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Items: 37

1.

Engineered resistance to Zika virus in transgenic Aedes aegypti expressing a polycistronic cluster of synthetic small RNAs.

Buchman A, Gamez S, Li M, Antoshechkin I, Li HH, Wang HW, Chen CH, Klein MJ, Duchemin JB, Paradkar PN, Akbari OS.

Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3656-3661. doi: 10.1073/pnas.1810771116. Epub 2019 Feb 5.

2.

Improved reference genome of Aedes aegypti informs arbovirus vector control.

Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC 4th, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB.

Nature. 2018 Nov;563(7732):501-507. doi: 10.1038/s41586-018-0692-z. Epub 2018 Nov 14.

3.

Integrated measurement of intracellular proteins and transcripts in single cells.

Xu AM, Liu Q, Takata KL, Jeoung S, Su Y, Antoshechkin I, Chen S, Thomson M, Heath JR.

Lab Chip. 2018 Oct 23;18(21):3251-3262. doi: 10.1039/c8lc00639c.

4.

The Caenorhabditis elegans Female-Like State: Decoupling the Transcriptomic Effects of Aging and Sperm Status.

Angeles-Albores D, Leighton DHW, Tsou T, Khaw TH, Antoshechkin I, Sternberg PW.

G3 (Bethesda). 2017 Sep 7;7(9):2969-2977. doi: 10.1534/g3.117.300080.

5.

Stepwise metamorphosis of the tubeworm Hydroides elegans is mediated by a bacterial inducer and MAPK signaling.

Shikuma NJ, Antoshechkin I, Medeiros JM, Pilhofer M, Newman DK.

Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):10097-102. doi: 10.1073/pnas.1603142113. Epub 2016 Aug 22.

6.

Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks.

Dillman AR, Macchietto M, Porter CF, Rogers A, Williams B, Antoshechkin I, Lee MM, Goodwin Z, Lu X, Lewis EE, Goodrich-Blair H, Stock SP, Adams BJ, Sternberg PW, Mortazavi A.

Genome Biol. 2015 Sep 21;16:200. doi: 10.1186/s13059-015-0746-6.

7.

Erratum: the genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families.

Schwarz EM, Hu Y, Antoshechkin I, Miller MM, Sternberg PW, Aroian RV.

Nat Genet. 2015 Jun;47(6):689. doi: 10.1038/ng0615-689a. No abstract available.

PMID:
26018900
8.

The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families.

Schwarz EM, Hu Y, Antoshechkin I, Miller MM, Sternberg PW, Aroian RV.

Nat Genet. 2015 Apr;47(4):416-22. doi: 10.1038/ng.3237. Epub 2015 Mar 2. Erratum in: Nat Genet. 2015 Jun;47(6):689.

9.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

10.

Pol II docking and pausing at growth and stress genes in C. elegans.

Maxwell CS, Kruesi WS, Core LJ, Kurhanewicz N, Waters CT, Lewarch CL, Antoshechkin I, Lis JT, Meyer BJ, Baugh LR.

Cell Rep. 2014 Feb 13;6(3):455-66. doi: 10.1016/j.celrep.2014.01.008. Epub 2014 Jan 30.

11.

Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network.

Simões-Costa M, Tan-Cabugao J, Antoshechkin I, Sauka-Spengler T, Bronner ME.

Genome Res. 2014 Feb;24(2):281-90. doi: 10.1101/gr.161182.113. Epub 2014 Jan 3.

12.

The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus.

Schwarz EM, Korhonen PK, Campbell BE, Young ND, Jex AR, Jabbar A, Hall RS, Mondal A, Howe AC, Pell J, Hofmann A, Boag PR, Zhu XQ, Gregory T, Loukas A, Williams BA, Antoshechkin I, Brown C, Sternberg PW, Gasser RB.

Genome Biol. 2013 Aug 28;14(8):R89. doi: 10.1186/gb-2013-14-8-r89.

13.

Transgene-free genome editing in Caenorhabditis elegans using CRISPR-Cas.

Chiu H, Schwartz HT, Antoshechkin I, Sternberg PW.

Genetics. 2013 Nov;195(3):1167-71. doi: 10.1534/genetics.113.155879. Epub 2013 Aug 26.

14.

Transcriptome profiling of Nasonia vitripennis testis reveals novel transcripts expressed from the selfish B chromosome, paternal sex ratio.

Akbari OS, Antoshechkin I, Hay BA, Ferree PM.

G3 (Bethesda). 2013 Sep 4;3(9):1597-605. doi: 10.1534/g3.113.007583.

15.

The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector.

Akbari OS, Antoshechkin I, Amrhein H, Williams B, Diloreto R, Sandler J, Hay BA.

G3 (Bethesda). 2013 Sep 4;3(9):1493-509. doi: 10.1534/g3.113.006742.

16.

Novel synthetic Medea selfish genetic elements drive population replacement in Drosophila; a theoretical exploration of Medea-dependent population suppression.

Akbari OS, Chen CH, Marshall JM, Huang H, Antoshechkin I, Hay BA.

ACS Synth Biol. 2014 Dec 19;3(12):915-28. doi: 10.1021/sb300079h. Epub 2012 Dec 28.

17.

Divergent mitochondrial biogenesis responses in human cardiomyopathy.

Ahuja P, Wanagat J, Wang Z, Wang Y, Liem DA, Ping P, Antoshechkin IA, Margulies KB, Maclellan WR.

Circulation. 2013 May 14;127(19):1957-67. doi: 10.1161/CIRCULATIONAHA.112.001219. Epub 2013 Apr 15.

18.

The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle.

Srinivasan J, Dillman AR, Macchietto MG, Heikkinen L, Lakso M, Fracchia KM, Antoshechkin I, Mortazavi A, Wong G, Sternberg PW.

Genetics. 2013 Apr;193(4):1279-95. doi: 10.1534/genetics.112.148809. Epub 2013 Feb 14.

19.

A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly.

Chen S, Oikonomou G, Chiu CN, Niles BJ, Liu J, Lee DA, Antoshechkin I, Prober DA.

Nucleic Acids Res. 2013 Feb 1;41(4):2769-78. doi: 10.1093/nar/gks1356. Epub 2013 Jan 8.

20.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

21.

Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans.

Maxwell CS, Antoshechkin I, Kurhanewicz N, Belsky JA, Baugh LR.

Genome Res. 2012 Oct;22(10):1920-9. doi: 10.1101/gr.133587.111. Epub 2012 Apr 26.

22.

Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator.

Huang W, Pérez-García P, Pokhilko A, Millar AJ, Antoshechkin I, Riechmann JL, Mas P.

Science. 2012 Apr 6;336(6077):75-9. doi: 10.1126/science.1219075. Epub 2012 Mar 8.

23.

Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint.

Budd ME, Antoshechkin IA, Reis C, Wold BJ, Campbell JL.

Cell Cycle. 2011 May 15;10(10):1690-8. Epub 2011 May 15.

24.

Scaffolding a Caenorhabditis nematode genome with RNA-seq.

Mortazavi A, Schwarz EM, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW.

Genome Res. 2010 Dec;20(12):1740-7. doi: 10.1101/gr.111021.110. Epub 2010 Oct 27.

25.

WormBase: a comprehensive resource for nematode research.

Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, Fernandes J, Han M, Kishore R, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW.

Nucleic Acids Res. 2010 Jan;38(Database issue):D463-7. doi: 10.1093/nar/gkp952. Epub 2009 Nov 12.

26.

WormBase 2007.

Rogers A, Antoshechkin I, Bieri T, Blasiar D, Bastiani C, Canaran P, Chan J, Chen WJ, Davis P, Fernandes J, Fiedler TJ, Han M, Harris TW, Kishore R, Lee R, McKay S, Müller HM, Nakamura C, Ozersky P, Petcherski A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW.

Nucleic Acids Res. 2008 Jan;36(Database issue):D612-7. Epub 2007 Nov 8.

27.

The versatile worm: genetic and genomic resources for Caenorhabditis elegans research.

Antoshechkin I, Sternberg PW.

Nat Rev Genet. 2007 Jul;8(7):518-32. Epub 2007 Jun 5. Review.

PMID:
17549065
28.

WormBase: new content and better access.

Bieri T, Blasiar D, Ozersky P, Antoshechkin I, Bastiani C, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Han M, Harris TW, Kishore R, Lee R, McKay S, Müller HM, Nakamura C, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Durbin R, Stein LD, Sternberg PW, Spieth J.

Nucleic Acids Res. 2007 Jan;35(Database issue):D506-10. Epub 2006 Nov 11.

29.

WormBook: the online review of Caenorhabditis elegans biology.

Girard LR, Fiedler TJ, Harris TW, Carvalho F, Antoshechkin I, Han M, Sternberg PW, Stein LD, Chalfie M.

Nucleic Acids Res. 2007 Jan;35(Database issue):D472-5. Epub 2006 Nov 11.

30.

WormBase: better software, richer content.

Schwarz EM, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Harris TW, Kenny EE, Kishore R, Lawson D, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Spooner W, Tuli MA, Van Auken K, Wang D, Durbin R, Spieth J, Stein LD, Sternberg PW.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D475-8.

31.

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics.

Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Canaran P, Chan J, Chen CK, Chen WJ, Cunningham F, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Pai S, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D383-9.

32.

WormBase: a multi-species resource for nematode biology and genomics.

Harris TW, Chen N, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Chan J, Chen CK, Chen WJ, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D411-7.

33.
35.
36.

Distinct roles for two purified factors in transcription of Xenopus mitochondrial DNA.

Antoshechkin I, Bogenhagen DF.

Mol Cell Biol. 1995 Dec;15(12):7032-42.

37.

Substrate specificity of Fpg protein. Recognition and cleavage of oxidatively damaged DNA.

Tchou J, Bodepudi V, Shibutani S, Antoshechkin I, Miller J, Grollman AP, Johnson F.

J Biol Chem. 1994 May 27;269(21):15318-24.

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