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Items: 46

1.

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.

Miraldi ER, Pokrovskii M, Watters A, Castro DM, De Veaux N, Hall JA, Lee JY, Ciofani M, Madar A, Carriero N, Littman DR, Bonneau R.

Genome Res. 2019 Mar;29(3):449-463. doi: 10.1101/gr.238253.118. Epub 2019 Jan 29.

2.

Early Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA.

Goldberg SB, Narayan A, Kole AJ, Decker RH, Teysir J, Carriero NJ, Lee A, Nemati R, Nath SK, Mane SM, Deng Y, Sukumar N, Zelterman D, Boffa DJ, Politi K, Gettinger SN, Wilson LD, Herbst RS, Patel AA.

Clin Cancer Res. 2018 Apr 15;24(8):1872-1880. doi: 10.1158/1078-0432.CCR-17-1341. Epub 2018 Jan 12.

PMID:
29330207
3.

Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility.

Chen X, Yu B, Carriero N, Silva C, Bonneau R.

Nucleic Acids Res. 2017 May 5;45(8):4315-4329. doi: 10.1093/nar/gkx174.

4.

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.

Karwacz K, Miraldi ER, Pokrovskii M, Madi A, Yosef N, Wortman I, Chen X, Watters A, Carriero N, Awasthi A, Regev A, Bonneau R, Littman D, Kuchroo VK.

Nat Immunol. 2017 Apr;18(4):412-421. doi: 10.1038/ni.3683. Epub 2017 Feb 6.

5.

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR.

Genomics Proteomics Bioinformatics. 2015 Feb;13(1):25-35. doi: 10.1016/j.gpb.2014.11.002. Epub 2015 Feb 21.

6.

Development of a novel method to create double-strand break repair fingerprints using next-generation sequencing.

Soong CP, Breuer GA, Hannon RA, Kim SD, Salem AF, Wang G, Yu R, Carriero NJ, Bjornson R, Sundaram RK, Bindra RS.

DNA Repair (Amst). 2015 Feb;26:44-53. doi: 10.1016/j.dnarep.2014.12.002. Epub 2014 Dec 19.

PMID:
25547252
7.

De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder.

Dong S, Walker MF, Carriero NJ, DiCola M, Willsey AJ, Ye AY, Waqar Z, Gonzalez LE, Overton JD, Frahm S, Keaney JF 3rd, Teran NA, Dea J, Mandell JD, Hus Bal V, Sullivan CA, DiLullo NM, Khalil RO, Gockley J, Yuksel Z, Sertel SM, Ercan-Sencicek AG, Gupta AR, Mane SM, Sheldon M, Brooks AI, Roeder K, Devlin B, State MW, Wei L, Sanders SJ.

Cell Rep. 2014 Oct 9;9(1):16-23. doi: 10.1016/j.celrep.2014.08.068. Epub 2014 Oct 2.

8.

Role of the Trypanosoma brucei HEN1 family methyltransferase in small interfering RNA modification.

Shi H, Barnes RL, Carriero N, Atayde VD, Tschudi C, Ullu E.

Eukaryot Cell. 2014 Jan;13(1):77-86. doi: 10.1128/EC.00233-13. Epub 2013 Nov 1.

9.

De novo mutations in histone-modifying genes in congenital heart disease.

Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, Carriero NJ, Cheung YH, Deanfield J, DePalma S, Fakhro KA, Glessner J, Hakonarson H, Italia MJ, Kaltman JR, Kaski J, Kim R, Kline JK, Lee T, Leipzig J, Lopez A, Mane SM, Mitchell LE, Newburger JW, Parfenov M, Pe'er I, Porter G, Roberts AE, Sachidanandam R, Sanders SJ, Seiden HS, State MW, Subramanian S, Tikhonova IR, Wang W, Warburton D, White PS, Williams IA, Zhao H, Seidman JG, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Seidman CE, Lifton RP.

Nature. 2013 Jun 13;498(7453):220-3. doi: 10.1038/nature12141. Epub 2013 May 12.

10.

Fossil slabs attached to unsubducted fragments of the Farallon plate.

Wang Y, Forsyth DW, Rau CJ, Carriero N, Schmandt B, Gaherty JB, Savage B.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5342-6. doi: 10.1073/pnas.1214880110. Epub 2013 Mar 18.

11.

The structure and repertoire of small interfering RNAs in Leishmania (Viannia) braziliensis reveal diversification in the trypanosomatid RNAi pathway.

Atayde VD, Shi H, Franklin JB, Carriero N, Notton T, Lye LF, Owens K, Beverley SM, Tschudi C, Ullu E.

Mol Microbiol. 2013 Feb;87(3):580-93. doi: 10.1111/mmi.12117. Epub 2012 Dec 26.

12.

Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing.

Narayan A, Carriero NJ, Gettinger SN, Kluytenaar J, Kozak KR, Yock TI, Muscato NE, Ugarelli P, Decker RH, Patel AA.

Cancer Res. 2012 Jul 15;72(14):3492-8. doi: 10.1158/0008-5472.CAN-11-4037. Epub 2012 May 10.

13.

De novo mutations revealed by whole-exome sequencing are strongly associated with autism.

Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, G√ľnel M, Roeder K, Geschwind DH, Devlin B, State MW.

Nature. 2012 Apr 4;485(7397):237-41. doi: 10.1038/nature10945.

14.

Deaths observed in Medicare beneficiaries: average attributable fraction and its longitudinal extension for many diseases.

Murphy TE, McAvay G, Carriero NJ, Gross CP, Tinetti ME, Allore HG, Lin H.

Stat Med. 2012 Nov 30;31(27):3313-9. doi: 10.1002/sim.5337. Epub 2012 Mar 13.

15.

Power of data mining methods to detect genetic associations and interactions.

Molinaro AM, Carriero N, Bjornson R, Hartge P, Rothman N, Chatterjee N.

Hum Hered. 2011;72(2):85-97. doi: 10.1159/000330579. Epub 2011 Sep 17.

16.

Segmental duplications in the human genome reveal details of pseudogene formation.

Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB.

Nucleic Acids Res. 2010 Nov;38(20):6997-7007. doi: 10.1093/nar/gkq587. Epub 2010 Jul 8.

17.

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.

Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB.

BMC Genomics. 2009 Oct 16;10:480. doi: 10.1186/1471-2164-10-480.

18.

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.

Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB.

Genome Biol. 2009 Feb 23;10(2):R23. doi: 10.1186/gb-2009-10-2-r23.

19.

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.

Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M.

Genome Biol. 2009;10(1):R2. doi: 10.1186/gb-2009-10-1-r2. Epub 2009 Jan 5.

20.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.

Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518. Epub 2009 Jan 4.

21.

Pseudofam: the pseudogene families database.

Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB.

Nucleic Acids Res. 2009 Jan;37(Database issue):D738-43. doi: 10.1093/nar/gkn758. Epub 2008 Oct 28.

22.

Keck Foundation Biotechnology Resource Laboratory, Yale University.

Stone KL, Bjornson RD, Blasko GG, Bruce C, Cofrancesco R, Carriero NJ, Colangelo CM, Crawford JK, Crawford JM, daSilva NC, Deluca JD, Elliott JI, Elliott MM, Flory PJ, Folta-Stogniew EJ, Gulcicek E, Kong Y, Lam TT, Lee JY, Lin A, LoPresti MB, Mane SM, McMurray WJ, Tikhonova IR, Westman S, Williams NA, Wu TL, Hongyu Z, Williams KR.

Yale J Biol Med. 2007 Dec;80(4):195-211. Review. No abstract available.

23.

X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers.

Bjornson RD, Carriero NJ, Colangelo C, Shifman M, Cheung KH, Miller PL, Williams K.

J Proteome Res. 2008 Jan;7(1):293-9. Epub 2007 Sep 29.

24.

Paired-end mapping reveals extensive structural variation in the human genome.

Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M.

Science. 2007 Oct 19;318(5849):420-6. Epub 2007 Sep 27.

25.

An efficient pseudomedian filter for tiling microrrays.

Royce TE, Carriero NJ, Gerstein MB.

BMC Bioinformatics. 2007 Jun 7;8:186.

26.

Hinge Atlas: relating protein sequence to sites of structural flexibility.

Flores SC, Lu LJ, Yang J, Carriero N, Gerstein MB.

BMC Bioinformatics. 2007 May 22;8:167.

27.

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.

Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M.

Nucleic Acids Res. 2007 Jan;35(Database issue):D55-60. Epub 2006 Nov 11.

28.

PseudoPipe: an automated pseudogene identification pipeline.

Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M.

Bioinformatics. 2006 Jun 15;22(12):1437-9. Epub 2006 Mar 30.

PMID:
16574694
29.
30.

Integrated pseudogene annotation for human chromosome 22: evidence for transcription.

Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M.

J Mol Biol. 2005 May 27;349(1):27-45. Epub 2005 Apr 2.

PMID:
15876366
31.

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.

Harrison PM, Zheng D, Zhang Z, Carriero N, Gerstein M.

Nucleic Acids Res. 2005 Apr 28;33(8):2374-83. Print 2005.

32.

A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.

Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M.

J Am Med Inform Assoc. 2005 Jan-Feb;12(1):90-8. Epub 2004 Oct 18.

33.

Comparative analysis of processed pseudogenes in the mouse and human genomes.

Zhang Z, Carriero N, Gerstein M.

Trends Genet. 2004 Feb;20(2):62-7. Review.

PMID:
14746985
34.

A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs.

Harrison PM, Carriero N, Liu Y, Gerstein M.

J Mol Biol. 2003 Nov 7;333(5):885-92.

PMID:
14583187
35.

Body mass index and effects of refeeding on liver tests in drug-dependent adults in a residential research unit.

Fontaine KR, Cheskin LJ, Carriero NJ, Jefferson L, Finley CJ, Gorelick DA.

J Am Diet Assoc. 2001 Dec;101(12):1467-9. No abstract available.

PMID:
11762745
36.

Pathological gambling among cocaine-dependent outpatients.

Hall GW, Carriero NJ, Takushi RY, Montoya ID, Preston KL, Gorelick DA.

Am J Psychiatry. 2000 Jul;157(7):1127-33.

PMID:
10873922
37.

Characteristics of smoked drug use among cocaine smokers.

Gorelick DA, Simmons MS, Carriero N, Tashkin DP.

Am J Addict. 1997 Summer;6(3):237-45.

PMID:
9256990
38.

Changes in cigarette smoking not observed following repeated cocaine self-administration.

Radzius A, Carriero NJ, Weinhold LL, Gorelick DA, Henningfield JE.

Exp Clin Psychopharmacol. 1997 Feb;5(1):51-3.

PMID:
9234039
39.

Parallelizing genetic linkage analysis: a case study for applying parallel computation in molecular biology.

Miller PL, Nadkarni P, Gelernter JE, Carriero N, Pakstis AJ, Kidd KK.

Comput Biomed Res. 1991 Jun;24(3):234-48.

PMID:
1868693
40.

A parallel computing approach to genetic sequence comparison: the master-worker paradigm with interworker communication.

Sittig DF, Foulser D, Carriero N, McCorkle G, Miller PL.

Comput Biomed Res. 1991 Apr;24(2):152-69.

PMID:
2036781
41.
42.
43.
44.

Cardiac deceleration as an indicator of correct performance.

Carriero NJ, Fite J Jr.

Percept Mot Skills. 1977 Feb;44(1):275-82.

PMID:
840599
45.

The effects of paced tapping on heart rate, skin conductance, and muscle potential.

Carriero NJ.

Psychophysiology. 1975 Mar;12(2):130-5. No abstract available.

PMID:
1135344
46.

A NOTE ON "ON SIMPLE METHODS OF SCORING TRACKING ERROR".

CARRIERO NJ.

Psychol Bull. 1964 Apr;61:303. No abstract available.

PMID:
14140336

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