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Items: 49

1.

Alterations to the Esophageal Microbiome Associated with Progression from Barrett's Esophagus to Esophageal Adenocarcinoma.

Snider EJ, Compres G, Freedberg DE, Khiabanian H, Nobel YR, Stump S, Uhlemann AC, Lightdale CJ, Abrams JA.

Cancer Epidemiol Biomarkers Prev. 2019 Aug 29. doi: 10.1158/1055-9965.EPI-19-0008. [Epub ahead of print]

PMID:
31466948
2.

TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer.

Singh A, Bhanot G, Khiabanian H.

Gigascience. 2019 Jun 1;8(6). pii: giz064. doi: 10.1093/gigascience/giz064.

3.

Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF.

Blasco MT, Navas C, Martín-Serrano G, Graña-Castro O, Lechuga CG, Martín-Díaz L, Djurec M, Li J, Morales-Cacho L, Esteban-Burgos L, Perales-Patón J, Bousquet-Mur E, Castellano E, Jacob HKC, Cabras L, Musteanu M, Drosten M, Ortega S, Mulero F, Sainz B Jr, Dusetti N, Iovanna J, Sánchez-Bueno F, Hidalgo M, Khiabanian H, Rabadán R, Al-Shahrour F, Guerra C, Barbacid M.

Cancer Cell. 2019 Apr 15;35(4):573-587.e6. doi: 10.1016/j.ccell.2019.03.002. Epub 2019 Apr 8.

PMID:
30975481
4.

Association of JAK2-V617F Mutations Detected by Solid Tumor Sequencing With Coexistent Myeloproliferative Neoplasms.

Riedlinger G, Hadigol M, Khiabanian H, Ganesan S.

JAMA Oncol. 2019 Feb 1;5(2):265-267. doi: 10.1001/jamaoncol.2018.6286. No abstract available.

PMID:
30605212
5.

Increasing Dietary Fiber Intake Is Associated with a Distinct Esophageal Microbiome.

Nobel YR, Snider EJ, Compres G, Freedberg DE, Khiabanian H, Lightdale CJ, Toussaint NC, Abrams JA.

Clin Transl Gastroenterol. 2018 Oct 25;9(10):199. doi: 10.1038/s41424-018-0067-7.

6.

Inference of Germline Mutational Status and Evaluation of Loss of Heterozygosity in High-Depth, Tumor-Only Sequencing Data.

Khiabanian H, Hirshfield KM, Goldfinger M, Bird S, Stein M, Aisner J, Toppmeyer D, Wong S, Chan N, Dhar K, Gheeya J, Vig H, Hadigol M, Pavlick D, Ansari S, Ali S, Xia B, Rodriguez-Rodriguez L, Ganesan S.

JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.17.00148. Epub 2018 Jan 19.

7.

On statistical modeling of sequencing noise in high depth data to assess tumor evolution.

Rabadan R, Bhanot G, Marsilio S, Chiorazzi N, Pasqualucci L, Khiabanian H.

J Stat Phys. 2018 Jul;172(1):143-155. doi: 10.1007/s10955-017-1945-1. Epub 2017 Dec 21.

8.

MERIT reveals the impact of genomic context on sequencing error rate in ultra-deep applications.

Hadigol M, Khiabanian H.

BMC Bioinformatics. 2018 Jun 8;19(1):219. doi: 10.1186/s12859-018-2223-1.

9.

Detection of clonal hematopoiesis of indeterminate potential in clinical sequencing of solid tumor specimens.

Severson EA, Riedlinger GM, Connelly CF, Vergilio JA, Goldfinger M, Ramkissoon S, Frampton GM, Ross JS, Fratella-Calabrese A, Gay L, Ali S, Miller V, Elvin J, Hadigol M, Hirshfield KM, Rodriguez-Rodriguez L, Ganesan S, Khiabanian H.

Blood. 2018 May 31;131(22):2501-2505. doi: 10.1182/blood-2018-03-840629. Epub 2018 Apr 20. No abstract available.

10.

Barrett's esophagus is associated with a distinct oral microbiome.

Snider EJ, Compres G, Freedberg DE, Giddins MJ, Khiabanian H, Lightdale CJ, Nobel YR, Toussaint NC, Uhlemann AC, Abrams JA.

Clin Transl Gastroenterol. 2018 Feb 20;9(3):135. doi: 10.1038/s41424-018-0005-8.

11.

Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia.

Tzoneva G, Dieck CL, Oshima K, Ambesi-Impiombato A, Sánchez-Martín M, Madubata CJ, Khiabanian H, Yu J, Waanders E, Iacobucci I, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Gastier-Foster JM, Loh ML, Kirschner-Schwabe R, Mullighan CG, Rabadan R, Ferrando AA.

Nature. 2018 Jan 25;553(7689):511-514. doi: 10.1038/nature25186. Epub 2018 Jan 17.

12.

Somatic CLL mutations occur at multiple distinct hematopoietic maturation stages: documentation and cautionary note regarding cell fraction purity.

Marsilio S, Khiabanian H, Fabbri G, Vergani S, Scuoppo C, Montserrat E, Shpall EJ, Hadigol M, Marin P, Rai KR, Rabadan R, Devereux S, Pasqualucci L, Chiorazzi N.

Leukemia. 2018 Apr;32(4):1041-1044. doi: 10.1038/leu.2017.343. Epub 2017 Dec 5. No abstract available.

13.

Gamma Secretase Inhibition by BMS-906024 Enhances Efficacy of Paclitaxel in Lung Adenocarcinoma.

Morgan KM, Fischer BS, Lee FY, Shah JJ, Bertino JR, Rosenfeld J, Singh A, Khiabanian H, Pine SR.

Mol Cancer Ther. 2017 Dec;16(12):2759-2769. doi: 10.1158/1535-7163.MCT-17-0439. Epub 2017 Oct 4.

14.

Lactobacillus rhamnosus GG probiotic enteric regimen does not appreciably alter the gut microbiome or provide protection against GVHD after allogeneic hematopoietic stem cell transplantation.

Gorshein E, Wei C, Ambrosy S, Budney S, Vivas J, Shenkerman A, Manago J, McGrath MK, Tyno A, Lin Y, Patel V, Gharibo M, Schaar D, Jenq RR, Khiabanian H, Strair R.

Clin Transplant. 2017 May;31(5). doi: 10.1111/ctr.12947. Epub 2017 Mar 31.

PMID:
28256022
15.

Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration.

Uhlemann AC, McAdam PR, Sullivan SB, Knox JR, Khiabanian H, Rabadan R, Davies PR, Fitzgerald JR, Lowy FD.

MBio. 2017 Jan 17;8(1). pii: e01375-16. doi: 10.1128/mBio.01375-16.

16.

Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas.

Abate F, da Silva-Almeida AC, Zairis S, Robles-Valero J, Couronne L, Khiabanian H, Quinn SA, Kim MY, Laginestra MA, Kim C, Fiore D, Bhagat G, Piris MA, Campo E, Lossos IS, Bernard OA, Inghirami G, Pileri S, Bustelo XR, Rabadan R, Ferrando AA, Palomero T.

Proc Natl Acad Sci U S A. 2017 Jan 24;114(4):764-769. doi: 10.1073/pnas.1608839114. Epub 2017 Jan 6.

17.

Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia.

Oshima K, Khiabanian H, da Silva-Almeida AC, Tzoneva G, Abate F, Ambesi-Impiombato A, Sanchez-Martin M, Carpenter Z, Penson A, Perez-Garcia A, Eckert C, Nicolas C, Balbin M, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Gastier-Foster JM, Devidas M, Loh ML, Kirschner-Schwabe R, Palomero T, Rabadan R, Ferrando AA.

Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11306-11311. Epub 2016 Sep 21.

18.

The genetics of nodal marginal zone lymphoma.

Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D.

Blood. 2016 Sep 8;128(10):1362-73. doi: 10.1182/blood-2016-02-696757. Epub 2016 Jun 22.

19.

A Case of T-cell Acute Lymphoblastic Leukemia Relapsed As Myeloid Acute Leukemia.

Paganin M, Buldini B, Germano G, Seganfreddo E, Meglio Ad, Magrin E, Grillo F, Pigazzi M, Rizzari C, Cazzaniga G, Khiabanian H, Palomero T, Rabadan R, Ferrando AA, Basso G.

Pediatr Blood Cancer. 2016 Sep;63(9):1660-3. doi: 10.1002/pbc.26054. Epub 2016 May 3.

PMID:
27149388
20.

Emerging Role of Genomic Rearrangements in Breast Cancer: Applying Knowledge from Other Cancers.

Paratala BS, Dolfi SC, Khiabanian H, Rodriguez-Rodriguez L, Ganesan S, Hirshfield KM.

Biomark Cancer. 2016 Feb 11;8(Supple 1):1-14. doi: 10.4137/BIC.S34417. eCollection 2016. Review.

21.

Clinical impact of small subclones harboring NOTCH1, SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia.

Rasi S, Khiabanian H, Ciardullo C, Terzi-di-Bergamo L, Monti S, Spina V, Bruscaggin A, Cerri M, Deambrogi C, Martuscelli L, Biasi A, Spaccarotella E, De Paoli L, Gattei V, Foà R, Rabadan R, Gaidano G, Rossi D.

Haematologica. 2016 Apr;101(4):e135-8. doi: 10.3324/haematol.2015.136051. Epub 2016 Jan 27. No abstract available.

22.

De novo transcriptome reconstruction and annotation of the Egyptian rousette bat.

Lee AK, Kulcsar KA, Elliott O, Khiabanian H, Nagle ER, Jones ME, Amman BR, Sanchez-Lockhart M, Towner JS, Palacios G, Rabadan R.

BMC Genomics. 2015 Dec 7;16:1033. doi: 10.1186/s12864-015-2124-x.

23.

The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome.

da Silva Almeida AC, Abate F, Khiabanian H, Martinez-Escala E, Guitart J, Tensen CP, Vermeer MH, Rabadan R, Ferrando A, Palomero T.

Nat Genet. 2015 Dec;47(12):1465-70. doi: 10.1038/ng.3442. Epub 2015 Nov 9.

24.

High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants.

Emmett KJ, Lee A, Khiabanian H, Rabadan R.

PLoS Curr. 2015 Feb 9;7. pii: ecurrents.outbreaks.c7fd7946ba606c982668a96bcba43c90. doi: 10.1371/currents.outbreaks.c7fd7946ba606c982668a96bcba43c90.

25.

Viral diversity and clonal evolution from unphased genomic data.

Khiabanian H, Carpenter Z, Kugelman J, Chan J, Trifonov V, Nagle E, Warren T, Iversen P, Bavari S, Palacios G, Rabadan R.

BMC Genomics. 2014;15 Suppl 6:S17. doi: 10.1186/1471-2164-15-S6-S17. Epub 2014 Oct 17.

26.

Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia.

Wang J, Khiabanian H, Rossi D, Fabbri G, Gattei V, Forconi F, Laurenti L, Marasca R, Del Poeta G, Foà R, Pasqualucci L, Gaidano G, Rabadan R.

Elife. 2014 Dec 11;3. doi: 10.7554/eLife.02869.

27.

Transcriptome reconstruction and annotation of cynomolgus and African green monkey.

Lee A, Khiabanian H, Kugelman J, Elliott O, Nagle E, Yu GY, Warren T, Palacios G, Rabadan R.

BMC Genomics. 2014 Oct 3;15:846. doi: 10.1186/1471-2164-15-846.

28.

Data-driven discovery of seasonally linked diseases from an Electronic Health Records system.

Melamed RD, Khiabanian H, Rabadan R.

BMC Bioinformatics. 2014;15 Suppl 6:S3. doi: 10.1186/1471-2105-15-S6-S3. Epub 2014 May 16.

29.

Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness.

Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes AB, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foà R.

Blood. 2014 Apr 10;123(15):2378-88. doi: 10.1182/blood-2013-10-534271. Epub 2014 Feb 18.

30.

Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia.

Rossi D, Khiabanian H, Spina V, Ciardullo C, Bruscaggin A, Famà R, Rasi S, Monti S, Deambrogi C, De Paoli L, Wang J, Gattei V, Guarini A, Foà R, Rabadan R, Gaidano G.

Blood. 2014 Apr 3;123(14):2139-47. doi: 10.1182/blood-2013-11-539726. Epub 2014 Feb 5.

31.

Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts.

Kode A, Manavalan JS, Mosialou I, Bhagat G, Rathinam CV, Luo N, Khiabanian H, Lee A, Murty VV, Friedman R, Brum A, Park D, Galili N, Mukherjee S, Teruya-Feldstein J, Raza A, Rabadan R, Berman E, Kousteni S.

Nature. 2014 Feb 13;506(7487):240-4. doi: 10.1038/nature12883. Epub 2014 Jan 15.

32.

Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas.

Palomero T, Couronné L, Khiabanian H, Kim MY, Ambesi-Impiombato A, Perez-Garcia A, Carpenter Z, Abate F, Allegretta M, Haydu JE, Jiang X, Lossos IS, Nicolas C, Balbin M, Bastard C, Bhagat G, Piris MA, Campo E, Bernard OA, Rabadan R, Ferrando AA.

Nat Genet. 2014 Feb;46(2):166-70. doi: 10.1038/ng.2873. Epub 2014 Jan 12.

33.

Genetics of follicular lymphoma transformation.

Pasqualucci L, Khiabanian H, Fangazio M, Vasishtha M, Messina M, Holmes AB, Ouillette P, Trifonov V, Rossi D, Tabbò F, Ponzoni M, Chadburn A, Murty VV, Bhagat G, Gaidano G, Inghirami G, Malek SN, Rabadan R, Dalla-Favera R.

Cell Rep. 2014 Jan 16;6(1):130-40. doi: 10.1016/j.celrep.2013.12.027. Epub 2014 Jan 2.

34.

Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome.

Fabbri G, Khiabanian H, Holmes AB, Wang J, Messina M, Mullighan CG, Pasqualucci L, Rabadan R, Dalla-Favera R.

J Exp Med. 2013 Oct 21;210(11):2273-88. doi: 10.1084/jem.20131448. Epub 2013 Oct 14.

35.

A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.

Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A.

Cell. 2013 Sep 26;155(1):70-80. doi: 10.1016/j.cell.2013.08.030.

36.

Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL.

Tzoneva G, Perez-Garcia A, Carpenter Z, Khiabanian H, Tosello V, Allegretta M, Paietta E, Racevskis J, Rowe JM, Tallman MS, Paganin M, Basso G, Hof J, Kirschner-Schwabe R, Palomero T, Rabadan R, Ferrando A.

Nat Med. 2013 Mar;19(3):368-71. doi: 10.1038/nm.3078. Epub 2013 Feb 3.

37.

Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia.

Rossi D, Rasi S, Spina V, Bruscaggin A, Monti S, Ciardullo C, Deambrogi C, Khiabanian H, Serra R, Bertoni F, Forconi F, Laurenti L, Marasca R, Dal-Bo M, Rossi FM, Bulian P, Nomdedeu J, Del Poeta G, Gattei V, Pasqualucci L, Rabadan R, Foà R, Dalla-Favera R, Gaidano G.

Blood. 2013 Feb 21;121(8):1403-12. doi: 10.1182/blood-2012-09-458265. Epub 2012 Dec 13.

38.

Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4.

Dapito DH, Mencin A, Gwak GY, Pradere JP, Jang MK, Mederacke I, Caviglia JM, Khiabanian H, Adeyemi A, Bataller R, Lefkowitch JH, Bower M, Friedman R, Sartor RB, Rabadan R, Schwabe RF.

Cancer Cell. 2012 Apr 17;21(4):504-16. doi: 10.1016/j.ccr.2012.02.007.

39.

Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness.

Rossi D, Bruscaggin A, Spina V, Rasi S, Khiabanian H, Messina M, Fangazio M, Vaisitti T, Monti S, Chiaretti S, Guarini A, Del Giudice I, Cerri M, Cresta S, Deambrogi C, Gargiulo E, Gattei V, Forconi F, Bertoni F, Deaglio S, Rabadan R, Pasqualucci L, Foà R, Dalla-Favera R, Gaidano G.

Blood. 2011 Dec 22;118(26):6904-8. doi: 10.1182/blood-2011-08-373159. Epub 2011 Oct 28.

40.

Discovering disease associations by integrating electronic clinical data and medical literature.

Holmes AB, Hawson A, Liu F, Friedman C, Khiabanian H, Rabadan R.

PLoS One. 2011;6(6):e21132. doi: 10.1371/journal.pone.0021132. Epub 2011 Jun 23.

41.

Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation.

Fabbri G, Rasi S, Rossi D, Trifonov V, Khiabanian H, Ma J, Grunn A, Fangazio M, Capello D, Monti S, Cresta S, Gargiulo E, Forconi F, Guarini A, Arcaini L, Paulli M, Laurenti L, Larocca LM, Marasca R, Gattei V, Oscier D, Bertoni F, Mullighan CG, Foá R, Pasqualucci L, Rabadan R, Dalla-Favera R, Gaidano G.

J Exp Med. 2011 Jul 4;208(7):1389-401. doi: 10.1084/jem.20110921. Epub 2011 Jun 13.

42.

Signs of the 2009 influenza pandemic in the New York-Presbyterian Hospital electronic health records.

Khiabanian H, Holmes AB, Kelly BJ, Gururaj M, Hripcsak G, Rabadan R.

PLoS One. 2010 Sep 9;5(9). pii: e12658. doi: 10.1371/journal.pone.0012658.

43.

ParMap, an algorithm for the identification of small genomic insertions and deletions in nextgen sequencing data.

Khiabanian H, Van Vlierberghe P, Palomero T, Ferrando AA, Rabadan R.

BMC Res Notes. 2010 May 27;3:147. doi: 10.1186/1756-0500-3-147.

44.

PHF6 mutations in T-cell acute lymphoblastic leukemia.

Van Vlierberghe P, Palomero T, Khiabanian H, Van der Meulen J, Castillo M, Van Roy N, De Moerloose B, Philippé J, González-García S, Toribio ML, Taghon T, Zuurbier L, Cauwelier B, Harrison CJ, Schwab C, Pisecker M, Strehl S, Langerak AW, Gecz J, Sonneveld E, Pieters R, Paietta E, Rowe JM, Wiernik PH, Benoit Y, Soulier J, Poppe B, Yao X, Cordon-Cardo C, Meijerink J, Rabadan R, Speleman F, Ferrando A.

Nat Genet. 2010 Apr;42(4):338-42. doi: 10.1038/ng.542. Epub 2010 Mar 14.

45.

Reassortment patterns in Swine influenza viruses.

Khiabanian H, Trifonov V, Rabadan R.

Version 2. PLoS Curr. 2009 Aug 21 [revised 2009 Jan 1];1:RRN1008.

46.

Reassortment patterns in Swine influenza viruses.

Khiabanian H, Trifonov V, Rabadan R.

PLoS One. 2009 Oct 7;4(10):e7366. doi: 10.1371/journal.pone.0007366.

47.

Differences in patient age distribution between influenza A subtypes.

Khiabanian H, Farrell GM, St George K, Rabadan R.

PLoS One. 2009 Aug 31;4(8):e6832. doi: 10.1371/journal.pone.0006832.

48.

Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus.

Trifonov V, Khiabanian H, Rabadan R.

N Engl J Med. 2009 Jul 9;361(2):115-9. doi: 10.1056/NEJMp0904572. Epub 2009 May 27. No abstract available.

49.

The origin of the recent swine influenza A(H1N1) virus infecting humans.

Trifonov V, Khiabanian H, Greenbaum B, Rabadan R.

Euro Surveill. 2009 Apr 30;14(17). pii: 19193.

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