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Items: 1 to 50 of 54

1.

svtools: population-scale analysis of structural variation.

Larson DE, Abel HJ, Chiang C, Badve A, Das I, Eldred JM, Layer RM, Hall IM.

Bioinformatics. 2019 Nov 1;35(22):4782-4787. doi: 10.1093/bioinformatics/btz492.

2.

A map of constrained coding regions in the human genome.

Havrilla JM, Pedersen BS, Layer RM, Quinlan AR.

Nat Genet. 2019 Jan;51(1):88-95. doi: 10.1038/s41588-018-0294-6. Epub 2018 Dec 10.

3.

Internal decompression of the acutely contused spinal cord: Differential effects of irrigation only versus biodegradable scaffold implantation.

Guest JD, Moore SW, Aimetti AA, Kutikov AB, Santamaria AJ, Hofstetter CP, Ropper AE, Theodore N, Ulich TR, Layer RT.

Biomaterials. 2018 Dec;185:284-300. doi: 10.1016/j.biomaterials.2018.09.025. Epub 2018 Sep 19.

PMID:
30265898
4.

Method and Apparatus for the Automated Delivery of Continuous Neural Stem Cell Trails Into the Spinal Cord of Small and Large Animals.

Kutikov AB, Moore SW, Layer RT, Podell PE, Sridhar N, Santamaria AJ, Aimetti AA, Hofstetter CP, Ulich TR, Guest JD.

Neurosurgery. 2019 Oct 1;85(4):560-573. doi: 10.1093/neuros/nyy379.

PMID:
30169668
5.

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy.

Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR.

NPJ Genom Med. 2018 Aug 13;3:22. doi: 10.1038/s41525-018-0061-8. eCollection 2018.

6.

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK.

Nucleic Acids Res. 2018 Jul 2;46(W1):W186-W193. doi: 10.1093/nar/gky474.

7.

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.

Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, Layer RM.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy064.

8.

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.

Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Wang HZ, Currall BB, Zhao X, Dea J, Duhn C, Erdman CA, Gilson MC, Yadav R, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Walker MF, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth GT, Roeder K, Devlin B, Talkowski ME, Sanders SJ.

Nat Genet. 2018 Apr 26;50(5):727-736. doi: 10.1038/s41588-018-0107-y.

9.

Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2018 Feb 5;9(1):572. doi: 10.1038/s41467-017-02383-6.

10.

GIGGLE: a search engine for large-scale integrated genome analysis.

Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR.

Nat Methods. 2018 Feb;15(2):123-126. doi: 10.1038/nmeth.4556. Epub 2018 Jan 8.

11.

Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3. Erratum in: Nat Commun. 2018 Feb 5;9(1):572.

12.

New Clinical-Pathological Classification of Intraspinal Injury Following Traumatic Acute Complete Thoracic Spinal Cord Injury: Postdurotomy/Myelotomy Observations From the INSPIRE Trial.

Layer RT, Ulich TR, Coric D, Arnold PM, Guest JD, Heary RH, Hsieh PC, Jenkins AL, Kim KD, Lee KS, Masuoka LK, Neff KM, Ray WZ, Theodore N, Fehlings MG.

Neurosurgery. 2017 Sep 1;64(CN_suppl_1):105-109. doi: 10.1093/neuros/nyx204. No abstract available.

PMID:
28899037
13.

A parallel algorithm for N-way interval set intersection.

Layer RM, Quinlan AR.

Proc IEEE Inst Electr Electron Eng. 2017 Mar;105(3):542-551. doi: 10.1109/JPROC.2015.2461494.

14.

Biodegradable scaffolds promote tissue remodeling and functional improvement in non-human primates with acute spinal cord injury.

Slotkin JR, Pritchard CD, Luque B, Ye J, Layer RT, Lawrence MS, O'Shea TM, Roy RR, Zhong H, Vollenweider I, Edgerton VR, Courtine G, Woodard EJ, Langer R.

Biomaterials. 2017 Apr;123:63-76. doi: 10.1016/j.biomaterials.2017.01.024. Epub 2017 Jan 25.

PMID:
28167393
15.

Vcfanno: fast, flexible annotation of genetic variants.

Pedersen BS, Layer RM, Quinlan AR.

Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5.

16.

Sustained Local Release of Methylprednisolone From a Thiol-Acrylate Poly(Ethylene Glycol) Hydrogel for Treating Chronic Compressive Radicular Pain.

Slotkin JR, Ness JK, Snyder KM, Skiles AA, Woodard EJ, O╩╝Shea T, Layer RT, Aimetti AA, Toms SA, Langer R, Tapinos N.

Spine (Phila Pa 1976). 2016 Apr;41(8):E441-8. doi: 10.1097/BRS.0000000000001309.

PMID:
26630427
17.

Efficient genotype compression and analysis of large genetic-variation data sets.

Layer RM, Kindlon N, Karczewski KJ; Exome Aggregation Consortium, Quinlan AR.

Nat Methods. 2016 Jan;13(1):63-5. doi: 10.1038/nmeth.3654. Epub 2015 Nov 9.

18.

SpeedSeq: ultra-fast personal genome analysis and interpretation.

Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM.

Nat Methods. 2015 Oct;12(10):966-8. doi: 10.1038/nmeth.3505. Epub 2015 Aug 10.

19.

MUNC, a long noncoding RNA that facilitates the function of MyoD in skeletal myogenesis.

Mueller AC, Cichewicz MA, Dey BK, Layer R, Reon BJ, Gagan JR, Dutta A.

Mol Cell Biol. 2015 Feb;35(3):498-513. doi: 10.1128/MCB.01079-14. Epub 2014 Nov 17.

20.

LUMPY: a probabilistic framework for structural variant discovery.

Layer RM, Chiang C, Quinlan AR, Hall IM.

Genome Biol. 2014 Jun 26;15(6):R84. doi: 10.1186/gb-2014-15-6-r84.

21.

Regulation of several androgen-induced genes through the repression of the miR-99a/let-7c/miR-125b-2 miRNA cluster in prostate cancer cells.

Sun D, Layer R, Mueller AC, Cichewicz MA, Negishi M, Paschal BM, Dutta A.

Oncogene. 2014 Mar 13;33(11):1448-57. doi: 10.1038/onc.2013.77. Epub 2013 Mar 18.

22.

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.

Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM.

Genome Res. 2013 May;23(5):762-76. doi: 10.1101/gr.143677.112. Epub 2013 Feb 14.

23.

Binary Interval Search: a scalable algorithm for counting interval intersections.

Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR.

Bioinformatics. 2013 Jan 1;29(1):1-7. doi: 10.1093/bioinformatics/bts652. Epub 2012 Nov 4.

24.

Notch3 and Mef2c proteins are mutually antagonistic via Mkp1 protein and miR-1/206 microRNAs in differentiating myoblasts.

Gagan J, Dey BK, Layer R, Yan Z, Dutta A.

J Biol Chem. 2012 Nov 23;287(48):40360-70. doi: 10.1074/jbc.M112.378414. Epub 2012 Oct 10.

25.

Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues.

Shibata Y, Kumar P, Layer R, Willcox S, Gagan JR, Griffith JD, Dutta A.

Science. 2012 Apr 6;336(6077):82-6. doi: 10.1126/science.1213307. Epub 2012 Mar 8. Erratum in: Science. 2012 Jun 22;336(6088):1506.

26.

MicroRNA-378 targets the myogenic repressor MyoR during myoblast differentiation.

Gagan J, Dey BK, Layer R, Yan Z, Dutta A.

J Biol Chem. 2011 Jun 3;286(22):19431-8. doi: 10.1074/jbc.M111.219006. Epub 2011 Apr 6.

27.

Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes.

Keaton MA, Taylor CM, Layer RM, Dutta A.

PLoS One. 2011 Mar 14;6(3):e17912. doi: 10.1371/journal.pone.0017912.

28.

Saturation analysis of ligand binding using a centrifugation procedure.

Layer RT.

Curr Protoc Neurosci. 2001 May;Chapter 7:Unit7.7. doi: 10.1002/0471142301.ns0707s02.

PMID:
18428533
29.

An assessment of the antinociceptive efficacy of intrathecal and epidural contulakin-G in rats and dogs.

Allen JW, Hofer K, McCumber D, Wagstaff JD, Layer RT, McCabe RT, Yaksh TL.

Anesth Analg. 2007 Jun;104(6):1505-13, table of contents.

PMID:
17513650
30.

Synthetic muO-conotoxin MrVIB blocks TTX-resistant sodium channel NaV1.8 and has a long-lasting analgesic activity.

Bulaj G, Zhang MM, Green BR, Fiedler B, Layer RT, Wei S, Nielsen JS, Low SJ, Klein BD, Wagstaff JD, Chicoine L, Harty TP, Terlau H, Yoshikami D, Olivera BM.

Biochemistry. 2006 Jun 13;45(23):7404-14.

PMID:
16752929
31.

Postischemic administration of CGX-1051, a peptide from cone snail venom, reduces infarct size in both rat and dog models of myocardial ischemia and reperfusion.

Lubbers NL, Campbell TJ, Polakowski JS, Bulaj G, Layer RT, Moore J, Gross GJ, Cox BF.

J Cardiovasc Pharmacol. 2005 Aug;46(2):141-6.

PMID:
16044024
32.

Conantokins: peptide antagonists of NMDA receptors.

Layer RT, Wagstaff JD, White HS.

Curr Med Chem. 2004 Dec;11(23):3073-84. Review.

PMID:
15579001
33.

Effects of conantokins on L-3,4-dihydroxyphenylalanine-induced behavior and immediate early gene expression.

Adams AC, Layer RT, McCabe RT, Keefe KA.

Eur J Pharmacol. 2000 Sep 22;404(3):303-13.

PMID:
10996596
34.

Isolation and characterization of a novel conus peptide with apparent antinociceptive activity.

McIntosh JM, Corpuz GO, Layer RT, Garrett JE, Wagstaff JD, Bulaj G, Vyazovkina A, Yoshikami D, Cruz LJ, Olivera BM.

J Biol Chem. 2000 Oct 20;275(42):32391-7.

35.

Conopeptides: From deadly venoms to novel therapeutics.

Shen GS, Layer RT, McCabe RT.

Drug Discov Today. 2000 Mar;5(3):98-106.

PMID:
10675883
36.

Felbamate increases [3H]glycine binding in rat brain and sections of human postmortem brain.

McCabe RT, Sofia RD, Layer RT, Leiner KA, Faull RL, Narang N, Wamsley JK.

J Pharmacol Exp Ther. 1998 Aug;286(2):991-9.

PMID:
9694960
37.

Chronic antidepressant treatments increase cytochrome b mRNA levels in mouse cerebral cortex.

Huang NY, Strakhova M, Layer RT, Skolnick P.

J Mol Neurosci. 1997 Dec;9(3):167-76.

PMID:
9481618
38.

Structure--activity studies for alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropanoic acid receptors: acidic hydroxyphenylalanines.

Hill RA, Wallace LJ, Miller DD, Weinstein DM, Shams G, Tai H, Layer RT, Willins D, Uretsky NJ, Danthi SN.

J Med Chem. 1997 Sep 26;40(20):3182-91.

PMID:
9379437
39.

Structurally modified ibogaine analogs exhibit differing affinities for NMDA receptors.

Layer RT, Skolnick P, Bertha CM, Bandarage UK, Kuehne ME, Popik P.

Eur J Pharmacol. 1996 Aug 8;309(2):159-65.

PMID:
8874134
40.

Adaptation of N-methyl-D-aspartate (NMDA) receptors following antidepressant treatment: implications for the pharmacotherapy of depression.

Skolnick P, Layer RT, Popik P, Nowak G, Paul IA, Trullas R.

Pharmacopsychiatry. 1996 Jan;29(1):23-6. Review.

PMID:
8852530
41.

[3H]1-aminocyclopropanecarboxylic acid, a novel probe for strychnine- insensitive glycine receptors.

Popik P, Lewin A, Berrang B, Nowak G, Layer R, Skolnick P.

Eur J Pharmacol. 1995 Nov 30;291(3):221-7.

PMID:
8719405
42.

Antidepressant-like actions of the polyamine site NMDA antagonist, eliprodil (SL-82.0715).

Layer RT, Popik P, Olds T, Skolnick P.

Pharmacol Biochem Behav. 1995 Nov;52(3):621-7.

PMID:
8545484
43.

NMDA antagonist properties of the putative antiaddictive drug, ibogaine.

Popik P, Layer RT, Fossom LH, Benveniste M, Geter-Douglass B, Witkin JM, Skolnick P.

J Pharmacol Exp Ther. 1995 Nov;275(2):753-60.

PMID:
7473163
44.

100 years of ibogaine: neurochemical and pharmacological actions of a putative anti-addictive drug.

Popik P, Layer RT, Skolnick P.

Pharmacol Rev. 1995 Jun;47(2):235-53. Review. No abstract available.

PMID:
7568327
45.

The putative anti-addictive drug ibogaine is a competitive inhibitor of [3H]MK-801 binding to the NMDA receptor complex.

Popik P, Layer RT, Skolnick P.

Psychopharmacology (Berl). 1994 May;114(4):672-4.

PMID:
7531855
46.

Adaptation of the N-methyl-D-aspartate receptor complex following chronic antidepressant treatments.

Paul IA, Nowak G, Layer RT, Popik P, Skolnick P.

J Pharmacol Exp Ther. 1994 Apr;269(1):95-102.

PMID:
8169857
47.

Adaptation of the NMDA receptor in rat cortex following chronic electroconvulsive shock or imipramine.

Paul IA, Layer RT, Skolnick P, Nowak G.

Eur J Pharmacol. 1993 Nov 15;247(3):305-11.

PMID:
7905831
48.
49.
50.

Adaptive changes in the N-methyl-D-aspartate receptor complex after chronic treatment with imipramine and 1-aminocyclopropanecarboxylic acid.

Nowak G, Trullas R, Layer RT, Skolnick P, Paul IA.

J Pharmacol Exp Ther. 1993 Jun;265(3):1380-6.

PMID:
8099620

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