Publications - McGill Computational Structural & Systems Biology Lab

Computational Structural & Systems Biology

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Structure-guided evolutionary analysis of interactome network rewiring at single residue resolution in yeasts. Pollet L, Xia Y. Journal of Molecular Biology 436: 168641 (2024).

Predicting depression risk in early adolescence via multimodal brain imaging. Gracia-Tabuenca Z, Barbeau EB, Xia Y, Chai X. NeuroImage: Clinical 42: 103604 (2024).

Comparative transcriptomic analyses of a Vero cell line in suspension versus adherent culture conditions. Sene MA, Xia Y, Kamen AA. International Journal of Cell Biology 2023: 9364689 (2023).

SSCAE: A neuromorphic SNN autoencoder for sc-RNA-seq dimensionality reduction. Zhang T, Amirsoleimani A, Eshraghian JK, Azghadi MR, Genov R, Xia Y. 2023 IEEE International Symposium on Circuits and Systems. 1-5 (2023). doi: 10.1109/ISCAS46773.2023.10181994.

From functional genomics of Vero cells to CRISPR-based genomic deletion for improved viral production rates. Sene MA, Xia Y, Kamen AA. Biotechnology and Bioengineering 119: 2794-2805 (2022).

Structural determinants of yeast protein-protein interaction interface evolution at the residue level. Pollet L, Lambourne L, Xia Y. Journal of Molecular Biology 434: 167750 (2022).

Overview of recent advances in Vero cells genomic characterization and engineering for high-throughput vaccine manufacturing. Sene MA, Xia Y, Kamen AA. Clinical and Translational Discovery 2: e40 (2022).

Are transient protein-protein interactions more dispensable? Ghadie MA, Xia Y. PLOS Computational Biology 18: e1010013 (2022).

Principal component analysis of alpha-helix deformations in transmembrane proteins. Bevacqua A, Bakshi S, Xia Y. PLOS ONE 16: e0257318 (2021).

Mutation edgotype drives fitness effect in human. Ghadie M, Xia Y. Frontiers in Bioinformatics 1: 690769 (2021).

Haplotype-resolved de novo assembly of the Vero cell line genome. Sene MA, Kiesslich S, Djambazian H, Ragoussis J, Xia Y, Kamen AA. npj Vaccines 6: 106 (2021).

Structural profiling of bacterial effectors reveals enrichment of host-interacting domains and motifs. Chen YF, Xia Y. Frontiers in Molecular Biosciences 8: 626600 (2021).
[Research Topic in memoriam of Cyrus Chothia]

Quantifying evolutionary importance of protein sites: a tale of two measures. Sharir-Ivry A, Xia Y. PLOS Genetics 17: e1009476 (2021).
[Selected by ISMB 2020 for a Best Talk Award to Avital Sharir-Ivry]

A pooled genome-wide screening strategy to identify and rank influenza host restriction factors in cell-based vaccine production platforms. Sharon DM, Nesdoly S, Yang HJ, Gelinas JF, Xia Y, Ansorge S, Kamen AA. Scientific Reports 10: 12166 (2020).

A reference map of the human binary protein interactome. Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Cote AG, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp JJ, Kovacs IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin SF, Choi SG, Colabella C, Coppin G, D'Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Tasan M, Tejeda A, Tropepe V, Twizere JC, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill DE, Vidal M, Roth FP, Calderwood MA. Nature 580: 402-408 (2020).

Non-catalytic binding sites induce weaker long-range evolutionary rate gradients than catalytic sites in enzymes. Sharir-Ivry A, Xia Y. Journal of Molecular Biology 431: 3860-3870 (2019).

Estimating dispensable content in the human interactome. Ghadie MA, Xia Y. Nature Communications 10: 3205 (2019).

Using pseudoenzymes to probe evolutionary design principles of enzymes. Sharir-Ivry A, Xia Y. Evolutionary Bioinformatics 15: 1-4 (2019).

Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes. Chen YF, Xia Y. PLOS Computational Biology 15: e1006762 (2019).

Nature of long-range evolutionary constraint in enzymes: insights from comparison to pseudoenzymes with similar structures. Sharir-Ivry A, Xia Y. Molecular Biology and Evolution 35: 2597-2606 (2018).
[Highlighted as a Fast Track article in Mol. Biol. Evol.]

Interactome evolution: insights from genome-wide analyses of protein-protein interactions. Ghadie MA, Coulombe-Huntington J, Xia Y. Current Opinion in Structural Biology 50: 42-48 (2018).
[Highlighted in Curr. Opin. Struct. Biol.]
A high-resolution genome-wide CRISPR/Cas9 viability screen reveals structural features and contextual diversity of the human cell-essential proteome. Bertomeu T, Coulombe-Huntington J, Chatr-aryamontri A, Bourdages KG, Coyaud E, Raught B, Xia Y, Tyers M. Molecular and Cellular Biology 38: e00302-17 (2018).

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. Ghadie MA, Lambourne L, Vidal M, Xia Y. PLOS Computational Biology 13: e1005717 (2017).

The impact of native state switching on protein sequence evolution. Sharir-Ivry A, Xia Y. Molecular Biology and Evolution 34: 1378-1390 (2017).

Upon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates. Jacobs C, Lambourne L, Xia Y, Segre D. PLOS ONE 12: e0170164 (2017).

Network centrality analysis in fungi reveals complex regulation of lost and gained genes. Coulombe-Huntington J, Xia Y. PLOS ONE 12: e0169459 (2017).

Worldwide malaria incidence and cancer mortality are inversely associated. Qin L, Chen C, Chen L, Xue R, Ou-Yang M, Zhou C, Zhao S, He Z, Xia Y, He J, Liu P, Zhong N, Chen X. Infectious Agents and Cancer 12: 14 (2017).

An inter-species protein-protein interaction network across vast evolutionary distance. Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Tasan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabasi AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M. Molecular Systems Biology 12: 865 (2016).

Widespread expansion of protein interaction capabilities by alternative splicing. Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M. Cell 164: 805-817 (2016).
[Highlighted in Nat. Methods and F1000]

A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human. Vo TV, Das J, Meyer MJ, Cordero NA, Akturk N, Wei X, Fair BJ, Degatano AG, Fragoza R, Liu LG, Matsuyama A, Trickey M, Horibata S, Grimson A, Yamano H, Yoshida M, Roth FP, Pleiss JA, Xia Y, Yu H. Cell 164: 310-323 (2016).

Widespread macromolecular interaction perturbations in human genetic disorders. Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovacs IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova A, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabasi AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M. Cell 161: 647-660 (2015).
[Highlighted in Curr. Opin. Struct. Biol. (1, 2), Curr. Opin. Genet. Dev., Curr. Opin. Biotechnol., and Curr. Opin. Syst. Biol.]

The Wnt signaling network in cancer. Apfel J, Parikh JR, Reischmann P, Ewing RM, Muller O, Xia Y, Dominguez I. Systems Biology of Cancer 222-255 (2015).

A proteome-scale map of the human interactome network. Rolland T, Tasan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabasi AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M. Cell 159: 1212-1226 (2014).
[Highlighted in Curr. Opin. Struct. Biol. (1, 2, 3), Curr. Opin. Biotechnol., and F1000]

Transcriptional correlates of disease outcome in anticoagulant-treated non-human primates infected with Ebolavirus. Garamszegi S, Yen JY, Honko AN, Geisbert JB, Robins KH, Geisbert TW, Xia Y, Hensley LE, Connor JH. PLOS Neglected Tropical Diseases 8: e3061 (2014).

A computational framework for heparan sulfate sequencing using high-resolution tandem mass spectra. Hu H, Huang Y, Mao Y, Yu X, Xu Y, Liu J, Zong C, Boons GJ, Lin C, Xia Y, Zaia J. Molecular & Cellular Proteomics 13: 2490-2502 (2014).

A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein Fur. Yu C, Lopez CA, Hu H, Xia Y, Freedman DS, Reddington AP, Daaboul GG, Unlu MS, Genco CA. PLOS ONE 9: e96832 (2014).

EPSLiM: Ensemble predictor for short linear motifs in nuclear hormone receptors. Xue R, Zakharov MN, Xia Y, Bhasin S, Costello JC, Jasuja R. Molecular Endocrinology 28: 768-777 (2014).

Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily. Pandya C, Dunaway-Mariano D, Xia Y, Allen KN. Proteins: Structure, Function, and Bioinformatics 82: 1896-1906 (2014).

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks. Garamszegi S, Franzosa EA, Xia Y. PLOS Pathogens 9: e1003778 (2013).
[Highlighted in Curr. Opin. Struct. Biol.]

Consequences of domain insertion on sequence-structure divergence in a superfold. Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN. Proceedings of the National Academy of Sciences USA 110: E3381-E3387 (2013).
[Highlighted in Curr. Opin. Struct. Biol.]

Quantitative residue-level structure-evolution relationships in the yeast membrane proteome. Franzosa EA, Xue R, Xia Y. Genome Biology and Evolution 5: 734-744 (2013).

Construction of functional linkage gene networks by data integration. Linghu B, Franzosa EA, Xia Y. Methods in Molecular Biology 939: 215-232 (2013).

Toward a three-dimensional view of protein networks between species. Franzosa EA, Garamszegi S, Xia Y. Frontiers in Microbiology 3: 428 (2012).

Regulatory network structure as a dominant determinant of transcription factor evolutionary rate. Coulombe-Huntington J, Xia Y. PLOS Computational Biology 8: e1002734 (2012).

Independent effects of protein core size and expression on residue-level structure-evolution relationships. Franzosa EA, Xia Y. PLOS ONE 7: e46602 (2012).

Multi-edge gene set networks reveal novel insights into global relationships between biological themes. Parikh JR, Xia Y, Marto JA. PLOS ONE 7: e45211 (2012).

Active clustering of biological sequences. Voevodski K, Balcan MF, Roglin H, Teng SH, Xia Y. Journal of Machine Learning Research 13: 203-225 (2012).
[Supplementary Material]

Structural models for host-pathogen protein-protein interactions: assessing coverage and bias. Franzosa EA, Xia Y. Pacific Symposium on Biocomputing 17: 287-298 (2012).

Heterozygous yeast deletion collection screens reveal essential targets of Hsp90. Franzosa EA, Albanese V, Frydman J, Xia Y, McClellan AJ. PLOS ONE 6: e28211 (2011).

Production of a reference transcriptome and a transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis. Traylor-Knowles N, Granger BR, Lubinski T, Parikh JR, Garamszegi S, Xia Y, Marto JA, Kaufman L, Finnerty JR. BMC Genomics 12: 585 (2011).

Therapeutics of Ebola hemorrhagic fever: whole-genome transcriptional analysis of successful disease mitigation. Yen JY, Garamszegi S, Geisbert JB, Rubins KH, Geisbert TW, Honko A, Xia Y, Connor JH, Hensley LE. Journal of Infectious Diseases 204: S1043-S1052 (2011).

Structural principles within the human-virus protein-protein interaction network. Franzosa EA, Xia Y. Proceedings of the National Academy of Sciences USA 108: 10538-10543 (2011).
[Highlighted in This Week in PNAS, Front. Microbiol., and Curr. Opin. Struct. Biol.]

Min-sum clustering of protein sequences with limited distance information. Voevodski K, Balcan MF, Roglin H, Teng SH, Xia Y. Proceedings of the 1st International Workshop on Similarity-Based Pattern Recognition 192-206 (2011).
[Published as Lecture Notes in Computer Science 7005: 192-206 (2011).]

Using functional linkage gene networks to study human diseases. Linghu B, Liu G, Xia Y. Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications 275-293 (2011).

Bioinformatics analysis of macrophages exposed to Porphyromonas gingivalis: implications in acute vs. chronic infections. Yu WH, Hu H, Zhou Q, Xia Y, Amar S. PLOS ONE 5: e15613 (2010).

Protein evolution in yeast transcription factor subnetworks. Wang Y, Franzosa EA, Zhang XS, Xia Y. Nucleic Acids Research 38: 5959-5969 (2010).

Discovering causal signaling pathways through gene-expression patterns. Parikh JR, Klinger B, Xia Y, Marto JA, Bluthgen N. Nucleic Acids Research 38: W109-W117 (2010).

Efficient clustering with limited distance information. Voevodski K, Balcan MF, Roglin H, Teng SH, Xia Y. Proceedings of the 26th Conference on Uncertainty in Artificial Intelligence 632-641 (2010).

Spectral affinity in protein networks. Voevodski K, Teng SH, Xia Y. BMC Systems Biology 3: 112 (2009).
[Protein Network Neighbor Search]

Precipitation patterns with polygonal boundaries between electrolytes. Pan C, Gao Q, Xie J, Xia Y, Epstein IR. Physical Chemistry Chemical Physics 11: 11033-11039 (2009).

Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Wang Y, Zhang XS, Xia Y. Nucleic Acids Research 37: 5943-5958 (2009).

Finding local communities in protein networks. Voevodski K, Teng SH, Xia Y. BMC Bioinformatics 10: 297 (2009).
[Local Community Finder (Command Line), Local Protein Community Finder]

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Linghu B, Snitkin ES, Hu Z, Xia Y, DeLisi C. Genome Biology 10: R91 (2009).

Structural determinants of protein evolution are context-sensitive at the residue level. Franzosa EA, Xia Y. Molecular Biology and Evolution 26: 2387-2395 (2009).
[Highlighted in Curr. Opin. Struct. Biol. and Nat. Rev. Genet.]

Integrated assessment of genomic correlates of protein evolutionary rate. Xia Y, Franzosa EA, Gerstein MB. PLOS Computational Biology 5: e1000413 (2009).
[Highlighted in Curr. Opin. Struct. Biol.]

A linear programming framework for inferring gene regulatory networks by integrating heterogeneous data. Wang Y, Wang RS, Joshi T, Xu D, Zhang XS, Chen L, Xia Y. Handbook of Research on Computational Methodologies in Gene Regulatory Networks 450-475 (2009).

Computational reconstruction of protein-protein interaction networks: algorithms and issues. Franzosa E, Linghu B, Xia Y. Methods in Molecular Biology 541: 89-100 (2009).

Structural correlates of protein melting temperature. Franzosa EA, Lynagh KJ, Xia Y. Proceedings of the 4th International Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations 99-106 (2009).

Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Yam AY, Xia Y, Lin HTJ, Burlingame A, Gerstein M, Frydman J. Nature Structural & Molecular Biology 15: 1255-1262 (2008).

Condition specific subnetwork identification using an optimization model. Wang Y, Xia Y. Proceedings of the 2nd International Symposium on Optimization and Systems Biology 333-340 (2008).
[Published as Lecture Notes in Operations Research 9: 333-340 (2008).]

The role of disorder in interaction networks: a structural analysis. Kim PM, Sboner A, Xia Y, Gerstein M. Molecular Systems Biology 4: 179 (2008).

High-precision high-coverage functional inference from integrated data sources. Linghu B, Snitkin ES, Holloway DT, Gustafson AM, Xia Y, DeLisi C. BMC Bioinformatics 9: 119 (2008).

Structural perspectives on protein evolution. Franzosa E, Xia Y. Annual Reports in Computational Chemistry 4: 3-21 (2008).

Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. McClellan AJ, Xia Y, Deutschbauer AM, Davis RW, Gerstein M, Frydman J. Cell 131: 121-135 (2007).
[Highlighted in Nat. Struct. Mol. Biol., Curr. Opin. Genet. Dev., and F1000]

Relating three-dimensional structures to protein networks provides evolutionary insights. Kim PM, Lu LJ, Xia Y, Gerstein MB. Science 314: 1938-1941 (2006).
[Highlighted in Science, Nat. Genet., Curr. Opin. Struct. Biol. (1, 2, 3), C&EN, and F1000]

Design principles of molecular networks revealed by global comparisons and composite motifs. Yu H, Xia Y, Trifonov V, Gerstein M. Genome Biology 7: R55 (2006).

Integrated prediction of the helical membrane protein interactome in yeast. Xia Y, Lu LJ, Gerstein M. Journal of Molecular Biology 357: 339-349 (2006).

Assessing the limits of genomic data integration for predicting protein networks. Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M. Genome Research 15: 945-953 (2005).
[Highlighted in F1000]

Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation. Huber D, Boyd D, Xia Y, Olma MH, Gerstein M, Beckwith J. Journal of Bacteriology 187: 2983-2991 (2005).

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms. Balasubramanian S, Xia Y, Freinkman E, Gerstein M. Nucleic Acids Research 33: 1710-1721 (2005).

Protein interaction prediction by integrating genomic features and protein interaction network analysis. Lu LJ, Xia Y, Yu H, Rives A, Lu H, Schubert F, Gerstein M. Data Analysis and Visualization in Genomics and Proteomics 61-81 (2005).

Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. Lehnert U, Xia Y, Royce TE, Goh CS, Liu Y, Senes A, Yu H, Zhang ZL, Engelman DM, Gerstein M. Quarterly Reviews of Biophysics 37: 121-146 (2004).

Analyzing cellular biochemistry in terms of molecular networks. Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M. Annual Review of Biochemistry 73: 1051-1087 (2004).

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M. Genome Research 14: 1107-1118 (2004).

Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor. Freeman-Cook LL, Dixon AM, Frank JB, Xia Y, Ely L, Gerstein M, Engelman DM, DiMaio D. Journal of Molecular Biology 338: 907-920 (2004).
[Highlighted in Curr. Opin. Genet. Dev.]

Simulating protein evolution in sequence and structure space. Xia Y, Levitt M. Current Opinion in Structural Biology 14: 202-207 (2004).
[Highlighted in Curr. Opin. Struct. Biol.]

Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution. Xia Y, Levitt M. Proteins: Structure, Function, and Bioinformatics 55: 107-114 (2004).

Physical, organizational and evolutionary principles of protein sequence-structure relationships. Xia Y. Ph.D. Thesis, Stanford University (2003).

Roles of mutation and recombination in the evolution of protein thermodynamics. Xia Y, Levitt M. Proceedings of the National Academy of Sciences USA 99: 10382-10387 (2002).
[Highlighted in F1000]

Design of an optimal Chebyshev-expanded discrimination function for globular proteins. Fain B, Xia Y, Levitt M. Protein Science 11: 2010-2021 (2002).

Determination of optimal Chebyshev-expanded hydrophobic discrimination function for globular proteins. Fain B, Xia Y, Levitt M. IBM Journal of Research and Development 45: 525-532 (2001).

Extracting knowledge-based energy functions from protein structures by error rate minimization: Comparison of methods using lattice model. Xia Y, Levitt M. Journal of Chemical Physics 113: 9318-9330 (2000).

Ab initio construction of protein tertiary structures using a hierarchical approach. Xia Y, Huang ES, Levitt M, Samudrala R. Journal of Molecular Biology 300: 171-185 (2000).
[Highlighted in Curr. Opin. Struct. Biol.]

Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches. Samudrala R, Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R. Pacific Symposium on Biocomputing 5: 176-187 (2000).

Ab initio protein structure prediction using a combined hierarchical approach. Samudrala R, Xia Y, Huang E, Levitt M. Proteins: Structure, Function, and Genetics 3S: 194-198 (1999).
[Highlighted in Mod. Drug Discov. and Curr. Opin. Struct. Biol.]

A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Samudrala R, Xia Y, Levitt M, Huang ES. Pacific Symposium on Biocomputing 4: 505-516 (1999).

Molecular modeling and design of invariant chain peptides with altered dissociation kinetics from class II MHC. Liang MN, Lee C, Xia Y, McConnell HM. Biochemistry 35: 14734-14742 (1996).

Photodissociation of methylazide: Observation of triplet methylnitrene radical. Ying L, Xia Y, Shang H, Zhao X, Tang Y. Journal of Chemical Physics 105: 5798-5805 (1996).

Photodissociation of CH₃N₃ - Spectral evidences for the formation of triplet CH₃N radical. Ying L, Xia Y, Shang H, Zhao X, Tang Y. Acta Physico-Chimica Sinica 11: 961-964 (1995).

Yu (Brandon) Xia Lab | Department of Bioengineering | McGill University