Research Topics
Genomes and Genes | Jimin PeiSummaryAffiliation: University of Texas Southwestern Medical Center Country: USA Publications
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Publications
Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteinsJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
Protein Sci 21:1172-84. 2012..Such a finding reinforces the evolutionary ties between the Wnt and Hedgehog signaling pathways and underscores the importance of gene duplications in creating essential signaling components in metazoan evolution...- Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptorsJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
Cell Signal 24:758-69. 2012..STMC6 proteins are likely transmembrane adaptors that regulate membrane proteins such as cell surface receptors... 
PROMALS: towards accurate multiple sequence alignments of distantly related proteinsJimin Pei
Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390 9050, USA
Bioinformatics 23:802-8. 2007..Although the alignment problem has attracted considerable attention, preparation of high-quality alignments for distantly related sequences remains a difficult task...- PROMALS web server for accurate multiple protein sequence alignmentsJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390 9050, USA
Nucleic Acids Res 35:W649-52. 2007..The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/.. - Sparse representation and Bayesian detection of genome copy number alterations from microarray dataRoger Pique-Regi
Signal and Image Processing Institute, Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, EEB 400, 3740 McClintock Ave, Los Angeles, CA 90089 2564, USA
Bioinformatics 24:309-18. 2008..This article proposes a novel detection technique that exploits the use of piece wise constant (PWC) vectors to represent genome copy number and sparse Bayesian learning (SBL) to detect CNA breakpoints... - PROMALS3D: a tool for multiple protein sequence and structure alignmentsJimin Pei
Howard Hughes Medical Institute, Dallas, TX 75390, USA
Nucleic Acids Res 36:2295-300. 2008..PROMALS3D outperforms a number of existing methods for constructing multiple sequence or structural alignments using both reference-dependent and reference-independent evaluation methods... 
Multiple protein sequence alignmentJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
Curr Opin Struct Biol 18:382-6. 2008..Here, I review methodologies and recent advances in the multiple protein sequence alignment field, with emphasis on the use of additional sequence and structural information to improve alignment quality...- CPDadh: a new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxinsJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
Protein Sci 18:856-62. 2009..In eukaryotes, catalytically inactive members of the CPDadh family are found in cell surface protein NELF (nasal embryonic LHRH factor) and some putative signaling proteins... - The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease foldJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
Proteins 77:413-9. 2009..Our results provide structural and mechanistic insights into several important proteins functioning in bacterial pathogenesis... - Remote homology between Munc13 MUN domain and vesicle tethering complexesJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
J Mol Biol 391:509-17. 2009.... - Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1Jimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390 9050, USA
J Mol Biol 410:18-26. 2011..Remote similarity between APH-1 and membrane proteases sheds light on APH-1's evolutionary origin and raises the possibility that APH-1 may possess proteolytic activity in the current or ancestral form of γ-secretase... - CREST--a large and diverse superfamily of putative transmembrane hydrolasesJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
Biol Direct 6:37. 2011..Recently, a group of putative transmembrane receptors called progestin and adipoQ receptors (PAQRs) were found to be distantly related to alkaline ceramidases, raising the possibility that they may also function as membrane enzymes... - MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural informationJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
Nucleic Acids Res 34:4364-74. 2006.... - COG3926 and COG5526: a tale of two new lysozyme-like protein familiesJimin Pei
Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
Protein Sci 14:2574-81. 2005..The predicted enzymatic activity is consistent with an experimental study on the zliS gene product from Zymomonas mobilis, suggesting that bacterial COG3926/DUF847 members might be activators of macromolecular secretion... - The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylasesJimin Pei
Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
Protein Sci 14:1370-4. 2005.... - Prediction of functional specificity determinants from protein sequences using log-likelihood ratiosJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA
Bioinformatics 22:164-71. 2006..AVAILABILITY: SPEL is freely available for non-commercial use. Its pre-compiled versions for several platforms and alignments used in this work are available at ftp://iole.swmed.edu/pub/SPEL/.. - Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coliJunmei Zhang
Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Mol Cell Proteomics 8:215-25. 2009..Furthermore, we demonstrate that bacterial lysine acetylation is regulated in response to stress stimuli... - Reconstruction of ancestral protein sequences and its applicationsWei Cai
Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
BMC Evol Biol 4:33. 2004..Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference... - Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5Demet Arac
Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
J Mol Biol 346:589-601. 2005.... - Combining evolutionary and structural information for local protein structure predictionJimin Pei
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA
Proteins 56:782-94. 2004..77), suggesting that it is a valid method for local protein structure prediction. Mixture of predicted structural frequencies and evolutionary frequencies improve the quality of local profile-to-profile alignment by COMPASS... - CASP5 assessment of fold recognition target predictionsLisa N Kinch
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
Proteins 53:395-409. 2003..We also compared the results of manual groups to those of automatic servers evaluated in parallel by CAFASP, showing that the top performing automated server structure predictions approached those of the best manual predictors... - Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus proteaseHua Cheng
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
Protein Sci 13:2260-9. 2004..Our study provides further support for the proposed evolutionary link between dsDNA bacteriophages and herpesviruses... - Structure prediction for CASP8 with all-atom refinement using RosettaSrivatsan Raman
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 77:89-99. 2009..These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy... - The ABC transporters in Candidatus Liberibacter asiaticusWenlin Li
Department of Biochemistry and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
Proteins 80:2614-28. 2012..L. asiaticus pathogenicity and the ABC transporter systems responsible for bacterial OM biosynthesis that are good drug targets... - An automatic method for CASP9 free modeling structure prediction assessmentQian Cong
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
Bioinformatics 27:3371-8. 2011..It is beneficial to incorporate the ideas behind manual inspection to an automatic score system, which could provide objective and reproducible assessment of structure models... - PROMALS3D web server for accurate multiple protein sequence and structure alignmentsJimin Pei
Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390 9050, USA
Nucleic Acids Res 36:W30-4. 2008..Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/... - CASP9 target classificationLisa N Kinch
Howard Hughes Medical Institute, University of Texas, Southwestern Medical Center, Dallas, TX 75390 9050, USA
Proteins 79:21-36. 2011.... - Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assembliesTina W Han
Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390 9152, USA
Cell 149:768-79. 2012..Phosphorylation of the LC domain of FUS prevented hydrogel retention, offering a conceptual means of dynamic, signal-dependent control of RNA granule assembly... - Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolasesJimin Pei
Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
Protein Sci 12:1131-5. 2003.... - Unusually rapid evolution of Neuroligin-4 in miceMarc F Bolliger
Departments of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Proc Natl Acad Sci U S A 105:6421-6. 2008.... - PCMA: fast and accurate multiple sequence alignment based on profile consistencyJimin Pei
Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
Bioinformatics 19:427-8. 2003..AVAILABILITY: PCMA is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/PCMA/... - C-terminal domain of gyrase A is predicted to have a beta-propeller structureYuan Qi
Department of Biochemistry, University of Texas Southwestern Medical Center, Texas 75390-9050, USA
Proteins 47:258-64. 2002..The prediction rationalizes available experimental data and sheds light on the spatial properties of the largest topoisomerase domain that lacks structural information... - Using protein design for homology detection and active site searchesJimin Pei
Department of Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Proc Natl Acad Sci U S A 100:11361-6. 2003..Our sequence selection criteria in evolutionary simulations introduce amino acid substitution rate variation among sites in a natural way, providing a better model to test phylogenetic methods... - Concerted regulation of myofiber-specific gene expression and muscle performance by the transcriptional repressor Sox6Daniel Quiat
Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Proc Natl Acad Sci U S A 108:10196-201. 2011..These results identify Sox6 as a robust regulator of muscle contractile phenotype and metabolism, and elucidate a mechanism by which functionally related muscle fiber-type specific gene isoforms are collectively controlled... - Substrate and functional diversity of lysine acetylation revealed by a proteomics surveySung Chan Kim
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
Mol Cell 23:607-18. 2006..The combined data sets offer a rich source for further characterization of the contribution of this modification to cellular physiology and human diseases... - Breaking the singleton of germination proteaseJimin Pei
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA
Protein Sci 11:691-7. 2002..Our analysis helps localize the active site of GPRs and provides insight into the catalytic mechanisms of a superfamily of putative metal-regulated proteases... - The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametesYanjie Liu
Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
Genes Dev 22:1051-68. 2008..Membrane dye experiments show that HAP2 is essential for membrane merger. Thus, in two distantly related eukaryotes, species-limited proteins govern access to a conserved protein essential for membrane fusion... - Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogelsMasato Kato
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390 9152, USA
Cell 149:753-67. 2012..These observations offer a framework for understanding the function of LC sequences as well as an organizing principle for cellular structures that are not membrane bound... - Prediction of a caspase-like fold in Tannerella forsythia virulence factor PrtHJimin Pei
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
Cell Cycle 8:1453-5. 2009..Our results offer structural and mechanistic insights into PrtH and its homologs, and help classification of this protease family...