, M., and Buchholz, F. (2013)
Hot1, a novel direct telomere-repeat binding protein, controls telomere length through interaction with active telomerase.
EMBO J. Jun 12;32(12):1681-701. PubMed

Niebuhr B., Kriebitzsch N., Fischer M., Behrens K., Günther T., Alawi M., Bergholz U., Müller U., Roscher S., Ziegler M., Buchholz F., Grundhoff A., Stocking C. (2013)
Runx1 is essential at two stages of early murine B-cell development.
Blood, Jul 18;122(3):413-23. PubMed

Caldarelli, A., Müller, J.P., Paskowski-Rogacz, M., Herrmann, K., Bauer,R., Koch, S., Henninger, A.K., Krastev, D., Ding, L., Kasper, S., Fischer,T., Brodhun,M., Böhmer, F.D. Buchholz F. (2013)
A genome-wide RNAi screen identifies proteins modulating aberrant FLT3-ITD signaling.
Leukemia, Mar 19. doi: 10.1038/leu.2013.83. PubMed

Thieme S., Gyárfás T., Richter C., Ozhan G., Fu J., Alexopulou D., Muders M.H., Michalk I., Jakob C., Dahl A., Klink B., Bandola J., Bachmann M., Schröck E., Buchholz F., Stewart A.F., Weidinger G., Anastassiadis K., Brenner S. (2013)
The histone demethylase UTX regulates stem cell migration and hematopoiesis.
Blood, Mar 28;121(13):2462-73. PubMed

Karimova, M., Abi-Ghanem, J., Berger, N., Surendranath, V., Pisabarro, M.T., Buchholz, F. (2013)
Vika/vox, a novel efficient and specific Cre/IoxP-like site-specific recombination system.
Nucleic Acids Res. 41(2):e37. PubMed

Abi-Ghanem J, Chusainow J, Karimova M, Spiegel C, Hofmann-Sieber H, Hauber J, Buchholz F., Pisabarro MT. (2013)
Engineering of a target site-specific recombinase by a combined evolution- and structure-guided approach.
Nucleic Acids Res. Feb 1;41(4):2394-403. PubMed

Buchholz F., Hauber J. (2013)
Engineered DNA modifying enzymes: Components of a future strategy to cure HIV/AIDS.
Antiviral Res. Feb;97(2):211-7. PubMed

Surendranath, V., Theis, M., Habermann, BH., Buchholz, F. (2013)
Designing efficient and specific endoribonuclease-prepared siRNAs.
Methods Mol Biol. 2013;942:193-204. PubMed

Hauber J, Hauber I, Buchholz F. (2013)
Revolutionizing HIV-therapy by Tre-Recombinase? Initial observations and current state of development.
MW Fortschr Med. Jun 13;155 Suppl 1:22-3. PubMed

2012

Tomczak A, Sontheimer J, Drechsel D, Hausdorf R, Gentzel M, Shevchenko A, Eichler S, Fahmy K, Buchholz F, Pisabarro MT. (2012)
3D Profile-Based Approach to Proteome-Wide Discovery of Novel Human Chemokines.
PLoS One. 2012;7(5):e36151. Epub 2012 May 7. PubMed

Ross, K., Sedello, A.K., Putz, G., Paszkowski-Rogacz M., Bird, A.W., Hubner, N., Mann, M., Waskow, C., Stocking, C., and Buchholz, F. (2012)
Polycomb group ring finger 1 cooperates with Runx1 in regulating differentiation and self renewal of hematopoietic cells.
Blood, 2012; 3;119(18):4152-61. PubMed

Mariyanna L, Priyadarshini P, Hofmann-Sieber H, Krepstakies M, Walz N, Grundhoff A, Buchholz F, Hildt E, Hauber J. (2012)
Excision of HIV-1 proviral DNA by recombinant cell permeable tre-recombinase.
PLoS One. 2012;7(2):e31576. Epub 2012 Feb 13. PubMed

Chakraborty, D., Kappei, D., Theis, M., Nitzsche, A., Ding, L., Paskowski-Rogacz, M., Surendranath, V., Berger, N., Schulz, H., Saar, K., Huebner, N., and Buchholz, F. (2012)
Combined RNAi and localization for functionally dissecting long noncoding RNAs.
Nature Methods. 12:9(4):360-2. PubMed

Gunal, G., Paszkowski-Rogacz, M., Singaravelu, K., Beyer, A., Buchholz, F., Jessberger, R. (2012)
Cohesin’s potential role in immunoglobulin class switching.
FEBS JOURNAL. Volume: 279, Special Issue: SI, Supplement: 1, Pages: 494-494, Published: SEP 2012

Ding L., Poser I., Paszkowski-Rogacz M., Buchholz F. (2012)
From RNAi Screens to Molecular Function in Embryonic Stem Cells.
Stem Cell Rev. 2012 Mar;8(1):32-42. PubMed

2011

Leushacke M., Spörle R., Bernemann C., Brouwer-Lehmitz A., Fritzmann J., Theis M., Buchholz F., Herrmann B.G., Morkel M. (2011)
An RNA interference phenotypic screen identifies a role for FGF signals in colon cancer progression.
PLoS One. 6(8):e23381. Epub 2011 Aug 11. PubMed

Krastev D.B., Slabicki M., Paszkowski-Rogacz M., Hubner N.C., Junqueira M., Shevchenko A., Mann M., Neugebauer K.M., Buchholz F. (2011)
A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly.
Nat Cell Biol. Jun 5;13(7):809-18. doi: 10.1038/ncb2264. PubMed

Nitzsche A., Paszkowski-Rogacz M., Matarese F., Janssen-Megens E.M., Hubner N.C., Schulz H., de Vries I., Ding L., Huebner N., Mann M., Stunnenberg HG., Buchholz F. (2011)
RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity.
PLoS One. May 12;6(5):e19470. PubMed

Krastev D.B., Buchholz F. (2011)
Ribosome biogenesis and p53: Who is regulating whom?
Cell Cycle. Oct 15;10(20):3417-8. PubMed

Theis M., Buchholz F. (2011)
High-throughput RNAi screening in mammalian cells with esiRNAs.
Methods. Apr;53(4):424-9. PubMed

Buchholz, F. and Hauber, J. (2011)
In Vitro Evolution and Analysis of HIV-1 LTR-Specific Recombinases.
Methods. 53 (1): 102-9. PubMed

2010

Surendranath V., Chusainow J., Hauber J., Buchholz F., Habermann B.H. (2010)
SeLOX–a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems.
Nucleic Acids Res. 1;38 Suppl:W293-8. PubMed

Slabicki, M.M., Theis, M., Krastev, D.B., Samsonov, E.M., Junqueira, M., Paszkowski-Rogacz, M., Teyra, J., Heninger, A.K., Poser, I., Prieur, F., Truchetto, J., Confavreux, C., Marelli, C., Durr, A., Camdessanche, J.P., Brice, A., Shevchenko, A., Pisabarro, M.T., Stevanin, G., Buchholz, F. (2010)
A genome-scale DNA repair RNAi screen identifies SPG47 as a novel gene associated with hereditary spastic paraplegia.
PLoS Biology. 29;8(6):e1000408. PubMed

Hutchins, J.R.A., Toyoda, Y., Hegemann, B., Poser, I., Heriche, J.K., Sykora, M.M., Augsburg, M., Hudecz, O., Buschhorn, B.A., Bulkescher, J., Comartin, D., Schleiffer, A., Sarov, M., Pozniakovsky, A., Slabicki, M.M., Schloissnig, S., Lawo, S., Pelletier, L., Stark, H., Nasmyth, K., Ellenberg, J., Durbin, R., Buchholz, F., Mechtler, K., Hyman, A.A., Peters, J.M. (2010)
Mitotic Protein Complexes in Human Cells.
Science. 30;328(5978):593-9. PubMed

Collinet, C., Stöter, M., Bradshaw, C. R., Samusik, N., Rink, J. C., Kenski, D., Habermann, B., Buchholz, F., Henschel, R., Mueller, M., Nagel, W. E., Fava, E., Kalaidzidis, Y., Zerial, M. (2010)
System Survey of Endocytosis by Functional Genomics and Quantitative Multi-Parametric Image Analysis.
Nature. 11;464(7286):243-9. PubMed

Theis M., Buchholz F. (2010)
MISSION esiRNA for RNAi screening in mammalian cells.
J Vis Exp. May 12;(39). pii: 2008. doi: 10.3791/2008. PubMed

Butter F., Kappei D., Buchholz F., Vermeulen M., Mann M. (2010)
A domesticated transposon mediates the effects of a single-nucleotide polymorphism responsible for enhanced muscle growth.
EMBO Rep. Apr;11(4):305-11. PubMed

Paszkowski-Rogacz M., Slabicki M., Pisabarro M.T., Buchholz F. (2010)
PhenoFam-gene set enrichment analysis through protein structural information.
BMC Bioinformatics. May 17;11:254. PubMed

2009

Theis, M., Paszkowski-Rogacz, M., Buchholz, F. (2009)
SKAnking with Ska3: essential role of Ska3 in cell division revealed by combined phenotypic profiling.
Cell Cycle. 1;8(21):3435-7. PubMed

Schulz, H., Kolde, R., Adler P, Aksoy I, Anastassiadis K, Bader M, Billon N, Boeuf H, Bourillot PY, Buchholz F, Dani C, Doss MX, Forrester L, Gitton M, Henrique D, Hescheler J, Himmelbauer H, Hübner N, Karantzali E, Kretsovali A, Lubitz S, Pradier L, Rai M, Reimand J, Rolletschek A, Sachinidis A, Savatier P, Stewart F, Storm MP, Trouillas M, Vilo J, Welham MJ, Winkler J, Wobus AM, Hatzopoulos AK (2009)
Functional Genomics in Embryonic Stem Cells Consortium.
The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation.
PLoS One. 3;4(9):e6804. PubMed

Anastassiadis, K., Fu, J., Patsch, C., Hu, S., Weidlich, S., Duerschke, K., Buchholz. F., Edenhofer, F., Stewart, A.F. (2009)
Dre recombinase, like Cre, is a highly efficient site-specific recombinase in E. coli, mammalian cells and mice.
Dis Model Mech. 2(9-10):508-15. PubMed

Lawo, S., Bashkurov, M., Mullin, M., Ferreria, M.G., Kittler, R., Habermann, B., Tagliaferro, A., Poser, I., Hutchins, J.R.A., Hegemann, B., Pinchev, D., Buchholz, F., Peters, J.M., Hyman, A.A., Gingras, A.C., and Pelletier, L. (2009)
HAUS, the 8-Subunit Human Augmin Complex, Regulates Centrosome and Spindle Integrity.
Current Biology. 19(10):816-26. PubMed

Ding, L., Paszkowski-Rogacz, M., Nitzsche, A., Slabicki, M.M., Heninger, A.K., Kittler, R., Junqueira, M., Shevchenko, A., Schulz, H., Hubner, N., Doss, M.X., Sachinidis, A., Hescheler, J., Caldarelli, A., Poser, I., Theis, M., and Buchholz, F. (2009)
A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity.
Cell Stem Cell. 8;4(5):403-15. PubMed

Theis, M., Slabicki, M., Junqueira, M., Paszkowski-Rogacz, M., Sontheimer, J., Kittler, R., Heninger, A. H., Glatter, T., Kruusmaa, K., Poser, I., Hyman, A. A., Pisabarro, M. T., Gstaiger, M., Aebersold, R., Shevchenko, A., and Buchholz, F. (2009)
Comparative Profiling Identifies C13orf3 as a Novel Component of the Ska Complex Required for Mammalian Cell Division.
EMBO J. 28(10):1453-65. PubMed

Buchert, M., Darido, C., Lagerqvist, E., Sedello, A., Cazevieille, C., Buchholz, F., Pannequin, J., Joubert, D., Hollande, F. (2009)
The symplekin/ZONAB complex inhibits intestinal cell differentiation via the repression of AML1/Runx1.
Gastroenterology. 137(1):156-64. PubMed

Trouillas, M., Saucourt, C., Guillotin, B., Gauthereau, X., Ding, L., Buchholz, F., Doss, M. X., Sachinidis, A., Hescheler, J., Hummel, O., Huebner, N., Kolde, R., Vilo, J., Schultz, H., and Boeuf, H. (2009)
Three LIF-dependent signatures and competency genes identified by gene profiling studies in mouse ES cells and early derivatives.
BMC Genomics. 9;10(1):73. PubMed

Buchholz, F. (2009)
Engineering DNA processing enzymes for the postgenomic era.
Curr Opin Biotechnol. 20(4):383-9. PubMed

2008

Buchholz, F. (2008)
Principles of Site-Specific Recombinase (SSR) Technology.
J Vis Exp. May 29;(15). PubMed

Kittler, R., Pelletier, L., and Buchholz, F. (2008)
Systems biology of mammalian cell division.
Cell Cycle. 7(14):2123-8. PubMed

Poser, I., Sarov, M., Hutchins, J., Heriche, J-K., Toyoda, Y., Nitzche, A., Pozniakovsky, A., Hegemann, B., Bird, A., Pelletier, L., Kittler, R., Naumann, R., Mechtler, K., Durbin, R., Stewart, A.F., Peters, J-M., Buchholz, F. and Hyman, A.A. (2008)
BAC TransgeneOmics: A high-throughput method for exploration of protein function in mammals.
Nature Methods. 5(5):409-15. PubMed

2007

Kittler, R., Pelletier, L., Heninger, AK Slabicki, M., Theis, M., Miroslaw, L., Poser, I., Grabner, H., Kozak, K., Wagner, J., Surendranath, V., Richter, C., Bowen, W., Habermann, B., Hyman, A.A., and Buchholz, F. (2007)
Genome-wide RNAi profiling of cell cycle progression in human tissue culture cells.
Nature Cell Biology. 9(12):1401-1412. PubMed

Gregan, J., Riedel, C.G., Petronczki, M., Cipak, L., Rumpf, C., Poser, I., Buchholz, F., Mechtler, K., and Nasmyth, K. (2007)
Tandem affinity purification of functional TAP-tagged proteins from human cells.
Nature Protocols. 2(5):1145-51. PubMed

Sarkar, I., Hauber, I., Hauber, J., and Buchholz, F. (2007)
HIV-1 Proviral DNA Excision Using an Evolved Recombinase.
Science. 29;316(5833):1912-5. PubMed
Faculty of 1000 Biology
Faculty of 1000 Medicine

Kittler, R., Surendranath, V., Heninger,A.K., Slabicki, M., Theis, M., Putz, G., Franke,K., Caldareli, A., Grabner, H., Kozak, K., Wagner, J., Rees, E., Korn, B., Sachse, C., Sönnichsen, B., Guo, J., Schelter, J., Burchard, J., Linsley, P.S., Jackson, A.L., Habermann, B., and Buchholz, F. (2007)
Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies.
Nature Methods. 4(4):337-344. PubMed

Cammenga, J., Niebuhr, B., Horn, S., Bergholz, U., Putz, G., Buchholz, F., Lohler, J., Stocking, C. (2007)
RUNX1 DNA-binding mutants, associated with minimally differentiated acute myelogenous leukemia, disrupt myeloid differentiation.
Cancer Research. 15;67(2):537-45. PubMed

2006

Echeverri, C.J., Beachy, P.A., Baum, B., Boutros, M., Buchholz, F., Chanda, S.K., Downward, J., Ellenberg, J., Fraser, A.G., Hacohen, N., Hahn, W.C., Jackson, A.L., Kiger, A., Linsley, P.S., Lum, L., Ma, Y., Mathey-Prevot, B., Root, D.E., Sabatini, D.M., Taipale, J., Perrimon, N., Bernards, R. (2006)
Minimizing the risk of reporting false positives in large-scale RNAi screens.
Nature Methods. 3(10):777-9. PubMed

Riedel , C.G., Katis, V.L., Katou ,Y., Mori, S., Itoh, T., Helmhart, W., Galova, M., Petronczki , M., Gregan, J., Cetin, B., Mudrak, I., Ogris, E., Mechtler, K., Pelletier, L., Buchholz , F., Shirahige, K., Nasmyth, K. (2006)
Protein phosphatase 2A protects centromeric sister chromatid cohesion during meiosis I.
Nature. 441(7089):53-61. PubMed
Faculty of 1000 Biology

Putz, G., Rosner, A., Nuesslein, I., Schmitz, N., and Buchholz, F. (2006)
AML1 deletion in adult mice causes splenomegaly and lymphomas.
Oncogene. 25(6):929-39. PubMed

Ding, L., and Buchholz, F. (2006)
RNAi in embryonic stem cells.
Stem Cell Reviews. 2 (1): 11-18. PubMed

Buchholz, F., Kittler, R., Slabicki, M., and Theis,M. (2006)
Enzymatically prepared RNAi libraries.
Nature Methods. 3(9):696-700. PubMed

Poser, I. and Buchholz, F. (2006)
A new approach to specify RNAi experiments.
European Pharmaceutical review. 3, 12-17.

2005

Kittler, R., Heninger, A. K., Franke, K., Habermann, B., and Buchholz, F. (2005)
Production of endoribonuclease-prepared short interfering RNAs for gene silencing in mammalian cells.
Nat Methods. 2, 779-784. PubMed

Zhang, D. J., Wang, Q., Wei, J., Baimukanova, G., Buchholz, F., Stewart, A. F., Mao, X., and Killeen, N. (2005)
Selective expression of the Cre recombinase in late-stage thymocytes using the distal promoter of the Lck gene.
J Immunol. 174, 6725-6731. PubMed

Kittler, R., and Buchholz, F. (2005)
Functional genomic analysis of cell division by endoribonuclease-prepared siRNAs.
Cell Cycle. 4, 564-567. PubMed

Kittler, R., Pelletier, L., Ma, C., Poser, I., Fischer, S., Hyman, A. A., and Buchholz, F. (2005)
RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells.
Proc Natl Acad Sci U S A. 102, 2396-2401. PubMed

Buchholz, F. (2005)
RNA-Interference in Mammalian Cells.
European Biotech News. 4, 39-42.

Krausz, E., Heninger, A.K., Kittler, R., Lohmann, A., Poser, I., Wagner, J., Franke, K., Kozak, K., Grabner, H., and Buchholz, F. (2005)
A genome-wide RNA-Interference library for the functional characterization of genes in cultured mammalian cells.
BioSpektrum. 4, 436-441.

Buchholz, F. (2005)
Functional Genomics in Mammalian Cells by RNAi: Opportunities and Challenges.
Laborwelt. 6, 18-21.

2004

Kittler, R., Putz, G., Pelletier, L., Poser, I., Heninger, A.K., Drechsel, D., Fischer, S., Konstantinova, I., Habermann, B., Grabner, H., Yaspo, M.L., Himmelbauer, H., Korn, B., Neugebauer, K., Pisabarro, M.T., Buchholz , F. (2004)
An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division.
Nature. 432, 1036-1040. PubMed
Faculty of 1000 Biology

Henschel, A., Buchholz, F., and Habermann, B. (2004)
DEQOR: a web-based tool for the design and quality control of siRNAs.
Nucleic Acids Res. 32, W113-120.

Kronke, J., Kittler, R., Buchholz, F., Windisch, M. P., Pietschmann, T., Bartenschlager, R., and Frese, M. (2004)
Alternative approaches for efficient inhibition of hepatitis C virus RNA replication by small interfering RNAs.
J Virol. 78, 3436-3446. PubMed

Calegari, F., Marzesco, A. M., Kittler, R., Buchholz, F., and Huttner, W. B. (2004)
Tissue-specific RNA interference in post-implantation mouse embryos using directional electroporation and whole embryo culture.
Differentiation. 72, 92-102. PubMed

2003

Ennifar, E., Meyer, J. E., Buchholz, F., Stewart, A. F., and Suck, D. (2003)
Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation.
Nucleic Acids Res. 31, 5449-5460. PubMed

Kittler, R. and Buchholz, F. (2003)
RNA interference: gene silencing in the fast lane.
Semin Cancer Biol. 13, 259-265. PubMed

2002

Calegari, F., Haubensak, W., Yang, D., Huttner, W. B., and Buchholz, F. (2002)
Tissue-specific RNA interference in postimplantation mouse embryos with endoribonuclease-prepared short interfering RNA.
Proc Natl Acad Sci U S A. 99, 14236-14240. PubMed

Yang, D., Buchholz, F., Huang, Z., Goga, A., Chen, C. Y., Brodsky, F. M., and Bishop, J. M. (2002)
Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells.
Proc Natl Acad Sci U S A. 99, 9942-9947. PubMed

Shimshek, D. R., Kim, J., Hubner, M. R., Spergel, D. J., Buchholz, F., Casanova, E., Stewart, A. F., Seeburg, P. H., and Sprengel, R. (2002)
Codon-improved Cre recombinase (iCre) expression in the mouse.
Genesis. 32, 19-26. PubMed

2001

Buchholz, F. and Stewart, A. F. (2001)
Alteration of Cre recombinase site specificity by substrate-linked protein evolution.
Nat Biotechnol. 19, 1047-1052. PubMed

Buchholz, F. and Bishop, M. (2001)
LoxP-directed cloning: use of Cre recombinase as a universal restriction enzyme.
Biotechniques. 31, 906-908, 910, 912, 914, 916, 918. PubMed

2000

Buchholz, F., Refaeli, Y., Trumpp, A., and Bishop, J. M. (2000)
Inducible chromosomal translocation of AML1 and ETO genes through Cre/loxP-mediated recombination in the mouse.
EMBO Rep. 1, 133-139. PubMed

Muyrers, J. P., Zhang, Y., Buchholz, F., and Stewart, A. F. (2000)
RecE/RecT and Redalpha/Redbeta initiate double-stranded break repair by specifically interacting with their respective partners.
Genes Dev. 14, 1971-1982. PubMed

Rodriguez, C. I., Buchholz, F., Galloway, J., Sequerra, R., Kasper, J., Ayala, R., Stewart, A. F., and Dymecki, S. M. (2000)
High-efficiency deleter mice show that FLPe is an alternative to Cre-loxP.
Nat Genet. 25, 139-140. PubMed

1998

Ringrose, L., Lounnas, V., Ehrlich, L., Buchholz, F., Wade, R., and Stewart, A. F. (1998)
Comparative kinetic analysis of FLP and cre recombinases: mathematical models for DNA binding and recombination.
J Mol Biol. 284, 363-384. PubMed

Zhang, Y., Buchholz, F., Muyrers, J. P., and Stewart, A. F. (1998)
A new logic for DNA engineering using recombination in Escherichia coli.
Nat Genet. 20, 123-128. PubMed

Angrand, P.O., Woodroofe, C. P., Buchholz, F., and Stewart, A. F. (1998)
Inducible expression based on regulated recombination: a single vector strategy for stable expression in cultured cells.
Nucleic Acids Res. 26, 3263-3269. PubMed

Buchholz, F., Angrand, P. O., and Stewart, A. F. (1998)
Improved properties of FLP recombinase evolved by cycling mutagenesis.
Nat Biotechnol. 16, 657-662. PubMed

1996

Buchholz, F., Ringrose, L., Angrand, P. O., Rossi, F. and Stewart, A. F. (1996)
Different thermostabilities of FLP and Cre recombinases: implications for applied site-specific recombination.
Nucleic Acids Res. 24, 4256-4262. PubMed

Buchholz, F., Angrand, P. O. and Stewart, A. F. (1996)
A simple assay to determine the functionality of Cre or FLP recombination targets in genomic manipulation constructs.
Nucleic Acids Res. 24, 3118-3119. PubMed

Jiang, Y., Yu, V. C., Buchholz, F., O’Connell, S., Rhodes, S. J., Candeloro, C., Xia, Y. R., Lusis, A. J. and Rosenfeld, M. G. (1996)
A novel family of Cys-Cys, His-Cys zinc finger transcription factors expressed in developing nervous system and pituitary gland.
J Biol Chem. 271, 10723-10730. PubMed

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