Publications

  1. Neuwald, A.F., Yang, H. and B.T. Nixon. 2022. SPARC: structural properties associated with residue constraints. Computational and Structural Biotechnology Journal. 20: 1702-1715.
  2. Chapoval,S.P., Lee, M., Lemmer, A., Oluwaseyi, A., Qi, X.,  Neuwald, A.F. and A. Keegan. 2022. Identifying function determining residues in neuroimmune semaphorin 4A. International Journal of Molecular Sciences.23(6):3024.
  3. Chen X., Neuwald A.F., Hilakivi-Clarke L., Clarke R., Xuan J. 2021.  ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements. PLoS Computational Biology 17(7):e1009203.
  4. Neuwald, A.F. 2021. Reflections on the Quest to Obtain Biological Information from Genomic Data. Quantitative Biology 9(3): 251–254.
  5. Shi, X, Wang, X., Neuwald, A.F., Hilakivi-Clarke, L., Clarke, R., and J. Xuan. 2021. A Bayesian approach for accurate de novo transcriptome assembly. Scientific Reports. 11(1):17663.
  6. Neuwald, A.F. and B. D. Kolaczkowski and S.F. Altschul. 2021. eCOMPASS: evaluative comparison of multiple protein alignments by statistical score. Bioinformatics  37(20):3456-63.
  7. Chen, X., Shi, X., Neuwald, A.F., Hilakivi-Clarke, L., Clarke, R., and J. Xuan. 2021. ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach. BMC Bioinformatics 22(1):193.
  8. Chen, X., Gu, J., Neuwald, A.F., Hilakivi-Clarke, L., Clarke, R., and J. Xuan. 2021. Identifying intracellular signaling modules and exploring pathways associated with breast cancer recurrence. Scientific Reports 11(1):385. doi: 10.1038/s41598-020-79603-5.
  9. Shi, X., Neuwald, A.F., Wang, X., Wang, T-L., Hilakivi-Clarke, L., Clarke, R. and J. Xuan. 2021. IntAPT: Integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. Bioinformatics. 37(5):650-658. PMID: 33016988.
  10. Neuwald, A.F., Lanczycki, C. J., Hodges, T.K., and A. Marchler-Bauer. 2020. Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments. DATABASE. doi:10.1093/database/baaa042.
  11. Tondnevis, F., Dudenhausen, E.E., Miller, A.M., McKenna, R., Altschu,l S.F., Bloom L.B. and A. F. Neuwald. 2020. Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity. Scientific Reports. 10(1):1691. doi: 10.1038/s41598-019-55118-6.
  12. Toshchakov, V.Y. and Neuwald, A.F. 2020. A Survey of TIR Domain Sequence and Structure Divergence. Immunogenetics. 72(3):181-203. doi: 10.1007/s00251-020-01157-7.
  13. Chen, X., Gu, J., Neuwald, A.F., Hilakivi-Clarke, L., Clarke, R., and J. Xuan. 2020. BICORN: An R package for integrative inference of de novo cis-regulatory modules. Scientific Reports 10(1):7960. doi: 10.1038/s41598-020-63043-2..
  14. Neuwald, A.F. and S. F. Altschul. 2018. Statistical Investigations of Protein Residue Direct Couplings. PLoS Computational Biology 14(12): e100623. doi: 10.1371/journal.pcbi.1006237
  15. Neuwald, A.F , Aravind, L. and S. F. Altschul. 2018. Inferring Joint Sequence-Structure Determinants of Protein Functional Specificity. eLife 7: e29880. doi: 10.7554/eLife.29880
  16. S. F. Altschul and Neuwald, A.F. 2018. Initial Cluster Analysis. Journal of Computational Biology 25(2):121-129.
  17. Neuwald, A.F and S. F. Altschul. 2016. Inference of Functionally-Relevant N-Acetyltransferase Residues Based on Statistical Correlations. Plos Comp. Biol. 12(12):e1005294.
  18. Neuwald, A.F and S. F. Altschul. 2016. Bayesian Top-down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties. Plos Comp. Biol. 12(5): e1004936.
  19. Neuwald, A.F. 2016. Gleaning structural and functional information from correlations in protein multiple sequence alignments. Current Opinion in Structural Biology. 38:1-8.
  20. Oruganty K., Talevich E.E., Neuwald A.F., Kannan N. 2016. Identification and classification of small molecule kinases: insights into substrate recognition and specificity. BMC Evol Biol. 16(1):7.
  21. Neuwald, A.F. 2014. Protein Domain Hierarchy Gibbs Sampling Strategies. Statistical Applications in Genetics and Molecular Biology 13(4):497-517.
  22. Neuwald, A.F. 2014. Evaluating, comparing and interpreting protein domain hierarchies. Journal of Computational Biology 21(4): 287-302.
  23. Neuwald, A.F. 2014. A Bayesian sampler for optimization of protein domain hierarchies. Journal of Computational Biology 21(3): 269-286.
  24. Neuwald, A.F., Lanczycki, C.J. and A. Marchler-Bauer. 2012. Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. BMC Bioinformatics 13:144.
  25. Neuwald, A.F. 2011. Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms. Statistical Applications in Genetics and Molecular Biology 10(1): Article 36. (30 pages)
  26. Neuwald, A.F. 2010. Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases. Biology Direct 5: 66 (17 pages).
  27. Iskow, R., McCabe, M., Mills, R., Torene, S., Pittard, W. S., Neuwald, A.F., Van Meir, E., Vertino, P. and S. E. Devine. 2010. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141(7):1253-1261.
  28. Ammerman, N.C., J. J. Gillespie, A. F. Neuwald, B. W. Sobral, A. F. Azad. 2009. A typhus group-specific serine protease defies the nature of reductive evolution in Rickettsia. Journal of Bacteriology 191:7609-7613.
  29. Neuwald, A.F. 2009. Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. Bioinformatics 25: 1869-1875
  30. Neuwald, A.F. 2009. The charge-dipole pocket: a defining feature of signaling pathway GTPase on-off switches. Journal of Molecular Biology 390: 142-153.
  31. Neuwald, A.F. 2009. The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops. BMC Structural Biology 9: 11.
  32. Kannan, N., J. Wu, G. S. Anand, S. Yooseph , A. F. Neuwald, J. C. Venter and S. S. Taylor. 2008. Evolution of allostery in the cyclic nucleotide binding module. Genome Biology 12(8): R264.
  33. Kannan, N., A.F. Neuwald and S. S. Taylor. 2007. Analogous regulatory sites within the αC-β4 loop regions of ZAP70 tyrosine kinase and AGC kinases. Biochimica et Biophysica Acta (BBA)-Proteins & Proteomics 1784(1):27-32.
  34. Neuwald A.F. 2007. Gα-Gβγ dissociation may be due to retraction of a buried lysine and disruption of an aromatic cluster by a GTP-sensing Arg-Trp pair. Protein Science 16(11): 2570-2577.
  35. Neuwald A.F.. 2007. The CHAIN program: forging evolutionary links to underlying mechanisms. Trends in Biochemical Sciences 32: 487-493.
  36. Kannan N., Haste N., Taylor S. S. and Neuwald A.F.. 2007. The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module. Proc. Natl. Acad. Sci., USA 104(4):1272-1277.
  37. Neuwald A.F. 2006. Hypothesis: bacterial clamp loader AAA+ ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine. Nucleic Acids Research 34(18): 5280-5290.
  38. Neuwald A.F. 2006. Bayesian shadows of molecular mechanisms cast in the light of evolution. Trends in Biochemical Sciences 31(7): 374-382.
  39. Kannan N. and Neuwald A.F. 2005. Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component? Journal of Molecular Biology 351: 956-972.
  40. Neuwald A.F. 2005. Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases. Nucleic Acids Research 33:3614-3628.
  41. Andersen J. N., Del Vecchio R.L., Kannan N., Gergel J., Neuwald A. F. and Tonks N. K. 2005. Computational analysis of protein tyrosine phophatases: practical guide to bioinformatics and data resources. Methods. 35: 90-114.
  42. Neuwald A.F. and Liu J. S. 2005. Measuring evolutionary constraints as protein properties reflecting underlying mechanisms. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, (eds. L.B. Jorde, P.R.R. Little, M.J. Dunn, and S. Subramaniam). John Wiley & Sons, Hoboken, NJ.
  43. Neuwald A.F. and Liu J.S. 2004. Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model. BMC Bioinformatics 5: 157 (16 pages).
  44. Kannan N. and Neuwald A.F. 2004. Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2α. Protein Science 13(8): 2059-2077.
  45. Saitoh N., Spahr C.S., Patterson S.D., Bubulya P., Neuwald A.F. and Spector D.L. 2004. Proteomic analysis of interchromatin granule clusters. Mol. Biol. Cell. 15(8): 3876-3890.
  46. Neuwald A.F., Kannan N., Poleksic A., Hata N., and Liu J.S. 2003. Ran’s C-terminal, basic patch and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras and Ran GTPases. Genome Research 13(4): 673-692.
  47. Ono T., Losada A., Hirano M., Myers M.P., Neuwald A.F. and Hirano T. 2003. Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells. Cell 115: 109-121.
  48. Neuwald A.F. 2003. Evolutionary clues to DNA polymerase III β clamp structural mechanisms. Nucleic Acids Research 31(15): 4503-4516.
  49. Neuwald A.F. and Hirano T. 2000. HEAT repeats associated with condensins, cohesins, and other complexes involved in chromosome-related functions. Genome Research 10(10): 1445-1452. This analysis led to the discovery of a new condensin component (see Ono, et al. 2003 above).
  50. Neuwald A.F. and Poleksic A. 2000. PSI-BLAST searches using hidden Markov models of structural repeats: Prediction of an unusual sliding DNA clamp and of β-propellers in UV-damaged DNA binding protein. Nucleic Acids Research 28(18): 3570-3580. This prediction of β-propeller domains in UV-DDB protein was confirmed experimentally by Li et al., Cell (2006) 124(1):105-117.
  51. Wilbur W.J. and Neuwald A.F. 2000. A theory of information with special application to search problems. Computers & Chemistry 24: 33-42.
  52. Aravind L., Neuwald A.F. and Ponting C.P. 1999. Sec14p-like domains in NF1 and Dbl-like proteins indicate lipid-regulation of Ras and Rho signaling. Current Biology 9:R195-197.
  53. Liu J. S., Neuwald A.F. and Lawrence C. E. 1999. Markovian structures in biological sequence alignments. Journal of the American Statistical Association 94: 1-15. This publication received the year 2000 Mitchell prize for the best Bayesian application paper.
  54. Neuwald A.F. 1999. The hexamerization domain of N-ethylmaleimide-sensitive factor: structural clues to chaperone function. Structure 7:R19-R23.
  55. Neuwald A.F., Aravind L., Spouge J. L. and Koonin E. V. 1999. AAA+: a class of chaperone-like ATPases associated with the assembly, operation and disassembly of protein complexes. Genome Research 9:27-43.
  56. Mintz P.J., Patterson S.D., Neuwald A.F., Spahr C.S., and Spector D.L. 1999. Purification and biochemical characterization of interchromatin granule clusters. EMBO J. 18(15): 4308-4320.
  57. Chung M. S., Neuwald A.F. and Wilbur W.J. 1998. Free energy analysis by unfolding applied to 125-mers on a cubic lattice. Journal of Folding and Design 3:51-65.
  58. Neuwald A.F. and Koonin E. V. 1998. Ataxin-2, global regulators of bacterial gene expression, and spliceosomal snRNP proteins share a conserved domain. Journal of Molecular Medicine 76:3-5.
  59. Neuwald, A.F. 1998. A probable solution to sequence-analysis problems. Trends in Biochemical Sciences 23(9):365-365.
  60. Neuwald A.F. 1997. Barth syndrome may be due to an acyltransferase deficiency. Current Biology 7: R465-R466. This prediction led to clinical confirmation (see J Pediatr. 2002. 141(5): 729-733) and to potential treatments for this disease (see J Lipid Res. 2003. 44(3): 560-566).
  61. Neuwald A.F. 1997. An unexpected structural relationship between integral membrane phosphatases and soluble haloperoxidases. Protein Science 6: 1764-1767.
  62. Neuwald A.F. 1997. A shared domain between a spindle assembly checkpoint protein and Ypt/Rab-specific GTPase-activators. Trends in Biochemical Sciences 22: 243-244.
  63. Neuwald A.F. and Landsman D.. 1997. GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Trends in Biochemical Sciences 22: 154-155.
  64. Neuwald A.F., Liu J.S., Lipman D.J. and Lawrence C.E. 1997. Extracting protein alignment models from the sequence database. Nucleic Acids Research 25: 1665-1677. 
  65. Bork P., Hofmann K., Bucher P., Neuwald A.F., Altschul S.F. and Koonin E.V. 1997. A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J. 11, 68-76.
  66. Mannella C.A., Neuwald A.F. and Lawrence C.E. 1996. Detection of likely transmembrane β-strand regions in sequences of mitochondrial pore proteins using the Gibbs sampler. Journal of Bioenergetics and Biomembranes 28: 163-169.
  67. Liu J.S., Neuwald A.F. and Lawrence C.E. 1995. Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. Journal of the American Statistical Association 90:1156-1170.
  68. Neuwald A.F., Liu J.S. and Lawrence C.E.. 1995. Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Science 4: 1618-1632. 
  69. Neuwald A.F. and Green P. 1994. Detecting Patterns in Protein Sequences. Journal of Molecular Biology 239: 698-712. 
  70. Lawrence C.E., Altschul S.F., Wootton J.C., Boguski M.S., Neuwald A.F. and Liu J.S. 1994. A Gibbs sampler for the detection of subtle motifs in multiple sequences.  Proceedings of the Twenty-seventh Hawaii International Conference on System Sciences pp. 245-254.
  71. Lawrence C.E., Altschul S.F., Boguski M.S., Liu J.S., Neuwald A.F. and Wootton J.C. 1993. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262: 208-214.
  72. Neuwald A.F., Krishnan B.R., Ahrweiler P.M., Frieden C., and Berg D.E. 1993. Conditional dihydrofolate reductase deficiency due to transposon Tn5tac1 insertion downstream from the folA gene in Escherichia coli. Gene 125: 69-73.
  73. Neuwald A.F., Krishnan B.R., Brikun I., Kulakauskas S., Suziedelis K., Tomcsanyi T., Leyh T.S. and Berg D.E.. 1992. cysQ, a gene needed for cysteine synthesis in Escherichia coli K-12 only during aerobic growth. Journal of Bacteriology 174: 415-425.
  74. Neuwald A.F., Berg D.E. and Stauffer G.V. 1992. Mutational analysis of the Escherichia coli serB promoter region reveals transcriptional linkage to a downstream gene. Gene 120: 1-9.
  75. Neuwald A.F., York J.D. and Majerus P.W. 1991. Diverse proteins homologous to inositol monophosphatase. FEBS Letters 294: 16-18.
  76. Neuwald A.F. and Stauffer G.V. 1990. IS30 activation of an smp’-lacZ gene fusion in Escherichia coli.  FEMS Microbiology Letters 56: 13-17.
  77. Neuwald A.F. and Stauffer G.V. 1989. An Escherichia coli membrane protein with a unique signal sequence.  Gene 82: 219-228.
  78. Neuwald A.F. and Stauffer G.V. 1985. DNA sequence and characterization of the   Escherichia coli serB gene.  Nucleic Acids Research 13: 7025-7039