Publications
2022
Evolutionary origin and sequence signatures of the heterodimeric ABCG5/ABCG8 transporter. Pei J., Cong Q. Protein Science. 31 (5): e4297.
Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera). Zhang J., Cong Q., Shen J., Grishin N.V. Insecta mundi. 2022 (921): 1409.
Co-Component Signal Transduction Systems: fast-evolving virulence regulation cassettes discovered in enteric bacteria. Kinch L.N., Cong Q., Jaishankar J., Orth K. bioRxiv
Towards a structurally resolved cancer interactome. Zhang J., Pei J., Durham J., Bos T., Cong Q. bioRxiv.
Genomics‐based higher classification of the species‐rich hairstreaks (Lepidoptera: Lycaenidae: Eumaeini). Robbins R.K., Cong Q., Zhang J., Shen J., Busby R.C., Faynel C., Duarte M., Martins A.R., Prieto C., Lamas G., Grishin N.V. Systematic Entomology. (online publication)
2021
Influence of the large‐Z effect during contact between butterfly sister species. Nelson E.D., Cong Q., Grishin N.V. Ecology and evolution. 11 (17): 11615-11626.
Accurate prediction of protein structures and interactions using a three-track neural network. Baek M., DiMaio F., Anishchenko I., Dauparas J., Ovchinnikov S., Lee G.R., Wang J., Cong Q., Kinch L.N., Schaeffer R.D., Millán C., Park H., Adams C., Glassman C.R., DeGiovanni A., Pereira J.H., Rodrigues A.V., Dijk A.A.V., Ebrecht A.C., Opperman D.J., Sagmeister T., Buhlheller C., Pavkov-Keller T., Rathinaswamy M.K., Dalwadi U., Yip C.K., Burke J.E., Garcia K.C., Grishin N.V., Adams P.D., Read R.J., Baker D. Science. 373 (6557): 871-876.
Comment (Case 3709)–Additional comments on the proposed conservation of names for western North American Hesperia comma-group subspecies through designation of neotypes. Calhoun J.V., Cong Q., Grishin N.V., Warren A.D. The Bulletin of Zoological Nomenclature. 78 (2): 131-132.
A uniquely patterned new species of Emesis from Honduras (Riodinidae). Gallardo R.J., Zhang J., Cong Q., Shen J., Grishin N.V. Tropical Lepidoptera Research. 31 (1): 53-59.
A covariation analysis reveals elements of selectivity in quorum sensing systems. Miranda S.W., Cong Q., Schaefer A.L., MacLeod E.K., Zimenko A., Baker D., Greenberg E.P. eLife. 10: e69169.
Genomics reveals the origins of historical specimens. Cong Q., Shen J., Zhang J., Li W., Kinch L.N., Calhoun J.V., Warren A.D., Grishin N.V. Molecular biology and evolution. 38 (5): 2166-2176.
A switch to feeding on cycads generates parallel accelerated evolution of toxin tolerance in two clades of Eumaeus caterpillars (Lepidoptera: Lycaenidae). Robbins R.K., Cong Q., Zhang J., Shen J., Riera J.Q., Murray D., Busby R.C., Faynel C., Hallwachs W., Janzen D.H., Grishin N.V. Proceedings of the National Academy of Sciences. 118 (7): e2018965118.
Computed structures of core eukaryotic protein complexes. Humphreys I.R., Pei J., Baek M., Krishnakumar A., Anishchenko I., Ovchinnikov S., Zhang J., Ness T.J., Banjade S., Bagde S.R., Stancheva V.G., Li X., Liu K., Zheng Z., Barrero D.J., Roy U., Kuper J., Fernández I.S., Szakal B., Branzei D., Rizo J., Kisker C., Greene E.C., Biggins S., Keeney S., Miller E.A., Fromme J.C., Hendrickson T.L., Cong Q., Baker D. Science. 374 (6573): eabm4805.
Two new species of Hermeuptychia from North America and three neotype designations (Nymphalidae: Satyrinae). Cong Q., Barbosa E.P., Marín M.A., Freitas A.V., Lamas G., Grishin N.V. The Taxonomic Report of the International Lepidoptera Survey. 9 (7).
Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling. Pei J., Zhang J., Cong Q. bioRxiv.
Genomics-guided refinement of butterfly taxonomy. Zhang J., Cong Q., Shen J., Opler P.A., Grishin N.V. The taxonomic report of the International Lepidoptera Survey. 9 (3).
2020
A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini). Zhang J., Brockmann E., Cong Q., Shen J., Grishin N.V. Zootaxa. 4748 (1).
Genomic evidence suggests further changes of butterfly names. Zhang J., Cong Q., Shen J., Opler P.A., Grishin N.V. The Taxonomic Report of the International Lepidoptera Survey 8 (7).
Speciation in North American Junonia from a genomic perspective. Cong Q., Zhang J., Shen J., Cao X., Brévignon C., Grishin N.V. Systematic entomology. 45 (4): 803-837.
Protein contact prediction using metagenome sequence data and residual neural networks. Wu Q., Peng Z., Anishchenko I., Cong Q., Baker D., Yang J. Bioinformatics. 36 (1): 41-48.
The meadow jumping mouse genome and transcriptome suggest mechanisms of hibernation. Cong Q., Brem E.A., Zhang J., Alföldi J., Johnson J., Karlsson E.K., Lindblad-Toh K., Malaney J.L., Israelsen W.J. bioRxiv.
The mitogenome of a Malagasy butterfly Malaza fastuosus (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (Lepidoptera) Zhang J., Lees D.C., Shen J., Cong Q., Huertas B., Martin G., Grishin N.V. Genome. 63 (4): 195-202.
2019
Genomic analysis of the tribe Emesidini (Lepidoptera: Riodinidae). Zhang J., Shen J., Cong Q., Grishin N.V. Zootaxa. 4668 (4): 475-488.
Assessing predictions on fitness effects of missense variants in calmodulin. Zhang J., Kinch L.N., Cong Q., Katsonis P., Lichtarge O., Savojardo C., Babbi G., Martelli P.L., Capriotti E., Casadio R., Garg A., Pal D., Weile J., Sun S., Verby M., Roth F.P., Grishin N.V. Human mutation. 40 (9): 1463-1473.
Protein interaction networks revealed by proteome coevolution. Cong Q., Anishchenko I., Ovchinnikov S., Baker D. Science. 365 (6449): 185-189.
Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae). Zhang J., Cong Q., Shen J., Brockmann E., Grishin N.V. Proceedings of the Royal Society B. 286 (1903): 20190609.
Functional expression and characterization of the envelope glycoprotein E1E2 heterodimer of hepatitis C virus. Cao L., Yu B., Kong D., Cong Q., Yu T., Chen Z., Hu Z., Chang H., Zhong J., Baker D., He Y. PLoS pathogens. 15 (5): e1007759.
Comment (Case 3709)–More comments on the proposed conservation of names for western North American Hesperia comma-group subspecies through designation of neotypes. Calhoun J.V., Cong Q., Grishin N.V., Warren A.D. The Bulletin of Zoological Nomenclature. 76 (1): 57-59.
Genomes of skipper butterflies reveal extensive convergence of wing patterns. Li W., Cong Q., Shen J., Zhang J., Hallwachs W., Janzen D.H., Grishin N.V. Proceedings of the National Academy of Sciences. 116 (13): 6232-6237.
The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots. Cong Q., Li W., Borek D., Otwinowski Z., Grishin N.V. Molecular Genetics and Genomics. 294 (1): 211-226.
Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking. Porter K.A., Padhorny D., Desta I., Ignatov M., Beglov D., Kotelnikov S., Sun Z., Alekseenko A., Anishchenko I., Cong Q., Ovchinnikov S., Baker D., Vajda S., Kozakov D. Proteins: Structure, Function, and Bioinformatics. 87 (12): 1241-1248.
High‐accuracy refinement using Rosetta in CASP13. Park H., Lee G.R., Kim D.E., Anishchenko I., Cong Q., Baker D. Proteins: Structure, Function, and Bioinformatics. 87 (12): 1276-1282
Fifty new genera of Hesperiidae (Lepidoptera). Cong Q., Zhang J., Shen J., Grishin N. Insecta mundi. 2019: 0731.
Gypsy moth genome provides insights into flight capability and virus–host interactions. Zhang J., Cong Q., Rex E.A., Hallwachs W., Janzen D.H., Grishin N.V., Gammon D.B. Proceedings of the National Academy of Sciences. 116 (5): 1669-1678.
Genomic determinants of speciation. Cong Q., Zhang J., Grishin N.V. bioRxiv. 837666.
Genomics of a complete butterfly continent. Zhang J., Cong Q., Shen J., Opler P.A., Grishin N.V. BioRxiv. 829887.
Changes to North American butterfly names. Zhang J., Cong Q., Shen J., Opler P.A., Grishin N.V. The taxonomic report of the International Lepidoptera Survey 8: (2).
Three new subfamilies of skipper butterflies (Lepidoptera, Hesperiidae). Zhang J., Cong Q., Shen J., Brockmann E., Grishin N.V. Zookeys. 861: 91-105.
2018
Expanding clinical phenotype in CACNA1C related disorders: From neonatal onset severe epileptic encephalopathy to late‐onset epilepsy. Bozarth X., Dines J.N., Cong Q., Mirzaa G.M., Foss K., Merritt J.L., Thies J., Mefford H.C., Novotny E. American Journal of Medical Genetics Part A. 176 (12): 2733-2739.
Comparative analysis of Swallowtail transcriptomes suggests molecular determinants for speciation and adaptation. Cong Q., Grishin N.V. Genome. 61 (12): 843-855.
2017
Assessing predictions of fitness effects of missense mutations in SUMO‐conjugating enzyme UBE2I. Zhang J., Kinch L.N., Cong Q., Weile J., Sun S., Cote A.G., Roth F.P., Grishin N.V. Human mutation. 38 (9): 1051-1063.
Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology. Janzen D.H., Burns J.M., Cong Q., Hallwachs W., Dapkey T., Manjunath R., Hajibabaei M., Hebert P.D., Grishin N.V. Proceedings of the National Academy of Sciences. 114 (31): 8313-8318.
Complete genome of Achalarus lyciades, the first representative of the Eudaminae subfamily of skippers. Shen J., Cong Q., Borek D., Otwinowski Z., Grishin N.V. Current Genomics. 18 (4): 366-374.
Acute hepatopancreatic necrosis disease-causing Vibrio parahaemolyticus strains maintain an antibacterial type VI secretion system with versatile effector repertoires. Li P., Kinch L.N., Ray A., Dalia A.B., Cong Q., Nunan L.M., Camilli A., Grishin N.V., Salomon D., Orth K. Applied and environmental microbiology. 83 (13): e00737-17.
When COI barcodes deceive: complete genomes reveal introgression in hairstreaks. Cong Q., Shen J., Borek D., Robbins R.K., Opler P.A., Otwinowski Z., Grishin N.V. Proceedings of the Royal Society B: Biological Sciences. 284 (1848): 20161735.
Mitogenomes of the four Agathymus holotypes collected 55 years ago. Zhang J., Cong Q., Shen J., Grishin N.V. Mitochondrial DNA Part B. 2 (2): 598-600.
The first complete genomes of Metalmarks and the classification of butterfly families. Cong Q., Shen J., Li W., Borek D., Otwinowski Z., Grishin N.V. Genomics. 109 (5-6): 485-493.
The complete mitogenome of Euschemon rafflesia (Lepidoptera: Hesperiidae). Zhang J., Cong Q., Shen J., Fan X., Wang M., Grishin N.V. Mitochondrial DNA Part B. 2 (1): 136-138.
The complete mitochondrial genome of a skipper Burara striata (Lepidoptera: Hesperiidae). Zhang J., Cong Q., Shen J., Wang R., Grishin N.V. Mitochondrial DNA Part B 2 (1): 145-147.
Mitogenomes of giant-skipper butterflies reveal an ancient split between deep and shallow root feeders. Zhang J., Cong Q., Fan X., Wang R., Wang M., Grishin N.V. F1000Research. 6: 222.
2016
Complete genomes of Hairstreak butterflies, their speciation and nucleo-mitochondrial incongruence. Cong Q., Shen J., Borek D., Robbins R.K., Otwinowski Z., Grishin N.V. Scientific reports. 6 (1): 1-15.
Speciation in cloudless sulphurs gleaned from complete genomes. Cong Q., Shen J., Warren A.D., Borek D., Otwinowski Z., Grishin N.V. Genome biology and evolution. 8 (3): 915-931.
The complete mitochondrial genome of Lerema accius and its phylogenetic implications. Cong Q., Grishin N.V. PeerJ. 4: e1546.
The complete mitogenome of Achalarus lyciades (Lepidoptera: Hesperiidae). Shen J., Cong Q., Grishin N.V. Mitochondrial DNA Part B. 1 (1): 581-583.
Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins. Shen J., Cong Q., Kinch L.N., Borek D., Otwinowski Z., Grishin N.V. F1000Research. 5: 2631.
2015
Predictive and comparative analysis of Ebolavirus proteins. Cong Q., Pei J., Grishin N.V. Cell Cycle. 14 (17): 2785-2797.
The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications. Shen J., Cong Q., Grishin N.V. Meta Gene. 5: 68-83.
Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation. Liu S., Cai X., Wu J., Cong Q., Chen X., Li T., Du F., Ren J., Wu Y., Grishin N.V., Chen Z.J. Science. 347 (6227): aaa2630.
Tiger swallowtail genome reveals mechanisms for speciation and caterpillar chemical defense. Cong Q., Borek D., Otwinowski Z., Grishin N.V. Cell reports. 10 (6): 910-919.
Skipper genome sheds light on unique phenotypic traits and phylogeny. Cong Q., Borek D., Otwinowski Z., Grishin N.V. BMC genomics. 16 (1): 1-13.
2014
A new Heraclides swallowtail (Lepidoptera, Papilionidae) from North America is recognized by the pattern on its neck. Shiraiwa K., Cong Q., Grishin N.V. Zookeys. 468: 85.
A new Hermeuptychia (Lepidoptera, Nymphalidae, Satyrinae) is sympatric and synchronic with H. sosybius in southeast US coastal plains, while another new Hermeuptychia species inhabits south Texas and northeast Mexico. Cong Q., Grishin N.V. ZooKeys. 379: 43.
2013
Seq2Ref: a web server to facilitate functional interpretation. Li W., Cong Q., Kinch L.N., Grishin N.V. BMC bioinformatics. 14 (1): 1-7.
M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci. Ji R., Cong Q., Li W., Grishin N.V. Bioinformatics. 29 (22): 2953-2954.
2012
Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome. Cong Q., Kinch L.N., Kim B., Grishin N.V. PloS one. 7 (7): e41071.
MESSA: MEta-server for protein sequence analysis. Cong Q., Grishin N.V. BMC biology. 10 (1): 1-12.
The ABC transporters in Candidatus Liberibacter asiaticus. Li W., Cong Q., Pei J., Kinch L.N., Grishin N.V. Proteins: Structure, Function, and Bioinformatics. 80 (11): 2614-2628.
2011
An automatic method for CASP9 free modeling structure prediction assessment. Cong Q., Kinch L.N., Pei J., Shi S., Grishin V.N., Li W., Grishin N.V. Bioinformatics. 27 (24): 3371-3378.
CASP9 target classification. Kinch L.N., Shi S., Cheng H., Cong Q., Pei J., Mariani V., Schwede T., Grishin N.V. PROTEINS: structure, function, and bioinformatics. 79 (S10): 21-36.
CASP9 assessment of free modeling target predictions. Kinch L., Shi S.Y., Cong Q., Cheng H., Liao Y., Grishin N.V. Proteins: Structure, Function, and Bioinformatics. 79 (S10): 59-73.
2010
HangOut: generating clean PSI-BLAST profiles for domains with long insertions. Kim B., Cong Q., Grishin N.V. Bioinformatics. 26 (12): 1564-1565.
Structural differences between proteins with similar sequences. Cong Q., Kim B., Kinch L.N., Grishin N.V. 2010 IEEE International Conference on BioInformatics and BioEngineering. 2010: 250-256.