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Items: 43

1.

Germline Genetic Risk Variants for Progressive Multifocal Leukoencephalopathy.

Eis PS, Bruno CD, Richmond TA, Koralnik IJ, Hanson BA, Major EO, Chow CR, Hendel-Chavez H, Stankoff B, Gasnault J, Taoufik Y, Hatchwell E.

Front Neurol. 2020 Mar 17;11:186. doi: 10.3389/fneur.2020.00186. eCollection 2020.

2.

Exploring the Sea Urchin Neuropeptide Landscape by Mass Spectrometry.

Monroe EB, Annangudi SP, Wadhams AA, Richmond TA, Yang N, Southey BR, Romanova EV, Schoofs L, Baggerman G, Sweedler JV.

J Am Soc Mass Spectrom. 2018 May;29(5):923-934. doi: 10.1007/s13361-018-1898-x. Epub 2018 Apr 17.

3.

Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal.

Turajlic S, Xu H, Litchfield K, Rowan A, Chambers T, Lopez JI, Nicol D, O'Brien T, Larkin J, Horswell S, Stares M, Au L, Jamal-Hanjani M, Challacombe B, Chandra A, Hazell S, Eichler-Jonsson C, Soultati A, Chowdhury S, Rudman S, Lynch J, Fernando A, Stamp G, Nye E, Jabbar F, Spain L, Lall S, Guarch R, Falzon M, Proctor I, Pickering L, Gore M, Watkins TBK, Ward S, Stewart A, DiNatale R, Becerra MF, Reznik E, Hsieh JJ, Richmond TA, Mayhew GF, Hill SM, McNally CD, Jones C, Rosenbaum H, Stanislaw S, Burgess DL, Alexander NR, Swanton C; PEACE; TRACERx Renal Consortium.

Cell. 2018 Apr 19;173(3):581-594.e12. doi: 10.1016/j.cell.2018.03.057. Epub 2018 Apr 12.

4.

Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System.

Wendt J, Rosenbaum H, Richmond TA, Jeddeloh JA, Burgess DL.

Methods Mol Biol. 2018;1708:383-405. doi: 10.1007/978-1-4939-7481-8_20.

PMID:
29224155
5.

Targeted LncRNA Sequencing with the SeqCap RNA Enrichment System.

Tan JC, Bouriakov VD, Feng L, Richmond TA, Burgess D.

Methods Mol Biol. 2016;1402:73-100. doi: 10.1007/978-1-4939-3378-5_8.

PMID:
26721485
6.

Genetic perturbation of the maize methylome.

Li Q, Eichten SR, Hermanson PJ, Zaunbrecher VM, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess DL, Richmond TA, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Kaeppler SM, Jeddeloh JA, Springer NM.

Plant Cell. 2014 Dec;26(12):4602-16. doi: 10.1105/tpc.114.133140. Epub 2014 Dec 19.

7.

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.

Evans J, Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR.

Plant J. 2014 Sep;79(6):993-1008. doi: 10.1111/tpj.12601. Epub 2014 Aug 11.

8.

Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays.

Forsström B, Axnäs BB, Stengele KP, Bühler J, Albert TJ, Richmond TA, Hu FJ, Nilsson P, Hudson EP, Rockberg J, Uhlen M.

Mol Cell Proteomics. 2014 Jun;13(6):1585-97. doi: 10.1074/mcp.M113.033308. Epub 2014 Apr 4.

9.

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.

Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KF, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N.

Plant J. 2013 Nov;76(3):494-505. doi: 10.1111/tpj.12294. Epub 2013 Aug 24.

10.

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome.

Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KF, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N.

Genome Biol. 2013 Jun 12;14(6):R58. doi: 10.1186/gb-2013-14-6-r58.

11.

Urotensin II in invertebrates: from structure to function in Aplysia californica.

Romanova EV, Sasaki K, Alexeeva V, Vilim FS, Jing J, Richmond TA, Weiss KR, Sweedler JV.

PLoS One. 2012;7(11):e48764. doi: 10.1371/journal.pone.0048764. Epub 2012 Nov 8.

12.

Microarray-based capture of novel expressed cell type-specific transfrags (CoNECT) to annotate tissue-specific transcription in Drosophila melanogaster.

Hong X, Doddapaneni H, Comeron JM, Rodesch MJ, Halvensleben HA, Nien CY, Bolei F, Metpally R, Richmond TA, Albert TJ, Manak JR.

G3 (Bethesda). 2012 Aug;2(8):873-82. doi: 10.1534/g3.112.003194. Epub 2012 Aug 1.

13.

Somatic retrotransposition alters the genetic landscape of the human brain.

Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ.

Nature. 2011 Oct 30;479(7374):534-7. doi: 10.1038/nature10531.

14.

Diversity of conotoxin types from Conus californicus reflects a diversity of prey types and a novel evolutionary history.

Elliger CA, Richmond TA, Lebaric ZN, Pierce NT, Sweedler JV, Gilly WF.

Toxicon. 2011 Feb;57(2):311-22. doi: 10.1016/j.toxicon.2010.12.008. Epub 2010 Dec 21.

15.

A diverse family of novel peptide toxins from an unusual cone snail, Conus californicus.

Gilly WF, Richmond TA, Duda TF Jr, Elliger C, Lebaric Z, Schulz J, Bingham JP, Sweedler JV.

J Exp Biol. 2011 Jan 1;214(Pt 1):147-61. doi: 10.1242/jeb.046086.

16.

Whole exome capture in solution with 3 Gbp of data.

Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu YQ, Newsham I, Richmond TA, Jeddeloh JA, Muzny D, Albert TJ, Gibbs RA.

Genome Biol. 2010;11(6):R62. doi: 10.1186/gb-2010-11-6-r62. Epub 2010 Jun 17.

17.

Acquired copy number alterations in adult acute myeloid leukemia genomes.

Walter MJ, Payton JE, Ries RE, Shannon WD, Deshmukh H, Zhao Y, Baty J, Heath S, Westervelt P, Watson MA, Tomasson MH, Nagarajan R, O'Gara BP, Bloomfield CD, Mrózek K, Selzer RR, Richmond TA, Kitzman J, Geoghegan J, Eis PS, Maupin R, Fulton RS, McLellan M, Wilson RK, Mardis ER, Link DC, Graubert TA, DiPersio JF, Ley TJ.

Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12950-5. doi: 10.1073/pnas.0903091106. Epub 2009 Jul 27.

18.

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers.

Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L, Green RD, Melnick A, Hatchwell E, Bouhassira EE, Verma A, Suzuki M, Greally JM.

Nucleic Acids Res. 2009 Jul;37(12):3829-39. doi: 10.1093/nar/gkp260. Epub 2009 Apr 22.

19.

Quantitative peptidomics reveal brain peptide signatures of behavior.

Brockmann A, Annangudi SP, Richmond TA, Ament SA, Xie F, Southey BR, Rodriguez-Zas SR, Robinson GE, Sweedler JV.

Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2383-8. doi: 10.1073/pnas.0813021106. Epub 2009 Jan 28.

20.

Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

Matejková P, Strouhal M, Smajs D, Norris SJ, Palzkill T, Petrosino JF, Sodergren E, Norton JE, Singh J, Richmond TA, Molla MN, Albert TJ, Weinstock GM.

BMC Microbiol. 2008 May 15;8:76. doi: 10.1186/1471-2180-8-76.

21.

An analytical pipeline for genomic representations used for cytosine methylation studies.

Thompson RF, Reimers M, Khulan B, Gissot M, Richmond TA, Chen Q, Zheng X, Kim K, Greally JM.

Bioinformatics. 2008 May 1;24(9):1161-7. doi: 10.1093/bioinformatics/btn096. Epub 2008 Mar 18.

22.

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data.

Cahan P, Godfrey LE, Eis PS, Richmond TA, Selzer RR, Brent M, McLeod HL, Ley TJ, Graubert TA.

Nucleic Acids Res. 2008 Apr;36(7):e41. doi: 10.1093/nar/gkn110. Epub 2008 Mar 11.

23.

Methods in high-resolution, array-based comparative genomic hybridization.

McCormick MR, Selzer RR, Richmond TA.

Methods Mol Biol. 2007;381:189-211.

PMID:
17984520
24.

Direct selection of human genomic loci by microarray hybridization.

Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, Gibbs RA.

Nat Methods. 2007 Nov;4(11):903-5. Epub 2007 Oct 14.

PMID:
17934467
25.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

26.

Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization.

Maydan JS, Flibotte S, Edgley ML, Lau J, Selzer RR, Richmond TA, Pofahl NJ, Thomas JH, Moerman DG.

Genome Res. 2007 Mar;17(3):337-47. Epub 2007 Jan 31.

27.

A high-resolution map of segmental DNA copy number variation in the mouse genome.

Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM, Ley TJ.

PLoS Genet. 2007 Jan 5;3(1):e3. Epub 2006 Nov 22.

28.

From the genome to the proteome: uncovering peptides in the Apis brain.

Hummon AB, Richmond TA, Verleyen P, Baggerman G, Huybrechts J, Ewing MA, Vierstraete E, Rodriguez-Zas SL, Schoofs L, Robinson GE, Sweedler JV.

Science. 2006 Oct 27;314(5799):647-9.

29.

Ultra-high resolution array painting facilitates breakpoint sequencing.

Gribble SM, Kalaitzopoulos D, Burford DC, Prigmore E, Selzer RR, Ng BL, Matthews NS, Porter KM, Curley R, Lindsay SJ, Baptista J, Richmond TA, Carter NP.

J Med Genet. 2007 Jan;44(1):51-8. Epub 2006 Sep 13.

30.

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.

Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J.

Genome Res. 2006 Oct;16(10):1299-309. Epub 2006 Sep 5.

31.

Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome.

Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA, Stewart H, Price SM, Blair E, Hennekam RC, Fitzpatrick CA, Segraves R, Richmond TA, Guiver C, Albertson DG, Pinkel D, Eis PS, Schwartz S, Knight SJ, Eichler EE.

Nat Genet. 2006 Sep;38(9):1038-42. Epub 2006 Aug 13.

PMID:
16906162
32.

Comparative isoschizomer profiling of cytosine methylation: the HELP assay.

Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM.

Genome Res. 2006 Aug;16(8):1046-55. Epub 2006 Jun 29.

33.

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays.

Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, Dorschner MO, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA.

Nat Methods. 2006 Jul;3(7):511-8.

PMID:
16791208
34.

Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori.

Albert TJ, Dailidiene D, Dailide G, Norton JE, Kalia A, Richmond TA, Molla M, Singh J, Green RD, Berg DE.

Nat Methods. 2005 Dec;2(12):951-3. Epub 2005 Nov 18.

PMID:
16299480
35.

Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH.

Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, Nair P, Brothman AR, Stallings RL.

Genes Chromosomes Cancer. 2005 Nov;44(3):305-19.

PMID:
16075461
36.

A high-resolution map of active promoters in the human genome.

Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B.

Nature. 2005 Aug 11;436(7052):876-80. Epub 2005 Jun 29.

37.

monitoring activity-dependent peptide release from the CNS using single-bead solid-phase extraction and MALDI TOF MS detection.

Hatcher NG, Richmond TA, Rubakhin SS, Sweedler JV.

Anal Chem. 2005 Mar 15;77(6):1580-7.

PMID:
15762560
38.

Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays.

Wong CW, Albert TJ, Vega VB, Norton JE, Cutler DJ, Richmond TA, Stanton LW, Liu ET, Miller LD.

Genome Res. 2004 Mar;14(3):398-405.

39.

Integrative approaches to determining Csl function.

Richmond TA, Somerville CR.

Plant Mol Biol. 2001 Sep;47(1-2):131-43.

PMID:
11554468
40.

The cellulose synthase superfamily.

Richmond TA, Somerville CR.

Plant Physiol. 2000 Oct;124(2):495-8. No abstract available.

41.

Engineered metal binding sites on green fluorescence protein.

Richmond TA, Takahashi TT, Shimkhada R, Bernsdorf J.

Biochem Biophys Res Commun. 2000 Feb 16;268(2):462-5.

PMID:
10679227
42.
43.

The fate of inflorescence meristems is controlled by developing fruits in Arabidopsis.

Hensel LL, Nelson MA, Richmond TA, Bleecker AB.

Plant Physiol. 1994 Nov;106(3):863-76.

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