Publications
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Unraveling the interplay between a small RNA and RNase E in bacteria Nucleic Acids Res. 2024 July 22:gkae621. doi: 10.1093/nar/gkae621
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RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae Nucleic Acids Res. 2024 May 28:gkae440. doi: 10.1093/nar/gkae440.
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TRS: a method for determining transcript termini from RNAtag-seq sequencing data Nat Commun. 2023 Nov 29;14(1):7843. doi: 10.1038/s41467-023-43534-2.
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Convergent Within-Host Adaptation of Pseudomonas aeruginosa through the Transcriptional Regulatory Network mSystems. 2023 Mar 28:e0002423. doi: 10.1128/msystems.00024-23. Online ahead of print.
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Inferring the contribution of small RNAs to changes in gene expression in response to stress NAR Genomics and Bioinformatics. 2022 Mar 4;4(1):lqac015. doi: 10.1093/nargab/lqac015. eCollection 2022 Mar.
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Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity Mol Cell. 2022 Feb 3;82(3):629-644.e4. doi: 10.1016/j.molcel.2021.12.030. Epub 2022 Jan 20.
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The impact of Hfq-mediated sRNA-mRNA interactome on the virulence of enteropathogenic Escherichia coli Sci Adv. 2021 Oct 29;7(44):eabi8228. doi: 10.1126/sciadv.abi8228. Epub 2021 Oct 27.
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Prediction of Novel Bacterial Small RNAs From RIL-Seq RNA–RNA Interaction Data. Front. Microbiol. 2021 May 21; doi: 10.3389/fmicb.2021.63507
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Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. Mol Biol Evol. 2021 Mar 9;38(3):1101-1121. doi: 10.1093/molbev/msaa278.
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Hierarchy in Hfq Chaperon Occupancy of Small RNA Targets Plays a Major Role in Their Regulation. Cell Rep 2020 Mar 3;30(9):3127-3138.e6. doi: 10.1016/j.celrep.2020.02.016.
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A Ubiquitous Platform for Bacterial Nanotube Biogenesis. Cell Rep 2019 Apr 9;27(2):334-342.e10. doi: 10.1016/j.celrep.2019.02.055. Epub 2019 Mar 28.
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In vivo cleavage rules and target repertoire of RNase III in Escherichia coli. Nucleic Acids Res. 2018 Aug 3. doi: 10.1093/nar/gky684.
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Assessing the functional association of intronic miRNAs with their host genes. RNA. 2018 Aug;24(8):991-1004. doi: 10.1261/rna.064386.117.
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Mapping the small RNA interactome in bacteria using RIL-seq. Nat Protoc. 2018 Jan;13(1):1-33. doi: 10.1038/nprot.2017.115.
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Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments. Nat Commun. 2017 Dec 11;8(1):2029. doi: 10.1038/s41467-017-02099-7.
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Integration of Bacterial Small RNAs in Regulatory Networks. Annu Rev Biophys. 2017 May 22;46:131-148. doi: 10.1146/annurev-biophys-070816-034058.
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Global Mapping of Small RNA-Target Interactions in Bacteria Mol Cell. 2016 Sep 1;63(5):884-97. doi: 10.1016/j.molcel.2016.07.026.
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Stochastic analysis of bistability in coherent mixed feedback loops combining transcriptional and posttranscriptional regulations Phys Rev E Stat Nonlin Soft Matter Phys. 2015 May;91(5):052706. Epub 2015 May 15.
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Degradation of Ndd1 by APC/C(Cdh1) generates a feed forward loop that times mitotic protein accumulation Nat Commun. 2015 May 11;6:7075. doi: 10.1038/ncomms8075.
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A defense-offense multi-layered regulatory switch in a pathogenic bacterium Nucleic Acids Res. 2015 Feb 18;43(3):1357-69
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Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions RNA. 2014 Jul;20(7):994-1003. doi: 10.1261/rna.043133.113. Epub 2014 May 27.
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Interactions between Distant ceRNAs in Regulatory Networks Biophys J. 2014 May 20;106(10):2254-66. doi: 10.1016/j.bpj.2014.03.040.
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Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics Nucleic Acids Res. 2014 Jun;42(10):6552-66. doi: 10.1093/nar/gku245. Epub 2014 Apr 29.
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Global Regulation of Transcription by a Small RNA: A Quantitative View Biophys J. 2014 Mar 4;106(5):1205-14. doi: 10.1016/j.bpj.2014.01.025.
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In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III Methods. 2013 Sep 15;63(2):135-43. doi: 10.1016/j.ymeth.2013.06.033. Epub 2013 Jul 9.
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A functional selection model explains evolutionary robustness despite plasticity in regulatory networks Mol Syst Biol. 2012 Oct 23;8:619. doi: 10.1038/msb.2012.50.
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Competition between small RNAs: a quantitative view. Biophys J. 2012 Apr 18;102(8):1712-21.
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Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids Nucleic Acids Res. 2012 Aug;40(15):7074-83. doi: 10.1093/nar/gks348. Epub 2012 May 11.
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Reduced polymorphism in domains involved in protein-protein interactions PLoS One. 2012;7(4):e34503. Epub 2012 Apr 3.
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A genome-wide view of the expression and processing patterns of Thermus thermophilus HB8 CRISPR RNAs RNA. 2012 Apr;18(4):783-94. Epub 2012 Feb 21.
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Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles Genome Biol. 2011 Oct 27;12(10):R109
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A wide repertoire of miRNA binding sites: prediction and functional implications Bioinformatics. 2011 Nov 15;27(22):3093-101. Epub 2011 Sep 27
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Comparative functional genomics of the fission yeasts Science. 2011 May 20;332(6032):930-6. Epub 2011 Apr 21
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Accessibility and Evolutionary Conservation Mark Bacterial Small-RNA Target-Binding Regions J Bacteriol. 2011 Apr;193(7):1690-701.
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RepTar: a database of predicted cellular targets of host and viral miRNAs Nucleic Acids Res. 2011 Jan;39(Database issue):D188-94.
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Cytomegalovirus microRNAs facilitate persistent virus infection in salivary glands PLoS Pathog. 2010 Oct 14;6(10):e1001150.
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Preferential use of protein domain pairs as interaction mediators: order and transitivity Bioinformatics. 2010 Oct 15;26(20):2564-70. Epub 2010 Aug 27.
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Modularity and directionality in genetic interaction maps Bioinformatics. 2010 Jun 15;26(12):i228-36.
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Legionella pneumophila 6S RNA optimizes intracellular multiplication Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7533-8. Epub 2010 Apr 5.
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Stochastic analysis of the SOS response in Escherichia coli PLoS One. 2009;4(5):e5363. Epub 2009 May 8.
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Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13292-7. Epub 2008 Aug 29.
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Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence Nucleic Acids Res. 2008 Apr;36(6):1913-27. doi: 10.1093/nar/gkn050. Epub 2008 Feb 11.
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A novel Bayesian DNA motif comparison method for clustering and retrieval PLoS Comput Biol. 2008 Feb 29;4(2):e1000010. doi: 10.1371/journal.pcbi.1000010.
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A melanoma multiepitope polypeptide induces specific CD8+ T-cell response Cell Immunol. 2007 Nov-Dec;250(1-2):24-30. doi: 10.1016/j.cellimm.2008.01.001. Epub 2008 Feb 13.
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Regulation of gene expression by small non-coding RNAs: a quantitative view Mol Syst Biol. 2007;3:138. Epub 2007 Sep 25.
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Host immune system gene targeting by a viral miRNA Science. 2007 July 20 317(5836):376-81
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Evolutionary conservation of domain-domain interactions Genome Biol. 2006;7(12):R125.
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Characterization and prediction of protein-protein interactions within and between complexes Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14718-23. Epub 2006 Sep 26.
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Co-evolution of transcription factors and their targets depends on mode of regulation Genome Biol. 2006 Jul 19;7(7):R62
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Towards an integrated protein-protein interaction network: a relational Markov network approach J Comput Biol. 2006 Mar;13(2):145-64.
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Proteins of the same fold and unrelated sequences have similar amino acid composition Proteins. 2006 Jul 1;64(1):275-9.
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Ab initio prediction of transcription factor targets using structural knowledge PLoS Comput Biol. 2005 Jun;1(1):e1. Epub 2005 Jun 24.
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Assigning functions to genes: identification of S-phase expressed genes in Leishmania major based on post-transcriptional control elements Nucleic Acids Res. 2005 Jul 28;33(13):4235-42. Print 2005.
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Clustering and conservation patterns of human microRNAs Nucleic Acids Res. 2005 May 12;33(8):2697-706. Print 2005.
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Chromosomal organization is shaped by the transcription regulatory network Trends Genet. 2005 Mar 21(3):138-42.
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Relative predicted protein levels of functionally associated proteins are conserved across organisms Nucleic Acids Res. 2005 Feb 17;33(3):1051-7. Print 2005.
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A structure-based approach for prediction of MHC-binding peptides Methods. 2004 Dec;34(4):454-9.
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Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):5934-9.
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IntAct: an open source molecular interaction database Nucleic Acids Res. 2004 Jan 1;32(Database issue):D452-5.
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Insights from MHC-bound peptides Novartis Found Symp. 2003;254:77-90; discussion 91-101, 216-22, 250-2.
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Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res. 2003 Dec;13(12):2665-73.
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Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation. Nucleic Acids Res. 2003 Oct 15;31(20):6053-61.
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Molecular basis for expression of common and rare fragile sites. Mol Cell Biol. 2003 Oct;23(20):7143-51.
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How reliable are experimental protein-protein interaction data? J Mol Biol. 2003 Apr 11;327(5):919-23.
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Conserved sequence elements associated with exon skipping. Nucleic Acids Res. 2003 Apr 1;31(7):1974-83.
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A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res. 2003 Apr 1;31(7):1813-20.
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PeCoP: automatic determination of persistently conserved positions in protein families. Bioinformatics. 2002 Sep;18(9):1276-7.
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Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function. Protein Sci. 2002 Feb 11(2):350-60
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Harnessing the cellular immune system to the gene-prediction cart. Trends Genet. 2001 Dec;17(12):732-4.
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Markovian domain fingerprinting: statistical segmentation of protein sequences. Bioinformatics. 2001 Oct;17(10):927-34.
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Possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins. Proteins. 2001 Oct 1;45(1):47-54.
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Correlated sequence-signatures as markers of protein-protein interaction J Mol Biol. 2001 Aug 24;311(4):681-92
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Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol. 2001 Jun 26;11(12):941-50.
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A structure-based approach for prediction of protein binding sites in gene upstream regions. Pac Symp Biocomput. 2001;:139-50
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Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments. Protein Sci. 2000 Nov;9(11):2278-84.
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Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles. Protein Sci. 2000 Sep;9(9):1838-46.
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Glimmers in the midnight zone: characterization of aligned identical residuesin sequence-dissimilar proteins sharing a common fold. Proc Int Conf Intell Syst Mol Biol. 2000;8:162-70.
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Sequence signals for generation of antigenic peptides by the proteasome: implications for proteasomal cleavage mechanism. J Mol Biol. 2000 Jan 28;295(4):879-90.
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Common fragile sites: G-band characteristics within an R-band. Am J Hum Genet. 1999 Mar;64(3):908-10.
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Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes. Fold Des. 1998;3(6):549-64.
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Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of a simian virus 40 integration site. Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8141-6.
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Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucleic Acids Res. 1998 May 15;26(10):2306-12.
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Role for CH...O interactions in protein-DNA recognition. J Mol Biol. 1998 Apr 17;277(5):1129-40.
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Structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets. Hum Immunol. 1997 Nov;58(1):1-11.
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Structure and function of the Pseudomonas putida integration host factor. J Bacteriol. 1996 Nov;178(21):6319-26.
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Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications. Proc Natl Acad Sci U S A. 1996 Jun 25;93(13):6470-5.
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Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. J Mol Biol. 1995 Oct 20;253(2):370-82.
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Periodic variation in side-chain polarities of T-cell antigenic peptides correlates with their structure and activity. Proc Natl Acad Sci U S A. 1995 Aug 29;92(18):8368-72.
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Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon. Comput Appl Biosci. 1995 Aug;11(4):379-87.
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Ranking potential binding peptides to MHC molecules by a computational threading approach. J Mol Biol. 1995 Jun 2;249(2):244-50.
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Conservation of salt bridges in protein families. J Mol Biol. 1995 Apr 21;248(1):125-35.
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Determination of common structural features in Escherichia coli promoters by computer analysis. Eur J Biochem. 1994 Aug 1;223(3):823-30.
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A complete Alu element within the coding sequence of a central gene. Cell. 1994 Jul 29;78(2):173-4.
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Sequence features that correlate with MHC restriction. Mol Immunol. 1994 Jan;31(1):1-19.
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Zinc fingers: conserved properties that can distinguish between spurious and actual DNA-binding motifs. J Biomol Struct Dyn. 1993 Dec;11(3):557-70.
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Comparative analysis of structurally defined heparin binding sequences reveals a distinct spatial distribution of basic residues. J Biol Chem. 1993 Sep 15;268(26):19228-31.
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Identification and characterization of E.coli ribosomal binding sites by free energy computation. Nucleic Acids Res. 1993 Aug 25;21(17):4019-23.
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Compilation of E. coli mRNA promoter sequences. Nucleic Acids Res. 1993 Apr 11;21(7):1507-16.
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Molecular analysis of HLA class II genes in primary Sjögren's syndrome. A study of Israeli Jewish and Greek non-Jewish patients. Hum Immunol. 1993 Apr;36(4):235-42.