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Items: 36

1.

Perinatal Nutritional Reprogramming of the Epigenome Promotes Subsequent Development of Nonalcoholic Steatohepatitis.

Gutierrez Sanchez LH, Tomita K, Guo Q, Furuta K, Alhuwaish H, Hirsova P, Baheti S, Alver B, Hlady R, Robertson KD, Ibrahim SH.

Hepatol Commun. 2018 Oct 1;2(12):1493-1512. doi: 10.1002/hep4.1265. eCollection 2018 Dec.

2.

Recurrent Genomic Alterations in Soft Tissue Perineuriomas.

Carter JM, Wu Y, Blessing MM, Folpe AL, Thorland EC, Spinner RJ, Jentoft ME, Wang C, Baheti S, Niu Z, Mauermann ML, Klein CJ.

Am J Surg Pathol. 2018 Dec;42(12):1708-1714. doi: 10.1097/PAS.0000000000001169.

PMID:
30303818
3.

Molecular profiling reveals immunogenic cues in anaplastic large cell lymphomas with DUSP22 rearrangements.

Luchtel RA, Dasari S, Oishi N, Pedersen MB, Hu G, Rech KL, Ketterling RP, Sidhu J, Wang X, Katoh R, Dogan A, Kip NS, Cunningham JM, Sun Z, Baheti S, Porcher JC, Said JW, Jiang L, Hamilton-Dutoit SJ, Møller MB, Nørgaard P, Bennani NN, Chng WJ, Huang G, Link BK, Facchetti F, Cerhan JR, d'Amore F, Ansell SM, Feldman AL.

Blood. 2018 Sep 27;132(13):1386-1398. doi: 10.1182/blood-2018-03-838524. Epub 2018 Aug 9.

PMID:
30093402
4.

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data.

Baheti S, Tang X, O'Brien DR, Chia N, Roberts LR, Nelson H, Boughey JC, Wang L, Goetz MP, Kocher JA, Kalari KR.

BMC Bioinformatics. 2018 Jul 17;19(1):271. doi: 10.1186/s12859-018-2260-9.

5.

Monoallelic Mutations to DNAJB11 Cause Atypical Autosomal-Dominant Polycystic Kidney Disease.

Cornec-Le Gall E, Olson RJ, Besse W, Heyer CM, Gainullin VG, Smith JM, Audrézet MP, Hopp K, Porath B, Shi B, Baheti S, Senum SR, Arroyo J, Madsen CD, Férec C, Joly D, Jouret F, Fikri-Benbrahim O, Charasse C, Coulibaly JM, Yu AS, Khalili K, Pei Y, Somlo S, Le Meur Y, Torres VE; Genkyst Study Group; HALT Progression of Polycystic Kidney Disease Group; Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease, Harris PC.

Am J Hum Genet. 2018 May 3;102(5):832-844. doi: 10.1016/j.ajhg.2018.03.013. Epub 2018 Apr 26.

6.

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations.

Druliner BR, Wang P, Bae T, Baheti S, Slettedahl S, Mahoney D, Vasmatzis N, Xu H, Kim M, Bockol M, O'Brien D, Grill D, Warner N, Munoz-Gomez M, Kossick K, Johnson R, Mouchli M, Felmlee-Devine D, Washechek-Aletto J, Smyrk T, Oberg A, Wang J, Chia N, Abyzov A, Ahlquist D, Boardman LA.

Sci Rep. 2018 Feb 16;8(1):3161. doi: 10.1038/s41598-018-21525-4.

7.

Network-directed cis-mediator analysis of normal prostate tissue expression profiles reveals downstream regulatory associations of prostate cancer susceptibility loci.

Larson NB, McDonnell SK, Fogarty Z, Larson MC, Cheville J, Riska S, Baheti S, Weber AM, Nair AA, Wang L, O'Brien D, Davila J, Schaid DJ, Thibodeau SN.

Oncotarget. 2017 Sep 8;8(49):85896-85908. doi: 10.18632/oncotarget.20717. eCollection 2017 Oct 17.

8.

Adipose tissue DNA methylome changes in development of new-onset diabetes after kidney transplantation.

Baheti S, Singh P, Zhang Y, Evans J, Jensen MD, Somers VK, Kocher JA, Sun Z, Chakkera HA.

Epigenomics. 2017 Nov;9(11):1423-1435. doi: 10.2217/epi-2017-0050. Epub 2017 Oct 2.

PMID:
28967791
9.

Statistical method evaluation for differentially methylated CpGs in base resolution next-generation DNA sequencing data.

Zhang Y, Baheti S, Sun Z.

Brief Bioinform. 2018 May 1;19(3):374-386. doi: 10.1093/bib/bbw133.

PMID:
28040747
10.

The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD).

Sarmento OF, Svingen PA, Xiong Y, Sun Z, Bamidele AO, Mathison AJ, Smyrk TC, Nair AA, Gonzalez MM, Sagstetter MR, Baheti S, McGovern DP, Friton JJ, Papadakis KA, Gautam G, Xavier RJ, Urrutia RA, Faubion WA.

J Biol Chem. 2017 Jan 13;292(2):706-722. doi: 10.1074/jbc.M116.749663. Epub 2016 Dec 1.

11.

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.

Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, Musolf A, Li Q, Holzinger E, Karyadi D, Cannon-Albright LA, Teerlink CC, Stanford JL, Isaacs WB, Xu J, Cooney KA, Lange EM, Schleutker J, Carpten JD, Powell IJ, Cussenot O, Cancel-Tassin G, Giles GG, MacInnis RJ, Maier C, Hsieh CL, Wiklund F, Catalona WJ, Foulkes WD, Mandal D, Eeles RA, Kote-Jarai Z, Bustamante CD, Schaid DJ, Hastie T, Ostrander EA, Bailey-Wilson JE, Radivojac P, Thibodeau SN, Whittemore AS, Sieh W.

Am J Hum Genet. 2016 Oct 6;99(4):877-885. doi: 10.1016/j.ajhg.2016.08.016. Epub 2016 Sep 22.

12.

Germline miRNA DNA variants and the risk of colorectal cancer by subtype.

Lindor NM, Larson MC, DeRycke MS, McDonnell SK, Baheti S, Fogarty ZC, Win AK, Potter JD, Buchanan DD, Clendenning M, Newcomb PA, Casey G, Gallinger S, Le Marchand L, Hopper JL, Jenkins MA, Goode EL, Thibodeau SN.

Genes Chromosomes Cancer. 2017 Mar;56(3):177-184. doi: 10.1002/gcc.22420. Epub 2016 Nov 30.

13.

Mutations in GANAB, Encoding the Glucosidase IIα Subunit, Cause Autosomal-Dominant Polycystic Kidney and Liver Disease.

Porath B, Gainullin VG, Cornec-Le Gall E, Dillinger EK, Heyer CM, Hopp K, Edwards ME, Madsen CD, Mauritz SR, Banks CJ, Baheti S, Reddy B, Herrero JI, Bañales JM, Hogan MC, Tasic V, Watnick TJ, Chapman AB, Vigneau C, Lavainne F, Audrézet MP, Ferec C, Le Meur Y, Torres VE; Genkyst Study Group, HALT Progression of Polycystic Kidney Disease Group; Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease, Harris PC.

Am J Hum Genet. 2016 Jun 2;98(6):1193-1207. doi: 10.1016/j.ajhg.2016.05.004.

14.

Target-enrichment sequencing and copy number evaluation in inherited polyneuropathy.

Wang W, Wang C, Dawson DB, Thorland EC, Lundquist PA, Eckloff BW, Wu Y, Baheti S, Evans JM, Scherer SS, Dyck PJ, Klein CJ.

Neurology. 2016 May 10;86(19):1762-71. doi: 10.1212/WNL.0000000000002659. Epub 2016 Apr 13.

15.

Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci.

Allen M, Burgess JD, Ballard T, Serie D, Wang X, Younkin CS, Sun Z, Kouri N, Baheti S, Wang C, Carrasquillo MM, Nguyen T, Lincoln S, Malphrus K, Murray M, Golde TE, Price ND, Younkin SG, Schellenberg GD, Asmann Y, Ordog T, Crook J, Dickson D, Ertekin-Taner N.

Acta Neuropathol. 2016 Aug;132(2):197-211. doi: 10.1007/s00401-016-1576-7. Epub 2016 Apr 26.

16.

Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data.

Baheti S, Kanwar R, Goelzenleuchter M, Kocher JP, Beutler AS, Sun Z.

BMC Genomics. 2016 Feb 27;17:149. doi: 10.1186/s12864-016-2494-8.

17.

Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set.

Thibodeau SN, French AJ, McDonnell SK, Cheville J, Middha S, Tillmans L, Riska S, Baheti S, Larson MC, Fogarty Z, Zhang Y, Larson N, Nair A, O'Brien D, Wang L, Schaid DJ.

Nat Commun. 2015 Nov 27;6:8653. doi: 10.1038/ncomms9653.

18.

Identification of differentially methylated regions in new genes associated with knee osteoarthritis.

Bonin CA, Lewallen EA, Baheti S, Bradley EW, Stuart MJ, Berry DJ, van Wijnen AJ, Westendorf JJ.

Gene. 2016 Jan 15;576(1 Pt 2):312-8. doi: 10.1016/j.gene.2015.10.037. Epub 2015 Oct 17.

19.

DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip.

Walker DL, Bhagwate AV, Baheti S, Smalley RL, Hilker CA, Sun Z, Cunningham JM.

Epigenomics. 2015;7(8):1287-302. doi: 10.2217/EPI.15.64. Epub 2015 Jul 20.

PMID:
26192535
20.

New DNA Methylation Markers for Pancreatic Cancer: Discovery, Tissue Validation, and Pilot Testing in Pancreatic Juice.

Kisiel JB, Raimondo M, Taylor WR, Yab TC, Mahoney DW, Sun Z, Middha S, Baheti S, Zou H, Smyrk TC, Boardman LA, Petersen GM, Ahlquist DA.

Clin Cancer Res. 2015 Oct 1;21(19):4473-81. doi: 10.1158/1078-0432.CCR-14-2469. Epub 2015 May 28.

21.

Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression.

Larson NB, McDonnell S, French AJ, Fogarty Z, Cheville J, Middha S, Riska S, Baheti S, Nair AA, Wang L, Schaid DJ, Thibodeau SN.

Am J Hum Genet. 2015 Jun 4;96(6):869-82. doi: 10.1016/j.ajhg.2015.04.015. Epub 2015 May 14.

22.

TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer.

Chien J, Sicotte H, Fan JB, Humphray S, Cunningham JM, Kalli KR, Oberg AL, Hart SN, Li Y, Davila JI, Baheti S, Wang C, Dietmann S, Atkinson EJ, Asmann YW, Bell DA, Ota T, Tarabishy Y, Kuang R, Bibikova M, Cheetham RK, Grocock RJ, Swisher EM, Peden J, Bentley D, Kocher JP, Kaufmann SH, Hartmann LC, Shridhar V, Goode EL.

Nucleic Acids Res. 2015 Aug 18;43(14):6945-58. doi: 10.1093/nar/gkv111. Epub 2015 Apr 27.

23.

The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.

Tang X, Baheti S, Shameer K, Thompson KJ, Wills Q, Niu N, Holcomb IN, Boutet SC, Ramakrishnan R, Kachergus JM, Kocher JP, Weinshilboum RM, Wang L, Thompson EA, Kalari KR.

Nucleic Acids Res. 2014 Dec 16;42(22):e172. doi: 10.1093/nar/gku1005. Epub 2014 Oct 28.

24.

RVboost: RNA-seq variants prioritization using a boosting method.

Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW.

Bioinformatics. 2014 Dec 1;30(23):3414-6. doi: 10.1093/bioinformatics/btu577. Epub 2014 Aug 27.

25.

Comprehensive assessment of genetic variants within TCF4 in Fuchs' endothelial corneal dystrophy.

Wieben ED, Aleff RA, Eckloff BW, Atkinson EJ, Baheti S, Middha S, Brown WL, Patel SV, Kocher JP, Baratz KH.

Invest Ophthalmol Vis Sci. 2014 Aug 28;55(9):6101-7. doi: 10.1167/iovs.14-14958.

26.

Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E.

Sun Z, Wu Y, Ordog T, Baheti S, Nie J, Duan X, Hojo K, Kocher JP, Dyck PJ, Klein CJ.

Epigenetics. 2014 Aug;9(8):1184-93. doi: 10.4161/epi.29676. Epub 2014 Jul 7.

27.

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.

Kalari KR, Nair AA, Bhavsar JD, O'Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP.

BMC Bioinformatics. 2014 Jun 27;15:224. doi: 10.1186/1471-2105-15-224.

28.

Reservoir complete denture in a patient with xerostomia secondary to radiotherapy for oral carcinoma: a case report and review of literature.

Ladda R, Kasat V, Gangadhar S, Baheti S, Bhandari A.

Ann Med Health Sci Res. 2014 Mar;4(2):271-5. doi: 10.4103/2141-9248.129062.

29.

From days to hours: reporting clinically actionable variants from whole genome sequencing.

Middha S, Baheti S, Hart SN, Kocher JP.

PLoS One. 2014 Feb 5;9(2):e86803. doi: 10.1371/journal.pone.0086803. eCollection 2014.

30.

SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

Hart SN, Sarangi V, Moore R, Baheti S, Bhavsar JD, Couch FJ, Kocher JP.

PLoS One. 2013 Dec 16;8(12):e83356. doi: 10.1371/journal.pone.0083356. eCollection 2013.

31.

An integrated model of the transcriptome of HER2-positive breast cancer.

Kalari KR, Necela BM, Tang X, Thompson KJ, Lau M, Eckel-Passow JE, Kachergus JM, Anderson SK, Sun Z, Baheti S, Carr JM, Baker TR, Barman P, Radisky DC, Joseph RW, McLaughlin SA, Chai HS, Camille S, Rossell D, Asmann YW, Thompson EA, Perez EA.

PLoS One. 2013 Nov 1;8(11):e79298. doi: 10.1371/journal.pone.0079298. eCollection 2013.

32.

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP.

Bioinformatics. 2012 Aug 15;28(16):2180-1. doi: 10.1093/bioinformatics/bts337. Epub 2012 Jun 10.

33.

Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations.

Kalari KR, Rossell D, Necela BM, Asmann YW, Nair A, Baheti S, Kachergus JM, Younkin CS, Baker T, Carr JM, Tang X, Walsh MP, Chai HS, Sun Z, Hart SN, Leontovich AA, Hossain A, Kocher JP, Perez EA, Reisman DN, Fields AP, Thompson EA.

Front Oncol. 2012 Feb 10;2:12. doi: 10.3389/fonc.2012.00012. eCollection 2012.

34.

Laparoscopic tubal sterilization reversal and fertility outcomes.

Jayakrishnan K, Baheti SN.

J Hum Reprod Sci. 2011 Sep;4(3):125-9. doi: 10.4103/0974-1208.92286.

35.

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.

Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP.

Bioinformatics. 2012 Jan 15;28(2):277-8. doi: 10.1093/bioinformatics/btr612. Epub 2011 Nov 15.

36.

Massive hematuria with hemodynamic instability--complication of oocyte retrieval.

Jayakrishnan K, Raman VK, Vijayalakshmi VK, Baheti S, Nambiar D.

Fertil Steril. 2011 Jul;96(1):e22-4. doi: 10.1016/j.fertnstert.2011.04.046. Epub 2011 May 19.

PMID:
21600575

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