Jimin Pei

Summary

Affiliation: University of Texas Southwestern Medical Center
Country: USA

Publications

  1. pmc PROMALS3D web server for accurate multiple protein sequence and structure alignments
    Jimin 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
  2. pmc A new family of predicted Krüppel-like factor genes and pseudogenes in placental mammals
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
    PLoS ONE 8:e81109. 2013
  3. pmc Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Protein Sci 21:1172-84. 2012
  4. pmc Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptors
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
    Cell Signal 24:758-69. 2012
  5. pmc Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1
    Jimin 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
  6. ncbi PROMALS: towards accurate multiple sequence alignments of distantly related proteins
    Jimin 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
  7. pmc PROMALS web server for accurate multiple protein sequence alignments
    Jimin 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
  8. pmc Sparse representation and Bayesian detection of genome copy number alterations from microarray data
    Roger 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
  9. pmc PROMALS3D: a tool for multiple protein sequence and structure alignments
    Jimin Pei
    Howard Hughes Medical Institute, Dallas, TX 75390, USA
    Nucleic Acids Res 36:2295-300. 2008
  10. ncbi Multiple protein sequence alignment
    Jimin 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

Collaborators

Detail Information

Publications42

  1. pmc PROMALS3D web server for accurate multiple protein sequence and structure alignments
    Jimin 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/...
  2. pmc A new family of predicted Krüppel-like factor genes and pseudogenes in placental mammals
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
    PLoS ONE 8:e81109. 2013
    ..They represent further expansions of KLF members in the murine lineage, most likely resulted from several events of retrotransposition and local gene duplication starting from an ancient spliced mRNA of KLF18. ..
  3. pmc Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins
    Jimin 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...
  4. pmc Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptors
    Jimin 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...
  5. pmc Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1
    Jimin 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...
  6. ncbi PROMALS: towards accurate multiple sequence alignments of distantly related proteins
    Jimin 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...
  7. pmc PROMALS web server for accurate multiple protein sequence alignments
    Jimin 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/..
  8. pmc Sparse representation and Bayesian detection of genome copy number alterations from microarray data
    Roger 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...
  9. pmc PROMALS3D: a tool for multiple protein sequence and structure alignments
    Jimin 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...
  10. ncbi Multiple protein sequence alignment
    Jimin 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...
  11. pmc CPDadh: a new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins
    Jimin 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...
  12. pmc The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold
    Jimin 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...
  13. pmc Remote homology between Munc13 MUN domain and vesicle tethering complexes
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    J Mol Biol 391:509-17. 2009
    ....
  14. pmc MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
    Jimin 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
    ....
  15. pmc COG3926 and COG5526: a tale of two new lysozyme-like protein families
    Jimin 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...
  16. pmc CREST--a large and diverse superfamily of putative transmembrane hydrolases
    Jimin 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...
  17. pmc The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases
    Jimin 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
    ....
  18. ncbi Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
    Jimin 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
    ....
  19. pmc Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli
    Junmei 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...
  20. pmc Reconstruction of ancestral protein sequences and its applications
    Wei 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...
  21. ncbi Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5
    Demet 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
    ....
  22. pmc Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease
    Hua 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...
  23. ncbi CASP5 assessment of fold recognition target predictions
    Lisa 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...
  24. ncbi Combining evolutionary and structural information for local protein structure prediction
    Jimin 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...
  25. pmc Structure prediction for CASP8 with all-atom refinement using Rosetta
    Srivatsan 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...
  26. ncbi PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information
    Jimin Pei
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
    Methods Mol Biol 1079:263-71. 2014
    ..PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D...
  27. pmc The ABC transporters in Candidatus Liberibacter asiaticus
    Wenlin 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...
  28. pmc An automatic method for CASP9 free modeling structure prediction assessment
    Qian 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...
  29. pmc CASP9 target classification
    Lisa N Kinch
    Howard Hughes Medical Institute, University of Texas, Southwestern Medical Center, Dallas, TX 75390 9050, USA
    Proteins 79:21-36. 2011
    ....
  30. doi Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies
    Tina 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...
  31. pmc Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases
    Jimin Pei
    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Protein Sci 12:1131-5. 2003
    ....
  32. pmc Unusually rapid evolution of Neuroligin-4 in mice
    Marc 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
    ....
  33. pmc Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates
    Jue Ning
    Department of Cell Biology, University of Texas Southwestern Medical School, Dallas, Texas 75390, USA
    Genes Dev 27:1198-215. 2013
    ..Our comparative transcriptomics approach provides a new resource for studying sexual development and demonstrates that exploiting the data can lead to the discovery of novel biology that is conserved across distant taxa...
  34. ncbi PCMA: fast and accurate multiple sequence alignment based on profile consistency
    Jimin 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
    ..PCMA balances speed and accuracy in a flexible way and is suitable for aligning large numbers of sequences...
  35. ncbi C-terminal domain of gyrase A is predicted to have a beta-propeller structure
    Yuan 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...
  36. pmc Concerted regulation of myofiber-specific gene expression and muscle performance by the transcriptional repressor Sox6
    Daniel 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...
  37. pmc Using protein design for homology detection and active site searches
    Jimin 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...
  38. ncbi Substrate and functional diversity of lysine acetylation revealed by a proteomics survey
    Sung 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...
  39. pmc Breaking the singleton of germination protease
    Jimin 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...
  40. pmc The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes
    Yanjie 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...
  41. doi Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels
    Masato 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...
  42. ncbi Prediction of a caspase-like fold in Tannerella forsythia virulence factor PrtH
    Jimin 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...