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Items: 1 to 50 of 293

1.

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 14. pii: 201818283. doi: 10.1073/pnas.1818283116. [Epub ahead of print]

PMID:
30642971
2.

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.

PMID:
30314968
3.

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.

PMID:
30298403
4.

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. 2018 Oct 6. doi: 10.1007/s00438-018-1494-6. [Epub ahead of print]

PMID:
30293092
5.

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.

PMID:
30270044
6.

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.

PMID:
30040199
7.

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.

PMID:
30011480
8.

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.

PMID:
29890119
9.

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.

PMID:
29866653
10.

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.

PMID:
29722076
11.

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.

PMID:
29690424
12.

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.

PMID:
29659718
13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

Long-Range Epistasis Mediated by Structural Change in a Model of Ligand Binding Proteins.

Nelson ED, Grishin NV.

PLoS One. 2016 Nov 21;11(11):e0166739. doi: 10.1371/journal.pone.0166739. eCollection 2016.

34.

Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei.

Leija C, Rijo-Ferreira F, Kinch LN, Grishin NV, Nischan N, Kohler JJ, Hu Z, Phillips MA.

PLoS Pathog. 2016 Nov 7;12(11):e1006010. doi: 10.1371/journal.ppat.1006010. eCollection 2016 Nov.

35.

Evolution of off-lattice model proteins under ligand binding constraints.

Nelson ED, Grishin NV.

Phys Rev E. 2016 Aug;94(2-1):022410. doi: 10.1103/PhysRevE.94.022410. Epub 2016 Aug 15.

PMID:
27627338
36.

Compact Structure Patterns in Proteins.

Chitturi B, Shi S, Kinch LN, Grishin NV.

J Mol Biol. 2016 Oct 23;428(21):4392-4412. doi: 10.1016/j.jmb.2016.07.022. Epub 2016 Aug 4.

PMID:
27498165
37.

Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus.

Ray A, Kinch LN, de Souza Santos M, Grishin NV, Orth K, Salomon D.

MBio. 2016 Jul 26;7(4). pii: e01077-16. doi: 10.1128/mBio.01077-16.

38.

HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing.

Liu H, Liang C, Kollipara RK, Matsui M, Ke X, Jeong BC, Wang Z, Yoo KS, Yadav GP, Kinch LN, Grishin NV, Nam Y, Corey DR, Kittler R, Liu Q.

Mol Cell. 2016 Aug 4;63(3):420-32. doi: 10.1016/j.molcel.2016.06.014. Epub 2016 Jul 14.

39.

Bile salt receptor complex activates a pathogenic type III secretion system.

Li P, Rivera-Cancel G, Kinch LN, Salomon D, Tomchick DR, Grishin NV, Orth K.

Elife. 2016 Jul 5;5. pii: e15718. doi: 10.7554/eLife.15718.

40.

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

Bromberg R, Grishin NV, Otwinowski Z.

PLoS Comput Biol. 2016 Jun 23;12(6):e1004985. doi: 10.1371/journal.pcbi.1004985. eCollection 2016 Jun.

41.

Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models.

Li W, Schaeffer RD, Otwinowski Z, Grishin NV.

PLoS One. 2016 May 5;11(5):e0154786. doi: 10.1371/journal.pone.0154786. eCollection 2016.

42.

Crystal structure of the human sterol transporter ABCG5/ABCG8.

Lee JY, Kinch LN, Borek DM, Wang J, Wang J, Urbatsch IL, Xie XS, Grishin NV, Cohen JC, Otwinowski Z, Hobbs HH, Rosenbaum DM.

Nature. 2016 May 26;533(7604):561-4. doi: 10.1038/nature17666. Epub 2016 May 4.

43.

Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence.

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

Sci Rep. 2016 Apr 28;6:24863. doi: 10.1038/srep24863.

44.

Direct Demonstration That Loop1 of Scap Binds to Loop7: A CRUCIAL EVENT IN CHOLESTEROL HOMEOSTASIS.

Zhang Y, Lee KM, Kinch LN, Clark L, Grishin NV, Rosenbaum DM, Brown MS, Goldstein JL, Radhakrishnan A.

J Biol Chem. 2016 Jun 10;291(24):12888-96. doi: 10.1074/jbc.M116.729798. Epub 2016 Apr 11.

45.

Speciation in Cloudless Sulphurs Gleaned from Complete Genomes.

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

Genome Biol Evol. 2016 Mar 30;8(3):915-31. doi: 10.1093/gbe/evw045.

46.

Absence of TLR11 in Mice Does Not Confer Susceptibility to Salmonella Typhi.

Song J, Wilhelm CL, Wangdi T, Maira-Litran T, Lee SJ, Raetz M, Sturge CR, Mirpuri J, Pei J, Grishin NV, McSorley SJ, Gewirtz AT, Bäumler AJ, Pier GB, Galán JE, Yarovinsky F.

Cell. 2016 Feb 25;164(5):827-8. doi: 10.1016/j.cell.2016.02.015. No abstract available.

47.

Assessment of CASP11 contact-assisted predictions.

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

Proteins. 2016 Sep;84 Suppl 1:164-80. doi: 10.1002/prot.25020. Epub 2016 Mar 9.

48.

Classification of proteins with shared motifs and internal repeats in the ECOD database.

Schaeffer RD, Kinch LN, Liao Y, Grishin NV.

Protein Sci. 2016 Jul;25(7):1188-203. doi: 10.1002/pro.2893. Epub 2016 Feb 21. Review.

49.

The complete mitochondrial genome of Lerema accius and its phylogenetic implications.

Cong Q, Grishin NV.

PeerJ. 2016 Jan 7;4:e1546. doi: 10.7717/peerj.1546. eCollection 2016.

50.

CASP 11 target classification.

Kinch LN, Li W, Schaeffer RD, Dunbrack RL, Monastyrskyy B, Kryshtafovych A, Grishin NV.

Proteins. 2016 Sep;84 Suppl 1:20-33. doi: 10.1002/prot.24982. Epub 2016 Jan 27.

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