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Items: 49

1.

Targeted in situ genome-wide profiling with high efficiency for low cell numbers.

Skene PJ, Henikoff JG, Henikoff S.

Nat Protoc. 2018 May;13(5):1006-1019. doi: 10.1038/nprot.2018.015. Epub 2018 Apr 12.

PMID:
29651053
2.

A unique chromatin complex occupies young α-satellite arrays of human centromeres.

Henikoff JG, Thakur J, Kasinathan S, Henikoff S.

Sci Adv. 2015 Feb 12;1(1). pii: e1400234.

3.

The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo.

Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang JP, Henikoff JG.

Elife. 2014 Apr 15;3:e01861. doi: 10.7554/eLife.01861.

4.

The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres.

Zhang T, Talbert PB, Zhang W, Wu Y, Yang Z, Henikoff JG, Henikoff S, Jiang J.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):E4875-83. doi: 10.1073/pnas.1319548110. Epub 2013 Nov 4.

5.

"Point" centromeres of Saccharomyces harbor single centromere-specific nucleosomes.

Henikoff S, Henikoff JG.

Genetics. 2012 Apr;190(4):1575-7. doi: 10.1534/genetics.111.137711. Epub 2012 Jan 10.

6.

Tripartite organization of centromeric chromatin in budding yeast.

Krassovsky K, Henikoff JG, Henikoff S.

Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):243-8. doi: 10.1073/pnas.1118898109. Epub 2011 Dec 19.

7.

Epigenome characterization at single base-pair resolution.

Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S.

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18318-23. doi: 10.1073/pnas.1110731108. Epub 2011 Oct 24.

8.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

9.

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.

10.

H2A.Z nucleosomes enriched over active genes are homotypic.

Weber CM, Henikoff JG, Henikoff S.

Nat Struct Mol Biol. 2010 Dec;17(12):1500-7. doi: 10.1038/nsmb.1926. Epub 2010 Nov 7.

11.

Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones.

Deal RB, Henikoff JG, Henikoff S.

Science. 2010 May 28;328(5982):1161-4. doi: 10.1126/science.1186777.

12.

A comprehensive map of insulator elements for the Drosophila genome.

Nègre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, Henikoff JG, Feng X, Ahmad K, Russell S, White RA, Stein L, Henikoff S, Kellis M, White KP.

PLoS Genet. 2010 Jan 15;6(1):e1000814. doi: 10.1371/journal.pgen.1000814.

13.

A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans.

Ooi SL, Henikoff JG, Henikoff S.

Nucleic Acids Res. 2010 Mar;38(4):e26. doi: 10.1093/nar/gkp1090. Epub 2009 Dec 4.

14.

Genome-wide profiling of salt fractions maps physical properties of chromatin.

Henikoff S, Henikoff JG, Sakai A, Loeb GB, Ahmad K.

Genome Res. 2009 Mar;19(3):460-9. doi: 10.1101/gr.087619.108. Epub 2008 Dec 16.

15.

Using the blocks database to recognize functional domains.

Henikoff JG, Greene EA, Taylor N, Henikoff S, Pietrokovski S.

Curr Protoc Bioinformatics. 2002 Aug;Chapter 2:Unit 2.2. doi: 10.1002/0471250953.bi0202s00.

PMID:
18792933
16.

Histone replacement marks the boundaries of cis-regulatory domains.

Mito Y, Henikoff JG, Henikoff S.

Science. 2007 Mar 9;315(5817):1408-11.

17.

High-throughput TILLING for Arabidopsis.

Till BJ, Colbert T, Codomo C, Enns L, Johnson J, Reynolds SH, Henikoff JG, Greene EA, Steine MN, Comai L, Henikoff S.

Methods Mol Biol. 2006;323:127-35.

PMID:
16739573
18.

Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis.

Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S.

Genome Biol. 2005;6(11):R90. Epub 2005 Oct 19.

19.

Genome-scale profiling of histone H3.3 replacement patterns.

Mito Y, Henikoff JG, Henikoff S.

Nat Genet. 2005 Oct;37(10):1090-7. Epub 2005 Sep 11.

PMID:
16155569
20.

DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes.

Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S.

Curr Biol. 2005 Jan 26;15(2):154-9.

21.

Suboptimal pharmacotherapeutic management of chronic stable angina in the primary care setting.

Wiest FC, Bryson CL, Burman M, McDonell MB, Henikoff JG, Fihn SD.

Am J Med. 2004 Aug 15;117(4):234-41.

PMID:
15308432
22.

High-throughput TILLING for functional genomics.

Till BJ, Colbert T, Tompa R, Enns LC, Codomo CA, Johnson JE, Reynolds SH, Henikoff JG, Greene EA, Steine MN, Comai L, Henikoff S.

Methods Mol Biol. 2003;236:205-20.

PMID:
14501067
23.

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design.

Rose TM, Henikoff JG, Henikoff S.

Nucleic Acids Res. 2003 Jul 1;31(13):3763-6.

24.

Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis.

Greene EA, Codomo CA, Taylor NE, Henikoff JG, Till BJ, Reynolds SH, Enns LC, Burtner C, Johnson JE, Odden AR, Comai L, Henikoff S.

Genetics. 2003 Jun;164(2):731-40.

25.

Large-scale discovery of induced point mutations with high-throughput TILLING.

Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE, Henikoff JG, Comai L, Henikoff S.

Genome Res. 2003 Mar;13(3):524-30.

26.

Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3.

Tompa R, McCallum CM, Delrow J, Henikoff JG, van Steensel B, Henikoff S.

Curr Biol. 2002 Jan 8;12(1):65-8.

27.

PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane.

Ng PC, Henikoff JG, Henikoff S.

Bioinformatics. 2000 Sep;16(9):760-6. Erratum in: Bioinformatics 2001 Mar;17(3):290.

PMID:
11108698
28.

Blocks-based methods for detecting protein homology.

Henikoff JG, Pietrokovski S, McCallum CM, Henikoff S.

Electrophoresis. 2000 May;21(9):1700-6.

PMID:
10870957
29.

Amino acid substitution matrices.

Henikoff S, Henikoff JG.

Adv Protein Chem. 2000;54:73-97. Review. No abstract available.

PMID:
10829225
30.

Drosophila genomic sequence annotation using the BLOCKS+ database.

Henikoff JG, Henikoff S.

Genome Res. 2000 Apr;10(4):543-6.

31.

Increased coverage of protein families with the blocks database servers.

Henikoff JG, Greene EA, Pietrokovski S, Henikoff S.

Nucleic Acids Res. 2000 Jan 1;28(1):228-30.

32.

Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.

Henikoff S, Henikoff JG, Pietrokovski S.

Bioinformatics. 1999 Jun;15(6):471-9.

PMID:
10383472
33.

New features of the Blocks Database servers.

Henikoff JG, Henikoff S, Pietrokovski S.

Nucleic Acids Res. 1999 Jan 1;27(1):226-8.

34.

Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences.

Rose TM, Schultz ER, Henikoff JG, Pietrokovski S, McCallum CM, Henikoff S.

Nucleic Acids Res. 1998 Apr 1;26(7):1628-35.

35.

Exploring protein homology with the Blocks server.

Pietrokovski S, Henikoff JG, Henikoff S.

Trends Genet. 1998 Apr;14(4):162-3. No abstract available.

PMID:
9594665
36.

Superior performance in protein homology detection with the Blocks Database servers.

Henikoff S, Pietrokovski S, Henikoff JG.

Nucleic Acids Res. 1998 Jan 1;26(1):309-12.

37.
38.

Recent enhancements to the Blocks Database servers.

Henikoff JG, Pietrokovski S, Henikoff S.

Nucleic Acids Res. 1997 Jan 1;25(1):222-5.

39.

The risk for and severity of bleeding complications in elderly patients treated with warfarin. The National Consortium of Anticoagulation Clinics.

Fihn SD, Callahan CM, Martin DC, McDonell MB, Henikoff JG, White RH.

Ann Intern Med. 1996 Jun 1;124(11):970-9.

PMID:
8624064
40.

Using substitution probabilities to improve position-specific scoring matrices.

Henikoff JG, Henikoff S.

Comput Appl Biosci. 1996 Apr;12(2):135-43.

PMID:
8744776
41.

Blocks database and its applications.

Henikoff JG, Henikoff S.

Methods Enzymol. 1996;266:88-105.

PMID:
8743679
42.

The Blocks database--a system for protein classification.

Pietrokovski S, Henikoff JG, Henikoff S.

Nucleic Acids Res. 1996 Jan 1;24(1):197-200.

43.

Automated construction and graphical presentation of protein blocks from unaligned sequences.

Henikoff S, Henikoff JG, Alford WJ, Pietrokovski S.

Gene. 1995 Oct 3;163(2):GC17-26.

PMID:
7590261
44.

Position-based sequence weights.

Henikoff S, Henikoff JG.

J Mol Biol. 1994 Nov 4;243(4):574-8.

PMID:
7966282
45.

A computerized intervention to improve timing of outpatient follow-up: a multicenter randomized trial in patients treated with warfarin. National Consortium of Anticoagulation Clinics.

Fihn SD, McDonell MB, Vermes D, Henikoff JG, Martin DC, Callahan CM, Kent DL, White RH.

J Gen Intern Med. 1994 Mar;9(3):131-9.

PMID:
8195911
46.

Protein family classification based on searching a database of blocks.

Henikoff S, Henikoff JG.

Genomics. 1994 Jan 1;19(1):97-107.

PMID:
8188249
47.

Performance evaluation of amino acid substitution matrices.

Henikoff S, Henikoff JG.

Proteins. 1993 Sep;17(1):49-61.

PMID:
8234244
48.

Amino acid substitution matrices from protein blocks.

Henikoff S, Henikoff JG.

Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9.

49.

Automated assembly of protein blocks for database searching.

Henikoff S, Henikoff JG.

Nucleic Acids Res. 1991 Dec 11;19(23):6565-72.

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