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Items: 31

1.

Iranian neonatal diabetes mellitus due to mutation in PDX1 gene: a case report.

Sahebi L, Niknafs N, Dalili H, Amini E, Esmaeilnia T, Amoli M, Farrokhzad N.

J Med Case Rep. 2019 Aug 1;13(1):258. doi: 10.1186/s13256-019-2149-x.

2.

Intraductal Papillary Mucinous Neoplasms Arise From Multiple Independent Clones, Each With Distinct Mutations.

Fischer CG, Beleva Guthrie V, Braxton AM, Zheng L, Wang P, Song Q, Griffin JF, Chianchiano PE, Hosoda W, Niknafs N, Springer S, Dal Molin M, Masica D, Scharpf RB, Thompson ED, He J, Wolfgang CL, Hruban RH, Roberts NJ, Lennon AM, Jiao Y, Karchin R, Wood LD.

Gastroenterology. 2019 Oct;157(4):1123-1137.e22. doi: 10.1053/j.gastro.2019.06.001. Epub 2019 Jun 5.

PMID:
31175866
3.

Genome-wide cell-free DNA fragmentation in patients with cancer.

Cristiano S, Leal A, Phallen J, Fiksel J, Adleff V, Bruhm DC, Jensen SØ, Medina JE, Hruban C, White JR, Palsgrove DN, Niknafs N, Anagnostou V, Forde P, Naidoo J, Marrone K, Brahmer J, Woodward BD, Husain H, van Rooijen KL, Ørntoft MW, Madsen AH, van de Velde CJH, Verheij M, Cats A, Punt CJA, Vink GR, van Grieken NCT, Koopman M, Fijneman RJA, Johansen JS, Nielsen HJ, Meijer GA, Andersen CL, Scharpf RB, Velculescu VE.

Nature. 2019 Jun;570(7761):385-389. doi: 10.1038/s41586-019-1272-6. Epub 2019 May 29.

PMID:
31142840
4.

The HEAVEN criteria predict laryngoscopic view and intubation success for both direct and video laryngoscopy: a cohort analysis.

Nausheen F, Niknafs NP, MacLean DJ, Olvera DJ, Wolfe AC Jr, Pennington TW, Davis DP.

Scand J Trauma Resusc Emerg Med. 2019 Apr 24;27(1):50. doi: 10.1186/s13049-019-0614-6.

5.

Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.

Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone K, Sivakumar IKA, Bruhm DC, Rosner S, Phallen J, Leal A, Adleff V, Smith KN, Cottrell TR, Rhymee L, Palsgrove DN, Hann CL, Levy B, Feliciano J, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Isbell JM, Sauter JL, Taube J, Scharpf RB, Karchin R, Pardoll DM, Chaft JE, Hellmann MD, Brahmer JR, Velculescu VE.

Cancer Res. 2019 Mar 15;79(6):1214-1225. doi: 10.1158/0008-5472.CAN-18-1127. Epub 2018 Dec 12.

6.

Tranexamic Acid in Civilian Trauma Care in the California Prehospital Antifibrinolytic Therapy Study.

Neeki MM, Dong F, Toy J, Vaezazizi R, Powell J, Wong D, Mousselli M, Rabiei M, Jabourian A, Niknafs N, Burgett-Moreno M, Vara R, Kissel S, Luo-Owen X, O'Bosky KR, Ludi D, Sporer K, Pennington T, Lee T, Borger R, Kwong E.

West J Emerg Med. 2018 Nov;19(6):977-986. doi: 10.5811/westjem.2018.8.39336. Epub 2018 Sep 10.

7.

Ethical and legal aspects of patient's safety: a clinical case report.

Kadivar M, Manookian A, Asghari F, Niknafs N, Okazi A, Zarvani A.

J Med Ethics Hist Med. 2017 Dec 30;10:15. eCollection 2017.

8.

A machine learning approach for somatic mutation discovery.

Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA Jr, Jones S, Sausen M, Velculescu VE, Angiuoli SV.

Sci Transl Med. 2018 Sep 5;10(457). pii: eaar7939. doi: 10.1126/scitranslmed.aar7939.

9.

Ipilimumab plus nivolumab and DNA-repair defects in AR-V7-expressing metastatic prostate cancer.

Boudadi K, Suzman DL, Anagnostou V, Fu W, Luber B, Wang H, Niknafs N, White JR, Silberstein JL, Sullivan R, Dowling D, Harb R, Nirschl TR, Veeneman BA, Tomlins SA, Wang Y, Jendrisak A, Graf RP, Dittamore R, Carducci MA, Eisenberger MA, Haffner MC, Meeker AK, Eshleman JR, Luo J, Velculescu VE, Drake CG, Antonarakis ES.

Oncotarget. 2018 Jun 19;9(47):28561-28571. doi: 10.18632/oncotarget.25564. eCollection 2018 Jun 19.

10.

Pathologic features of response to neoadjuvant anti-PD-1 in resected non-small-cell lung carcinoma: a proposal for quantitative immune-related pathologic response criteria (irPRC).

Cottrell TR, Thompson ED, Forde PM, Stein JE, Duffield AS, Anagnostou V, Rekhtman N, Anders RA, Cuda JD, Illei PB, Gabrielson E, Askin FB, Niknafs N, Smith KN, Velez MJ, Sauter JL, Isbell JM, Jones DR, Battafarano RJ, Yang SC, Danilova L, Wolchok JD, Topalian SL, Velculescu VE, Pardoll DM, Brahmer JR, Hellmann MD, Chaft JE, Cimino-Mathews A, Taube JM.

Ann Oncol. 2018 Aug 1;29(8):1853-1860. doi: 10.1093/annonc/mdy218.

11.

Epigenetic Therapy Ties MYC Depletion to Reversing Immune Evasion and Treating Lung Cancer.

Topper MJ, Vaz M, Chiappinelli KB, DeStefano Shields CE, Niknafs N, Yen RC, Wenzel A, Hicks J, Ballew M, Stone M, Tran PT, Zahnow CA, Hellmann MD, Anagnostou V, Strissel PL, Strick R, Velculescu VE, Baylin SB.

Cell. 2017 Nov 30;171(6):1284-1300.e21. doi: 10.1016/j.cell.2017.10.022.

12.

High grade serous ovarian carcinomas originate in the fallopian tube.

Labidi-Galy SI, Papp E, Hallberg D, Niknafs N, Adleff V, Noe M, Bhattacharya R, Novak M, Jones S, Phallen J, Hruban CA, Hirsch MS, Lin DI, Schwartz L, Maire CL, Tille JC, Bowden M, Ayhan A, Wood LD, Scharpf RB, Kurman R, Wang TL, Shih IM, Karchin R, Drapkin R, Velculescu VE.

Nat Commun. 2017 Oct 23;8(1):1093. doi: 10.1038/s41467-017-00962-1.

13.

Association of SP-B gene 9306 A/G polymorphism (rs7316) and risk of RDS.

Fatahi N, Niknafs N, Kalani M, Dalili H, Shariat M, Amini E, Esmaeilnia Shirvani T, Hardani AK, Taheritafti R, Ghasemi-Fakhr N, Ghadami M, Tavakkoly-Bazzaz J, Rashidi-Nezhad R, Nayeri F, Rashidi-Nezhad A.

J Matern Fetal Neonatal Med. 2018 Nov;31(22):2965-2970. doi: 10.1080/14767058.2017.1359829. Epub 2017 Aug 7.

PMID:
28738720
14.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins RA, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD.

Hum Mutat. 2017 Sep;38(9):1266-1276. doi: 10.1002/humu.23265. Epub 2017 Jun 19.

15.

Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.

Anagnostou V, Smith KN, Forde PM, Niknafs N, Bhattacharya R, White J, Zhang T, Adleff V, Phallen J, Wali N, Hruban C, Guthrie VB, Rodgers K, Naidoo J, Kang H, Sharfman W, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf RB, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE.

Cancer Discov. 2017 Mar;7(3):264-276. doi: 10.1158/2159-8290.CD-16-0828. Epub 2016 Dec 28.

16.

Association of SP-C gene codon 186 polymorphism (rs1124) and risk of RDS.

Fatahi N, Dalili H, Kalani M, Niknafs N, Shariat M, Tavakkoly-Bazzaz J, Amini E, Esmaeilnia Shirvani T, Hardani AK, Taheritafti R, Ghasemi-Fakhr N, Ghadami M, Nayeri F, Rashidi-Nezhad A.

J Matern Fetal Neonatal Med. 2017 Nov;30(21):2585-2589. doi: 10.1080/14767058.2016.1256994. Epub 2016 Nov 24.

PMID:
27884070
17.

Intraventricular Hemorrhage in a Term Neonate: Manifestation of Protein S Deficiency- A Case Report.

Sahriarian S, Akbari P, Amini E, Dalili H, Esmaeilnia Shrivany T, Niknafs N, Shariat M, Ghorban Sabagh V.

Iran J Public Health. 2016 Apr;45(4):531-4.

18.

Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R.

Cancer Res. 2016 Jul 1;76(13):3719-31. doi: 10.1158/0008-5472.CAN-15-3190. Epub 2016 Apr 28.

19.

Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma.

Rettig EM, Talbot CC Jr, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig EJ, Wheelan SJ, Marchionni L, Considine M, Ling S, Fakhry C, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N.

Cancer Prev Res (Phila). 2016 Apr;9(4):265-74. doi: 10.1158/1940-6207.CAPR-15-0316. Epub 2016 Feb 9. Erratum in: Cancer Prev Res (Phila). 2018 Apr;11(4):249.

20.

Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer.

Roberts NJ, Norris AL, Petersen GM, Bondy ML, Brand R, Gallinger S, Kurtz RC, Olson SH, Rustgi AK, Schwartz AG, Stoffel E, Syngal S, Zogopoulos G, Ali SZ, Axilbund J, Chaffee KG, Chen YC, Cote ML, Childs EJ, Douville C, Goes FS, Herman JM, Iacobuzio-Donahue C, Kramer M, Makohon-Moore A, McCombie RW, McMahon KW, Niknafs N, Parla J, Pirooznia M, Potash JB, Rhim AD, Smith AL, Wang Y, Wolfgang CL, Wood LD, Zandi PP, Goggins M, Karchin R, Eshleman JR, Papadopoulos N, Kinzler KW, Vogelstein B, Hruban RH, Klein AP.

Cancer Discov. 2016 Feb;6(2):166-75. doi: 10.1158/2159-8290.CD-15-0402. Epub 2015 Dec 9.

21.

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing.

Niknafs N, Beleva-Guthrie V, Naiman DQ, Karchin R.

PLoS Comput Biol. 2015 Oct 5;11(10):e1004416. doi: 10.1371/journal.pcbi.1004416. eCollection 2015 Oct.

22.

The genomic landscape of response to EGFR blockade in colorectal cancer.

Bertotti A, Papp E, Jones S, Adleff V, Anagnostou V, Lupo B, Sausen M, Phallen J, Hruban CA, Tokheim C, Niknafs N, Nesselbush M, Lytle K, Sassi F, Cottino F, Migliardi G, Zanella ER, Ribero D, Russolillo N, Mellano A, Muratore A, Paraluppi G, Salizzoni M, Marsoni S, Kragh M, Lantto J, Cassingena A, Li QK, Karchin R, Scharpf R, Sartore-Bianchi A, Siena S, Diaz LA Jr, Trusolino L, Velculescu VE.

Nature. 2015 Oct 8;526(7572):263-7. doi: 10.1038/nature14969. Epub 2015 Sep 30.

23.

A combination of molecular markers and clinical features improve the classification of pancreatic cysts.

Springer S, Wang Y, Dal Molin M, Masica DL, Jiao Y, Kinde I, Blackford A, Raman SP, Wolfgang CL, Tomita T, Niknafs N, Douville C, Ptak J, Dobbyn L, Allen PJ, Klimstra DS, Schattner MA, Schmidt CM, Yip-Schneider M, Cummings OW, Brand RE, Zeh HJ, Singhi AD, Scarpa A, Salvia R, Malleo G, Zamboni G, Falconi M, Jang JY, Kim SW, Kwon W, Hong SM, Song KB, Kim SC, Swan N, Murphy J, Geoghegan J, Brugge W, Fernandez-Del Castillo C, Mino-Kenudson M, Schulick R, Edil BH, Adsay V, Paulino J, van Hooft J, Yachida S, Nara S, Hiraoka N, Yamao K, Hijioka S, van der Merwe S, Goggins M, Canto MI, Ahuja N, Hirose K, Makary M, Weiss MJ, Cameron J, Pittman M, Eshleman JR, Diaz LA Jr, Papadopoulos N, Kinzler KW, Karchin R, Hruban RH, Vogelstein B, Lennon AM.

Gastroenterology. 2015 Nov;149(6):1501-10. doi: 10.1053/j.gastro.2015.07.041. Epub 2015 Aug 4.

24.

Early onset of tuberous sclerosis with chylous ascites: a case report.

Dalili H, Amini E, Akbari Asbagh P, Esmaeilnia Shrivany T, Niknafs N, Nayyeri F, Shariat M, Talebian S, Akbari Asbagh N, Ghorban Sabagh V.

Iran J Public Health. 2015 Mar;44(3):407-11.

25.

A probabilistic model to predict clinical phenotypic traits from genome sequencing.

Chen YC, Douville C, Wang C, Niknafs N, Yeo G, Beleva-Guthrie V, Carter H, Stenson PD, Cooper DN, Li B, Mooney S, Karchin R.

PLoS Comput Biol. 2014 Sep 4;10(9):e1003825. doi: 10.1371/journal.pcbi.1003825. eCollection 2014 Sep.

26.

Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas.

Jiao Y, Pawlik TM, Anders RA, Selaru FM, Streppel MM, Lucas DJ, Niknafs N, Guthrie VB, Maitra A, Argani P, Offerhaus GJA, Roa JC, Roberts LR, Gores GJ, Popescu I, Alexandrescu ST, Dima S, Fassan M, Simbolo M, Mafficini A, Capelli P, Lawlor RT, Ruzzenente A, Guglielmi A, Tortora G, de Braud F, Scarpa A, Jarnagin W, Klimstra D, Karchin R, Velculescu VE, Hruban RH, Vogelstein B, Kinzler KW, Papadopoulos N, Wood LD.

Nat Genet. 2013 Dec;45(12):1470-1473. doi: 10.1038/ng.2813. Epub 2013 Nov 3.

27.

Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing.

Hoang ML, Chen CH, Sidorenko VS, He J, Dickman KG, Yun BH, Moriya M, Niknafs N, Douville C, Karchin R, Turesky RJ, Pu YS, Vogelstein B, Papadopoulos N, Grollman AP, Kinzler KW, Rosenquist TA.

Sci Transl Med. 2013 Aug 7;5(197):197ra102. doi: 10.1126/scitranslmed.3006200.

28.

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.

Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Stenson PD, Cooper DN, Karchin R.

Hum Genet. 2013 Nov;132(11):1235-43. doi: 10.1007/s00439-013-1325-0. Epub 2013 Jun 23.

29.

CRAVAT: cancer-related analysis of variants toolkit.

Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R.

Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16.

30.

Biomechanical factors in planning of periacetabular osteotomy.

Niknafs N, Murphy RJ, Armiger RS, Lepistö J, Armand M.

Front Bioeng Biotechnol. 2013 Dec 10;1:20. doi: 10.3389/fbioe.2013.00020. eCollection 2013.

31.

Adult colo-colonic intussusception incidentally detected by emergency bedside gallbladder sonography.

Summers S, Habicht M, Fox JC, Niknafs N.

J Emerg Med. 2011 Dec;41(6):668-71. doi: 10.1016/j.jemermed.2009.07.036. Epub 2009 Sep 18. No abstract available.

PMID:
19766435

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