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Predicting Sequence Features, Function, and Structure of Proteins Using MESSA.

Bhat AS, Grishin NV.

Curr Protoc Bioinformatics. 2019 Sep;67(1):e84. doi: 10.1002/cpbi.84.


pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes.

Lee Y, Baumhardt JM, Pei J, Chook YM, Grishin NV.

Bioinformatics. 2019 Aug 22. pii: btz657. doi: 10.1093/bioinformatics/btz657. [Epub ahead of print]


Three new subfamilies of skipper butterflies (Lepidoptera, Hesperiidae).

Zhang J, Cong Q, Shen J, Brockmann E, Grishin NV.

Zookeys. 2019 Jul 8;861:91-105. doi: 10.3897/zookeys.861.34686. eCollection 2019.


CASP13 target classification into tertiary structure prediction categories.

Kinch LN, Kryshtafovych A, Monastyrskyy B, Grishin NV.

Proteins. 2019 Jul 11. doi: 10.1002/prot.25775. [Epub ahead of print]


Assessing predictions on fitness effects of missense variants in calmodulin.

Zhang J, Kinch LN, Cong Q, Katsonis P, Lichtarge O, Savojardo C, Babbi G, Martelli PL, Capriotti E, Casadio R, Garg A, Pal D, Weile J, Sun S, Verby M, Roth FP, Grishin NV.

Hum Mutat. 2019 Sep;40(9):1463-1473. doi: 10.1002/humu.23857. Epub 2019 Sep 3.


ECOD: identification of distant homology among multidomain and transmembrane domain proteins.

Schaeffer RD, Kinch L, Medvedev KE, Pei J, Cheng H, Grishin N.

BMC Mol Cell Biol. 2019 Jun 21;20(1):18. doi: 10.1186/s12860-019-0204-5.


Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae).

Zhang J, Cong Q, Shen J, Brockmann E, Grishin NV.

Proc Biol Sci. 2019 May 29;286(1903):20190609. doi: 10.1098/rspb.2019.0609.


Functional Assessment of Lipoyltransferase-1 Deficiency in Cells, Mice, and Humans.

Ni M, Solmonson A, Pan C, Yang C, Li D, Notzon A, Cai L, Guevara G, Zacharias LG, Faubert B, Vu HS, Jiang L, Ko B, Morales NM, Pei J, Vale G, Rakheja D, Grishin NV, McDonald JG, Gotway GK, McNutt MC, Pascual JM, DeBerardinis RJ.

Cell Rep. 2019 Apr 30;27(5):1376-1386.e6. doi: 10.1016/j.celrep.2019.04.005.


Structural prerequisites for CRM1-dependent nuclear export signaling peptides: accessibility, adapting conformation, and the stability at the binding site.

Lee Y, Pei J, Baumhardt JM, Chook YM, Grishin NV.

Sci Rep. 2019 Apr 29;9(1):6627. doi: 10.1038/s41598-019-43004-0.


Unveiling one of the rarest 'butterflies' ever (Lepidoptera: Hesperiidae, Noctuidae).

Zilli A, Grishin NV.

Syst Entomol. 2019 Apr;44(2):384-395. doi: 10.1111/syen.12330. Epub 2018 Nov 3.


How Often Do Protein Genes Navigate Valleys of Low Fitness?

Nelson ED, Grishin NV.

Genes (Basel). 2019 Apr 8;10(4). pii: E283. doi: 10.3390/genes10040283.


Genomes of skipper butterflies reveal extensive convergence of wing patterns.

Li W, Cong Q, Shen J, Zhang J, Hallwachs W, Janzen DH, Grishin NV.

Proc Natl Acad Sci U S A. 2019 Mar 26;116(13):6232-6237. doi: 10.1073/pnas.1821304116. Epub 2019 Mar 15.


Identification of residues critical for topology inversion of the transmembrane protein TM4SF20 through regulated alternative translocation.

Wang J, Kinch LN, Denard B, Lee CE, Esmaeilzadeh Gharehdaghi E, Grishin N, Ye J.

J Biol Chem. 2019 Apr 12;294(15):6054-6061. doi: 10.1074/jbc.RA119.007681. Epub 2019 Feb 26.


Gypsy moth genome provides insights into flight capability and virus-host interactions.

Zhang J, Cong Q, Rex EA, Hallwachs W, Janzen DH, Grishin NV, Gammon DB.

Proc Natl Acad Sci U S A. 2019 Jan 29;116(5):1669-1678. doi: 10.1073/pnas.1818283116. Epub 2019 Jan 14.


Comparative analysis of swallowtail transcriptomes suggests molecular determinants for speciation and adaptation.

Cong Q, Grishin NV.

Genome. 2018 Dec;61(12):843-855. doi: 10.1139/gen-2018-0084. Epub 2018 Oct 26.


Combined Blockade of Activating ERBB2 Mutations and ER Results in Synthetic Lethality of ER+/HER2 Mutant Breast Cancer.

Croessmann S, Formisano L, Kinch LN, Gonzalez-Ericsson PI, Sudhan DR, Nagy RJ, Mathew A, Bernicker EH, Cristofanilli M, He J, Cutler RE Jr, Lalani AS, Miller VA, Lanman RB, Grishin NV, Arteaga CL.

Clin Cancer Res. 2019 Jan 1;25(1):277-289. doi: 10.1158/1078-0432.CCR-18-1544. Epub 2018 Oct 12.


Identification of Protein Homologs and Domain Boundaries by Iterative Sequence Alignment.

Schaeffer D, Grishin NV.

Methods Mol Biol. 2019;1851:277-286. doi: 10.1007/978-1-4939-8736-8_15.


The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots.

Cong Q, Li W, Borek D, Otwinowski Z, Grishin NV.

Mol Genet Genomics. 2019 Feb;294(1):211-226. doi: 10.1007/s00438-018-1494-6. Epub 2018 Oct 6.


Protein AMPylation by an Evolutionarily Conserved Pseudokinase.

Sreelatha A, Yee SS, Lopez VA, Park BC, Kinch LN, Pilch S, Servage KA, Zhang J, Jiou J, Karasiewicz-Urbańska M, Łobocka M, Grishin NV, Orth K, Kucharczyk R, Pawłowski K, Tomchick DR, Tagliabracci VS.

Cell. 2018 Oct 18;175(3):809-821.e19. doi: 10.1016/j.cell.2018.08.046. Epub 2018 Sep 27.


Searching ECOD for Homologous Domains by Sequence and Structure.

Schaeffer RD, Liao Y, Grishin NV.

Curr Protoc Bioinformatics. 2018 Mar;61(1):e45. doi: 10.1002/cpbi.45.


Inference of epistatic effects in a key mitochondrial protein.

Nelson ED, Grishin NV.

Phys Rev E. 2018 Jun;97(6-1):062404. doi: 10.1103/PhysRevE.97.062404.


FlyXCDB-A Resource for Drosophila Cell Surface and Secreted Proteins and Their Extracellular Domains.

Pei J, Kinch LN, Grishin NV.

J Mol Biol. 2018 Sep 14;430(18 Pt B):3353-3411. doi: 10.1016/j.jmb.2018.06.002. Epub 2018 Jun 8.


Truncated Adenomatous Polyposis Coli Mutation Induces Asef-Activated Golgi Fragmentation.

Kim SB, Zhang L, Yoon J, Lee J, Min J, Li W, Grishin NV, Moon YA, Wright WE, Shay JW.

Mol Cell Biol. 2018 Aug 15;38(17). pii: e00135-18. doi: 10.1128/MCB.00135-18. Print 2018 Sep 1.


Functional and evolutionary analysis of viral proteins containing a Rossmann-like fold.

Medvedev KE, Kinch LN, Grishin NV.

Protein Sci. 2018 Aug;27(8):1450-1463. doi: 10.1002/pro.3438. Epub 2018 Jun 13.


[Pancreatoduodenectomy: learning curve within single multi-field center].

Kaprin AD, Kostin AA, Nikiforov PV, Egorov VI, Grishin NA, Lozhkin MV, Petrov LO, Bykasov SA, Sidorov DV.

Khirurgiia (Mosk). 2018;(4):17-23. doi: 10.17116/hirurgia2018417-23. Russian.


A new species of Wahydra from Ecuador (Hesperiidae, Hesperiinae, Anthoptini).

Carneiro E, Dolibaina DR, Grishin NV, Warren AD.

Zootaxa. 2018 Mar 7;4392(1):196-200. doi: 10.11646/zootaxa.4392.1.11.


A sequence family database built on ECOD structural domains.

Liao Y, Schaeffer RD, Pei J, Grishin NV.

Bioinformatics. 2018 Sep 1;34(17):2997-3003. doi: 10.1093/bioinformatics/bty214.


Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni.

Wendt GR, Collins JN, Pei J, Pearson MS, Bennett HM, Loukas A, Berriman M, Grishin NV, Collins JJ 3rd.

Elife. 2018 Mar 20;7. pii: e33221. doi: 10.7554/eLife.33221.


The complete mitochondrial genome of a skipper Burara striata (Lepidoptera: Hesperiidae).

Zhang J, Cong Q, Shen J, Wang R, Grishin NV.

Mitochondrial DNA B Resour. 2017;2(1):145-147. doi: 10.1080/23802359.2017.1298416. Epub 2017 Mar 10.


Species richness of Eurasian Zephyrus hairstreaks (Lepidoptera: Lycaenidae: Theclini) with implications on historical biogeography: An NDM/VNDM approach.

Zhuang H, Yago M, Settele J, Li X, Ueshima R, Grishin NV, Wang M.

PLoS One. 2018 Jan 19;13(1):e0191049. doi: 10.1371/journal.pone.0191049. eCollection 2018.


Targeting the Conserved Fusion Loop of HAP2 Inhibits the Transmission of Plasmodium berghei and falciparum.

Angrisano F, Sala KA, Da DF, Liu Y, Pei J, Grishin NV, Snell WJ, Blagborough AM.

Cell Rep. 2017 Dec 5;21(10):2868-2878. doi: 10.1016/j.celrep.2017.11.024.


Complete Genome of Achalarus lyciades, The First Representative of the Eudaminae Subfamily of Skippers.

Shen J, Cong Q, Borek D, Otwinowski Z, Grishin NV.

Curr Genomics. 2017 Aug;18(4):366-374. doi: 10.2174/1389202918666170426113315.


Requirement of the fusogenic micropeptide myomixer for muscle formation in zebrafish.

Shi J, Bi P, Pei J, Li H, Grishin NV, Bassel-Duby R, Chen EH, Olson EN.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):11950-11955. doi: 10.1073/pnas.1715229114. Epub 2017 Oct 23.


Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I.

Zhang J, Kinch LN, Cong Q, Weile J, Sun S, Cote AG, Roth FP, Grishin NV.

Hum Mutat. 2017 Sep;38(9):1051-1063. doi: 10.1002/humu.23293.


Pet10p is a yeast perilipin that stabilizes lipid droplets and promotes their assembly.

Gao Q, Binns DD, Kinch LN, Grishin NV, Ortiz N, Chen X, Goodman JM.

J Cell Biol. 2017 Oct 2;216(10):3199-3217. doi: 10.1083/jcb.201610013. Epub 2017 Aug 11.


A new species of Oxynetra from Mexico (Hesperiidae, Pyrginae, Pyrrhopygini).

Warren AD, Grishin NV.

Zookeys. 2017 Apr 10;(667):155-164. doi: 10.3897/zookeys.667.6080. eCollection 2017. Review.


The first complete genomes of Metalmarks and the classification of butterfly families.

Cong Q, Shen J, Li W, Borek D, Otwinowski Z, Grishin NV.

Genomics. 2017 Oct;109(5-6):485-493. doi: 10.1016/j.ygeno.2017.07.006. Epub 2017 Jul 28.


Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology.

Janzen DH, Burns JM, Cong Q, Hallwachs W, Dapkey T, Manjunath R, Hajibabaei M, Hebert PDN, Grishin NV.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8313-8318. doi: 10.1073/pnas.1621504114. Epub 2017 Jul 17.


Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor.

Hou Z, Su L, Pei J, Grishin NV, Zhang H.

Structure. 2017 Aug 1;25(8):1187-1194.e3. doi: 10.1016/j.str.2017.05.023. Epub 2017 Jun 29.


Acute Hepatopancreatic Necrosis Disease-Causing Vibrio parahaemolyticus Strains Maintain an Antibacterial Type VI Secretion System with Versatile Effector Repertoires.

Li P, Kinch LN, Ray A, Dalia AB, Cong Q, Nunan LM, Camilli A, Grishin NV, Salomon D, Orth K.

Appl Environ Microbiol. 2017 Jun 16;83(13). pii: e00737-17. doi: 10.1128/AEM.00737-17. Print 2017 Jul 1.


Mitogenomes of Giant-Skipper Butterflies reveal an ancient split between deep and shallow root feeders.

Zhang J, Cong Q, Fan XL, Wang R, Wang M, Grishin NV.

F1000Res. 2017 Mar 6;6:222. doi: 10.12688/f1000research.10970.1. eCollection 2017.


The Ancient Gamete Fusogen HAP2 Is a Eukaryotic Class II Fusion Protein.

Fédry J, Liu Y, Péhau-Arnaudet G, Pei J, Li W, Tortorici MA, Traincard F, Meola A, Bricogne G, Grishin NV, Snell WJ, Rey FA, Krey T.

Cell. 2017 Feb 23;168(5):904-915.e10. doi: 10.1016/j.cell.2017.01.024.


When COI barcodes deceive: complete genomes reveal introgression in hairstreaks.

Cong Q, Shen J, Borek D, Robbins RK, Opler PA, Otwinowski Z, Grishin NV.

Proc Biol Sci. 2017 Feb 8;284(1848). pii: 20161735. doi: 10.1098/rspb.2016.1735.


Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins.

Shen J, Cong Q, Kinch LN, Borek D, Otwinowski Z, Grishin NV.

F1000Res. 2016 Nov 3;5:2631. doi: 10.12688/f1000research.9765.1. eCollection 2016.


The complete mitogenome of Euschemon rafflesia (Lepidoptera: Hesperiidae).

Zhang J, Cong Q, Shen J, Fan XL, Wang M, Grishin NV.

Mitochondrial DNA B Resour. 2017;2(1):136-138. doi: 10.1080/23802359.2017.1292478. Epub 2017 Feb 23.


Mitogenomes of the four Agathymus holotypes collected 55 years ago.

Zhang J, Cong Q, Shen J, Grishin NV.

Mitochondrial DNA B Resour. 2017;2(2):598-600. doi: 10.1080/23802359.2017.1372701. Epub 2017 Sep 4.


Expansion of divergent SEA domains in cell surface proteins and nucleoporin 54.

Pei J, Grishin NV.

Protein Sci. 2017 Mar;26(3):617-630. doi: 10.1002/pro.3096. Epub 2017 Feb 13.


Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog.

Volkov OA, Kinch L, Ariagno C, Deng X, Zhong S, Grishin N, Tomchick DR, Chen Z, Phillips MA.

Elife. 2016 Dec 15;5. pii: e20198. doi: 10.7554/eLife.20198.


ECOD: new developments in the evolutionary classification of domains.

Schaeffer RD, Liao Y, Cheng H, Grishin NV.

Nucleic Acids Res. 2017 Jan 4;45(D1):D296-D302. doi: 10.1093/nar/gkw1137. Epub 2016 Nov 29.


Structure of protein O-mannose kinase reveals a unique active site architecture.

Zhu Q, Venzke D, Walimbe AS, Anderson ME, Fu Q, Kinch LN, Wang W, Chen X, Grishin NV, Huang N, Yu L, Dixon JE, Campbell KP, Xiao J.

Elife. 2016 Nov 23;5. pii: e22238. doi: 10.7554/eLife.22238.

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