Krzysztof Ginalski

Krzysztof Ginalski

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Krzysztof Ginalski

Publications by authors named "Krzysztof Ginalski"

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MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading.

Mol Cell 2020 Jan 20;77(2):395-410.e3. Epub 2019 Nov 20.

Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.10.029DOI Listing
January 2020

Correction to: Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.

BMC Psychiatry 2019 Jul 16;19(1):221. Epub 2019 Jul 16.

Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.

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http://dx.doi.org/10.1186/s12888-019-2207-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6631896PMC
July 2019

qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing.

Nat Commun 2019 05 24;10(1):2313. Epub 2019 May 24.

Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, Texas, 77555, USA.

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http://dx.doi.org/10.1038/s41467-019-10332-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6534554PMC
May 2019

Transposable elements contribute to fungal genes and impact fungal lifestyle.

Sci Rep 2019 Mar 13;9(1):4307. Epub 2019 Mar 13.

Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland.

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http://dx.doi.org/10.1038/s41598-019-40965-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416283PMC
March 2019

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.

BMC Evol Biol 2018 12 22;18(1):199. Epub 2018 Dec 22.

Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.

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http://dx.doi.org/10.1186/s12862-018-1309-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303947PMC
December 2018

Hypermethylation of and Influences Cell Death Signaling in Familial Alzheimer's Disease.

Oxid Med Cell Longev 2018 4;2018:6918797. Epub 2018 Apr 4.

Laboratory of Neurogenetics, Department of Neurodegenerative Disorders, Mossakowski Medical Research Centre of the Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warsaw, Poland.

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http://dx.doi.org/10.1155/2018/6918797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5904768PMC
October 2018

Predicting proteome dynamics using gene expression data.

Sci Rep 2018 09 14;8(1):13866. Epub 2018 Sep 14.

Department of Biochemistry and Molecular Biology, Institute for Translational Sciences, and Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA.

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http://www.nature.com/articles/s41598-018-31752-4
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http://dx.doi.org/10.1038/s41598-018-31752-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6138643PMC
September 2018

Exome scale map of genetic alterations promoting metastasis in colorectal cancer.

BMC Genet 2018 09 19;19(1):85. Epub 2018 Sep 19.

Depatment of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.

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http://dx.doi.org/10.1186/s12863-018-0673-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146521PMC
September 2018

Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer.

BMC Genomics 2018 Aug 20;19(1):621. Epub 2018 Aug 20.

Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France.

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-018-4978-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6102843PMC
August 2018

Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution.

Genome Biol 2018 03 15;19(1):34. Epub 2018 Mar 15.

LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118, route de Narbonne, Toulouse, 31062, France.

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http://dx.doi.org/10.1186/s13059-018-1411-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5856001PMC
March 2018

Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.

Biochemistry 2018 02 26;57(6):963-977. Epub 2018 Jan 26.

Department of Molecular Physiology and Biological Physics, University of Virginia , 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.

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http://dx.doi.org/10.1021/acs.biochem.7b01137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469932PMC
February 2018

Cut-and-Paste Transposons in Fungi with Diverse Lifestyles.

Genome Biol Evol 2017 12;9(12):3463-3477

Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Poland.

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http://dx.doi.org/10.1093/gbe/evx261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751038PMC
December 2017

Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing.

Genes Dev 2017 12 12;31(23-24):2405-2415. Epub 2018 Jan 12.

State Key Laboratory of Agro-Biotechnology, Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China.

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http://genesdev.cshlp.org/lookup/doi/10.1101/gad.306571.117
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http://dx.doi.org/10.1101/gad.306571.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5795786PMC
December 2017

A heterozygous mutation in GOT1 is associated with familial macro-aspartate aminotransferase.

J Hepatol 2017 11 15;67(5):1026-1030. Epub 2017 Jul 15.

Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw 01-813, Poland; Department of Genetics, Cancer Center-Institute, Warsaw 02-781, Poland. Electronic address:

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http://dx.doi.org/10.1016/j.jhep.2017.07.003DOI Listing
November 2017

Systematic classification of the His-Me finger superfamily.

Nucleic Acids Res 2017 Nov;45(20):11479-11494

Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.

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http://dx.doi.org/10.1093/nar/gkx924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714182PMC
November 2017

Fungal lifestyle reflected in serine protease repertoire.

Sci Rep 2017 08 22;7(1):9147. Epub 2017 Aug 22.

Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland.

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http://dx.doi.org/10.1038/s41598-017-09644-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567314PMC
August 2017

Comprehensive classification of the PIN domain-like superfamily.

Nucleic Acids Res 2017 Jul;45(12):6995-7020

University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089 Warsaw, Poland.

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http://dx.doi.org/10.1093/nar/gkx494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499597PMC
July 2017

Towards Engineering Novel PE-Based Immunotoxins by Targeting Them to the Nucleus.

Toxins (Basel) 2016 11 10;8(11). Epub 2016 Nov 10.

Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, Warsaw 02-089, Poland.

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http://dx.doi.org/10.3390/toxins8110321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127118PMC
November 2016

Diverse cap-binding properties of Drosophila eIF4E isoforms.

Biochim Biophys Acta 2016 10 29;1864(10):1292-303. Epub 2016 Jun 29.

Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland. Electronic address:

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http://dx.doi.org/10.1016/j.bbapap.2016.06.015DOI Listing
October 2016

Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study.

Proc Natl Acad Sci U S A 2016 07 11;113(29):E4190-9. Epub 2016 Jul 11.

Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 1L7

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http://dx.doi.org/10.1073/pnas.1603980113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961139PMC
July 2016

FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases.

Nucleic Acids Res 2016 05 7;44(8):3534-48. Epub 2016 Apr 7.

Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland

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http://dx.doi.org/10.1093/nar/gkw222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857005PMC
May 2016

Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform.

PLoS One 2015 10;10(4):e0120520. Epub 2015 Apr 10.

Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX, 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX, 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX, 77555, USA.

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https://pdfs.semanticscholar.org/5603/902ef4a635b2b8c8a4fb86
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http://dx.plos.org/10.1371/journal.pone.0120520
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120520PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393298PMC
April 2016

A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis.

Plant Physiol 2015 Nov 8;169(3):2080-101. Epub 2015 Sep 8.

Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)

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http://www.plantphysiol.org/content/early/2015/09/08/pp.15.0
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http://www.plantphysiol.org/content/169/3/2080.full.pdf
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http://www.plantphysiol.org/lookup/doi/10.1104/pp.15.00493
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http://dx.doi.org/10.1104/pp.15.00493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634048PMC
November 2015

Five eIF4E isoforms from Arabidopsis thaliana are characterized by distinct features of cap analogs binding.

Biochem Biophys Res Commun 2015 Jan 18;456(1):47-52. Epub 2014 Nov 18.

Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0006291X140204
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http://dx.doi.org/10.1016/j.bbrc.2014.11.032DOI Listing
January 2015

DIRS and Ngaro Retrotransposons in Fungi.

PLoS One 2013 25;8(9):e76319. Epub 2013 Sep 25.

Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Warsaw, Poland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076319PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388PMC
July 2014

The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast.

Mol Cell 2014 May;54(4):691-7

Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France; Equipe Labellisée Ligue Contre le Cancer, 14 rue Corvisart, 75013 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.04.032DOI Listing
May 2014

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification.

Nucleic Acids Res 2014 Apr 23;42(7):4160-79. Epub 2014 Jan 23.

Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt1414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985635PMC
April 2014

HarmonyDOCK: the structural analysis of poses in protein-ligand docking.

J Comput Biol 2014 Mar 20;21(3):247-56. Epub 2010 Nov 20.

1 Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw , Warsaw, Poland .

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http://www.liebertpub.com/doi/10.1089/cmb.2009.0111
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http://dx.doi.org/10.1089/cmb.2009.0111DOI Listing
March 2014

Probabilistic approach to predicting substrate specificity of methyltransferases.

PLoS Comput Biol 2014 Mar 20;10(3):e1003514. Epub 2014 Mar 20.

Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, United States of America; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1003514
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http://dx.doi.org/10.1371/journal.pcbi.1003514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961171PMC
March 2014

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification.

Genes Dev 2012 Sep 16;26(17):1911-25. Epub 2012 Aug 16.

Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.

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http://dx.doi.org/10.1101/gad.193169.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435495PMC
September 2012

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.

Nucleic Acids Res 2012 Aug 25;40(15):7016-45. Epub 2012 May 25.

Laboratory of Bioinformatics and Systems Biology, CENT, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.

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http://dx.doi.org/10.1093/nar/gks382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424549PMC
August 2012

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome.

PLoS One 2011 9;6(8):e23168. Epub 2011 Aug 9.

Laboratory of Bioinformatics and Systems Biology, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023168PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3153492PMC
February 2012

The C2H2 zinc finger transcription factors are likely targets for Ni(II) toxicity.

Metallomics 2011 Nov 25;3(11):1227-31. Epub 2011 Aug 25.

Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.

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http://dx.doi.org/10.1039/c1mt00081kDOI Listing
November 2011

Extending the aerolysin family: from bacteria to vertebrates.

PLoS One 2011 8;6(6):e20349. Epub 2011 Jun 8.

Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020349PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110756PMC
October 2011

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

Proc Natl Acad Sci U S A 2011 Jun 23;108(23):9443-8. Epub 2011 May 23.

Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1073/pnas.1015399108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111281PMC
June 2011

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.

J Comput Chem 2011 Mar 1;32(4):742-55. Epub 2010 Sep 1.

Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a Street, 02-106 Warsaw, Poland.

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http://dx.doi.org/10.1002/jcc.21643DOI Listing
March 2011

VoteDock: consensus docking method for prediction of protein-ligand interactions.

J Comput Chem 2011 Mar 1;32(4):568-81. Epub 2010 Sep 1.

Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a Street, 02-106 Warsaw, Poland.

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http://doi.wiley.com/10.1002/jcc.21642
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http://dx.doi.org/10.1002/jcc.21642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510457PMC
March 2011

Novel transmembrane lipases of alpha/beta hydrolase fold.

FEBS Lett 2011 Mar 17;585(6):870-4. Epub 2011 Feb 17.

Laboratory of Bioinformatics and Systems Biology, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.

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http://dx.doi.org/10.1016/j.febslet.2011.02.016DOI Listing
March 2011

Detailed mechanism of squalene epoxidase inhibition by terbinafine.

J Chem Inf Model 2011 Feb 13;51(2):455-62. Epub 2011 Jan 13.

BioInfoBank Institute, Poznań, Poland.

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http://dx.doi.org/10.1021/ci100403bDOI Listing
February 2011

TOS1 is circularly permuted 1,3-beta-glucanase.

Cell Cycle 2010 Jan 3;9(1):201-4. Epub 2010 Jan 3.

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http://dx.doi.org/10.4161/cc.9.1.10510DOI Listing
January 2010

Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human.

Nucleic Acids Res 2009 Dec;37(22):7701-14

Laboratory of Bioinformatics and Bioengineering, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.

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http://dx.doi.org/10.1093/nar/gkp854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794190PMC
December 2009

A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome.

Bioinform Biol Insights 2009 Oct 5;3:109-27. Epub 2009 Oct 5.

The Linnaeus Centre for Bioinformatics, Uppsala University BMC, Box 598, Husargatan 3, SE-751 24 Uppsala, Sweden.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808174PMC
http://dx.doi.org/10.4137/bbi.s3382DOI Listing
October 2009

Virtual high throughput screening using combined random forest and flexible docking.

Comb Chem High Throughput Screen 2009 Jun;12(5):484-9

Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.

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http://dx.doi.org/10.2174/138620709788489000DOI Listing
June 2009

The interactome: predicting the protein-protein interactions in cells.

Cell Mol Biol Lett 2009 6;14(1):1-22. Epub 2008 Oct 6.

Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland.

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http://www.degruyter.com/view/j/cmble.2009.14.issue-1/s11658
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http://dx.doi.org/10.2478/s11658-008-0024-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6275871PMC
January 2009

Snf2 proteins in plants: gene silencing and beyond.

Trends Plant Sci 2008 Oct 9;13(10):557-65. Epub 2008 Sep 9.

Laboratory of Bioinformatics and Bioengineering, Interdisciplinary Center for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1016/j.tplants.2008.08.004DOI Listing
October 2008

Prediction of signal peptides in protein sequences by neural networks.

Acta Biochim Pol 2008 26;55(2):261-7. Epub 2008 May 26.

Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warszawa, Poland.

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September 2008

Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440.

Proc Natl Acad Sci U S A 2008 Aug 4;105(32):11329-34. Epub 2008 Aug 4.

Departments of Molecular Microbiology and Protein Science, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.

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http://dx.doi.org/10.1073/pnas.0802273105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516282PMC
August 2008

Mitochondrial release factor in yeast: interplay of functional domains.

Curr Genet 2008 Mar 26;53(3):185-92. Epub 2008 Jan 26.

Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.

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http://dx.doi.org/10.1007/s00294-008-0177-yDOI Listing
March 2008

AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update.

J Mol Model 2008 Jan 8;14(1):69-76. Epub 2007 Nov 8.

Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.

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http://dx.doi.org/10.1007/s00894-007-0250-3DOI Listing
January 2008

HSV-1 UL45 encodes a carbohydrate binding C-type lectin protein.

Cell Cycle 2008 Jan 18;7(2):269-71. Epub 2007 Nov 18.

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http://dx.doi.org/10.4161/cc.7.2.5324DOI Listing
January 2008

Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.

BMC Struct Biol 2007 Jun 20;7:40. Epub 2007 Jun 20.

Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5a, Warsaw, Poland.

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http://dx.doi.org/10.1186/1472-6807-7-40DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913061PMC
June 2007

In silico prediction of SARS protease inhibitors by virtual high throughput screening.

Chem Biol Drug Des 2007 Apr;69(4):269-79

Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5a Street, 02-106 Warsaw, Poland.

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http://dx.doi.org/10.1111/j.1747-0285.2007.00475.xDOI Listing
April 2007

Target specific compound identification using a support vector machine.

Comb Chem High Throughput Screen 2007 Mar;10(3):189-96

BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland.

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http://dx.doi.org/10.2174/138620707780126705DOI Listing
March 2007

Efficacy of 2-halogen substituted D-glucose analogs in blocking glycolysis and killing "hypoxic tumor cells".

Cancer Chemother Pharmacol 2006 Dec 23;58(6):725-34. Epub 2006 Mar 23.

School of Medicine and Sylvester Cancer Center, The University of Miami, Miami, FL, USA.

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http://dx.doi.org/10.1007/s00280-006-0207-8DOI Listing
December 2006

Novel SARS unique AdoMet-dependent methyltransferase.

Cell Cycle 2006 Oct 16;5(20):2414-6. Epub 2006 Oct 16.

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http://dx.doi.org/10.4161/cc.5.20.3361DOI Listing
October 2006

Comparative modeling for protein structure prediction.

Curr Opin Struct Biol 2006 Apr 28;16(2):172-7. Epub 2006 Feb 28.

Centre for Mathematical and Computational Modelling, Warsaw University, Pawińskiego 5a, 02-106 Warsaw, Poland.

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http://dx.doi.org/10.1016/j.sbi.2006.02.003DOI Listing
April 2006

Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease.

J Virol 2006 Mar;80(5):2575-7

Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Poland.

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http://dx.doi.org/10.1128/JVI.80.5.2575-2577.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1395385PMC
March 2006

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.

BMC Bioinformatics 2006 Feb 6;7:53. Epub 2006 Feb 6.

Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-7-53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1409798PMC
February 2006

Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade.

Protein Sci 2006 Jan 1;15(1):84-93. Epub 2005 Dec 1.

Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1110/ps.051766506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242371PMC
January 2006

Bacillus subtilis YkuK protein is distantly related to RNase H.

FEMS Microbiol Lett 2005 Oct;251(2):341-6

Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawińskiego 5A, 02-106 Warsaw, Poland.

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https://academic.oup.com/femsle/article-lookup/doi/10.1016/j
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http://dx.doi.org/10.1016/j.femsle.2005.08.020DOI Listing
October 2005

Identification of novel restriction endonuclease-like fold families among hypothetical proteins.

Nucleic Acids Res 2005 22;33(11):3598-605. Epub 2005 Jun 22.

Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA.

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http://dx.doi.org/10.1093/nar/gki676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1157100PMC
July 2005

Protein domain of unknown function DUF1023 is an alpha/beta hydrolase.

Proteins 2005 Apr;59(1):1-6

Department of Biochemistry, University of Texas, Southwestern Medical Center, Dallas, Texas 75390-9038, USA.

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http://dx.doi.org/10.1002/prot.20388DOI Listing
April 2005

Practical lessons from protein structure prediction.

Nucleic Acids Res 2005 1;33(6):1874-91. Epub 2005 Apr 1.

BioInfoBank Institute ul. Limanowskiego 24A, 60-744 Poznań, Poland.

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http://dx.doi.org/10.1093/nar/gki327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1074308PMC
April 2005

A comprehensive update of the sequence and structure classification of kinases.

BMC Struct Biol 2005 Mar 16;5. Epub 2005 Mar 16.

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, USA.

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http://dx.doi.org/10.1186/1472-6807-5-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1079889PMC
March 2005

Raptor protein contains a caspase-like domain.

Trends Biochem Sci 2004 Oct;29(10):522-4

Biochemistry Department, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S096800040400207
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http://dx.doi.org/10.1016/j.tibs.2004.08.006DOI Listing
October 2004

ECEPE proteins: a novel family of eukaryotic cysteine proteinases.

Trends Biochem Sci 2004 Oct;29(10):524-6

Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawińskiego 5a, 02-106 Warsaw, Poland.

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http://linkinghub.elsevier.com/retrieve/pii/S096800040400204
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http://dx.doi.org/10.1016/j.tibs.2004.08.003DOI Listing
October 2004

Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity.

Proc Natl Acad Sci U S A 2004 Oct 27;101(40):14385-9. Epub 2004 Sep 27.

Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0405913101
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http://dx.doi.org/10.1073/pnas.0405913101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC521941PMC
October 2004

BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases.

Trends Biochem Sci 2004 Aug;29(8):392-5

Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA.

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http://dx.doi.org/10.1016/j.tibs.2004.06.001DOI Listing
August 2004

Detecting distant homology with Meta-BASIC.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W576-81

Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA.

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http://dx.doi.org/10.1093/nar/gkh370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441508PMC
July 2004

DCC proteins: a novel family of thiol-disulfide oxidoreductases.

Trends Biochem Sci 2004 Jul;29(7):339-42

Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.

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http://dx.doi.org/10.1016/j.tibs.2004.04.003DOI Listing
July 2004

Sequence-structure mapping errors in the PDB: OB-fold domains.

Protein Sci 2004 Jun 7;13(6):1594-602. Epub 2004 May 7.

Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, L-448, PO Box 808, Livermore, CA 94551, USA.

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http://dx.doi.org/10.1110/ps.04634604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279972PMC
June 2004

BOF: a novel family of bacterial OB-fold proteins.

FEBS Lett 2004 Jun;567(2-3):297-301

Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.

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http://dx.doi.org/10.1016/j.febslet.2004.04.086DOI Listing
June 2004

Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomes.

J Biol Chem 2004 Apr 19;279(14):14096-103. Epub 2004 Jan 19.

Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawiñskiego 5A, 02-106 Warsaw, Poland.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M312856200
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April 2004

Protein structure prediction for the male-specific region of the human Y chromosome.

Proc Natl Acad Sci U S A 2004 Feb;101(8):2305-10

Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC356946PMC
http://dx.doi.org/10.1073/pnas.0306306101DOI Listing
February 2004

Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment.

Proteins 2003 ;53 Suppl 6:410-7

Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland.

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http://doi.wiley.com/10.1002/prot.10548
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http://dx.doi.org/10.1002/prot.10548DOI Listing
January 2004

Application of 3D-Jury, GRDB, and Verify3D in fold recognition.

Proteins 2003 ;53 Suppl 6:418-23

BioInfoBank Institute, Poznan, Poland.

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http://dx.doi.org/10.1002/prot.10547DOI Listing
January 2004

Detection of reliable and unexpected protein fold predictions using 3D-Jury.

Nucleic Acids Res 2003 Jul;31(13):3291-2

Bioinformatics Laboratory, BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168910PMC
http://dx.doi.org/10.1093/nar/gkg503DOI Listing
July 2003

3D-Jury: a simple approach to improve protein structure predictions.

Bioinformatics 2003 May;19(8):1015-8

BioInfoBank Institute, Limanowskiego 24A, 60-744 Poznan, Poland.

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http://dx.doi.org/10.1093/bioinformatics/btg124DOI Listing
May 2003

Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III.

J Mol Biol 2002 Feb;316(3):853-66

Molecular and Structural Biology Division, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.

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http://dx.doi.org/10.1006/jmbi.2001.5382DOI Listing
February 2002