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Items: 1 to 50 of 109

1.

Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma.

Kurtz DM, Scherer F, Jin MC, Soo J, Craig AFM, Esfahani MS, Chabon JJ, Stehr H, Liu CL, Tibshirani R, Maeda LS, Gupta NK, Khodadoust MS, Advani RH, Levy R, Newman AM, Dührsen U, Hüttmann A, Meignan M, Casasnovas RO, Westin JR, Roschewski M, Wilson WH, Gaidano G, Rossi D, Diehn M, Alizadeh AA.

J Clin Oncol. 2018 Aug 20:JCO2018785246. doi: 10.1200/JCO.2018.78.5246. [Epub ahead of print]

PMID:
30125215
2.

Surgical and molecular characterization of primary and metastatic disease in a neuroendocrine tumor arising in a tailgut cyst.

Erdrich J, Schaberg K, Khodadoust MS, Zhou L, Shelton AA, Visser BC, Ford JM, Alizadeh AA, Quake SR, Kunz PL, Beausang JF.

Cold Spring Harb Mol Case Stud. 2018 Aug 7. pii: mcs.a003004. doi: 10.1101/mcs.a003004. [Epub ahead of print]

3.

Combination Approach for Detecting Different Types of Alterations in Circulating Tumor DNA in Leiomyosarcoma.

Przybyl J, Chabon JJ, Spans L, Ganjoo KN, Vennam S, Newman AM, Forgó E, Varma S, Zhu S, Debiec-Rychter M, Alizadeh AA, Diehn M, van de Rijn M.

Clin Cancer Res. 2018 Jun 1;24(11):2688-2699. doi: 10.1158/1078-0432.CCR-17-3704. Epub 2018 Feb 20.

PMID:
29463554
4.

Profiling Tumor Infiltrating Immune Cells with CIBERSORT.

Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA.

Methods Mol Biol. 2018;1711:243-259. doi: 10.1007/978-1-4939-7493-1_12.

PMID:
29344893
5.

The evaluation of Cr-curcumin-DNA complexation by experimental and theoretical approaches.

Ahmadi F, Vahedpour T, Alizadeh AA.

Nucleosides Nucleotides Nucleic Acids. 2018 Jan 2;37(1):35-52. doi: 10.1080/15257770.2017.1414241. Epub 2018 Jan 16.

PMID:
29336691
6.

KLHL6 Is Preferentially Expressed in Germinal Center-Derived B-Cell Lymphomas.

Kunder CA, Roncador G, Advani RH, Gualco G, Bacchi CE, Sabile JM, Lossos IS, Nie K, Tibshirani RJ, Green MR, Alizadeh AA, Natkunam Y.

Am J Clin Pathol. 2017 Nov 20;148(6):465-476. doi: 10.1093/ajcp/aqx099.

PMID:
29140403
7.

Enhanced sciatic nerve regeneration by human endometrial stem cells in an electrospun poly (ε-caprolactone)/collagen/NBG nerve conduit in rat.

Mohamadi F, Ebrahimi-Barough S, Nourani MR, Mansoori K, Salehi M, Alizadeh AA, Tavangar SM, Sefat F, Sharifi S, Ai J.

Artif Cells Nanomed Biotechnol. 2017 Nov 8:1-13. doi: 10.1080/21691401.2017.1391823. [Epub ahead of print]

PMID:
29117721
8.

An Alignment-Independent 3D-QSAR Study of FGFR2 Tyrosine Kinase Inhibitors.

Jafari B, Hamzeh-Mivehroud M, Alizadeh AA, Sharifi M, Dastmalchi S.

Adv Pharm Bull. 2017 Sep;7(3):409-418. doi: 10.15171/apb.2017.049. Epub 2017 Sep 25.

9.

Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling.

Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Khodadoust MS, Esfahani MS, Liu CL, Zhou L, Scherer F, Kurtz DM, Say C, Carter JN, Merriott DJ, Dudley JC, Binkley MS, Modlin L, Padda SK, Gensheimer MF, West RB, Shrager JB, Neal JW, Wakelee HA, Loo BW Jr, Alizadeh AA, Diehn M.

Cancer Discov. 2017 Dec;7(12):1394-1403. doi: 10.1158/2159-8290.CD-17-0716. Epub 2017 Sep 24.

10.

Data normalization considerations for digital tumor dissection.

Newman AM, Gentles AJ, Liu CL, Diehn M, Alizadeh AA.

Genome Biol. 2017 Jul 5;18(1):128. doi: 10.1186/s13059-017-1257-4.

11.

High-throughput sequencing for noninvasive disease detection in hematologic malignancies.

Scherer F, Kurtz DM, Diehn M, Alizadeh AA.

Blood. 2017 Jul 27;130(4):440-452. doi: 10.1182/blood-2017-03-735639. Epub 2017 Jun 9. Review.

12.

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens.

Khodadoust MS, Olsson N, Wagar LE, Haabeth OA, Chen B, Swaminathan K, Rawson K, Liu CL, Steiner D, Lund P, Rao S, Zhang L, Marceau C, Stehr H, Newman AM, Czerwinski DK, Carlton VE, Moorhead M, Faham M, Kohrt HE, Carette J, Green MR, Davis MM, Levy R, Elias JE, Alizadeh AA.

Nature. 2017 Mar 30;543(7647):723-727. doi: 10.1038/nature21433. Epub 2017 Mar 22.

13.

Distinct patterns of B-cell receptor signaling in non-Hodgkin lymphomas identified by single-cell profiling.

Myklebust JH, Brody J, Kohrt HE, Kolstad A, Czerwinski DK, Wälchli S, Green MR, Trøen G, Liestøl K, Beiske K, Houot R, Delabie J, Alizadeh AA, Irish JM, Levy R.

Blood. 2017 Feb 9;129(6):759-770. doi: 10.1182/blood-2016-05-718494. Epub 2016 Dec 23.

14.

Corrigendum: Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients.

Chabon JJ, Simmons AD, Lovejoy AF, Esfahani MS, Newman AM, Haringsma HJ, Kurtz DM, Stehr H, Scherer F, Karlovich CA, Harding TC, Durkin KA, Otterson GA, Thomas Purcell W, Ross Camidge D, Goldman JW, Sequist LV, Piotrowska Z, Wakelee HA, Neal JW, Alizadeh AA, Diehn M.

Nat Commun. 2016 Nov 14;7:13513. doi: 10.1038/ncomms13513. No abstract available.

15.

Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA.

Scherer F, Kurtz DM, Newman AM, Stehr H, Craig AF, Esfahani MS, Lovejoy AF, Chabon JJ, Klass DM, Liu CL, Zhou L, Glover C, Visser BC, Poultsides GA, Advani RH, Maeda LS, Gupta NK, Levy R, Ohgami RS, Kunder CA, Diehn M, Alizadeh AA.

Sci Transl Med. 2016 Nov 9;8(364):364ra155.

16.

Identification of novel peptides against TNF-α using phage display technique and in silico modeling of their modes of binding.

Alizadeh AA, Hamzeh-Mivehroud M, Farajzadeh M, Dastmalchi S.

Eur J Pharm Sci. 2017 Jan 1;96:490-498. doi: 10.1016/j.ejps.2016.10.005. Epub 2016 Oct 5.

PMID:
27720899
17.

Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance.

Jeong Y, Hoang NT, Lovejoy A, Stehr H, Newman AM, Gentles AJ, Kong W, Truong D, Martin S, Chaudhuri A, Heiser D, Zhou L, Say C, Carter JN, Hiniker SM, Loo BW Jr, West RB, Beachy P, Alizadeh AA, Diehn M.

Cancer Discov. 2017 Jan;7(1):86-101. doi: 10.1158/2159-8290.CD-16-0127. Epub 2016 Sep 23.

18.

High-throughput genomic profiling of tumor-infiltrating leukocytes.

Newman AM, Alizadeh AA.

Curr Opin Immunol. 2016 Aug;41:77-84. doi: 10.1016/j.coi.2016.06.006. Epub 2016 Jun 30. Review.

19.

Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients.

Chabon JJ, Simmons AD, Lovejoy AF, Esfahani MS, Newman AM, Haringsma HJ, Kurtz DM, Stehr H, Scherer F, Karlovich CA, Harding TC, Durkin KA, Otterson GA, Purcell WT, Camidge DR, Goldman JW, Sequist LV, Piotrowska Z, Wakelee HA, Neal JW, Alizadeh AA, Diehn M.

Nat Commun. 2016 Jun 10;7:11815. doi: 10.1038/ncomms11815. Erratum in: Nat Commun. 2016 Nov 14;7:13513.

20.

Integrated digital error suppression for improved detection of circulating tumor DNA.

Newman AM, Lovejoy AF, Klass DM, Kurtz DM, Chabon JJ, Scherer F, Stehr H, Liu CL, Bratman SV, Say C, Zhou L, Carter JN, West RB, Sledge GW, Shrager JB, Loo BW Jr, Neal JW, Wakelee HA, Diehn M, Alizadeh AA.

Nat Biotechnol. 2016 May;34(5):547-555. doi: 10.1038/nbt.3520. Epub 2016 Mar 28.

21.

Production and Purification of a Novel Anti-TNF-α Single Chain Fragment Variable Antibody.

Alizadeh AA, Hamzeh-Mivehroud M, Dastmalchi S.

Adv Pharm Bull. 2015 Dec;5(Suppl 1):667-72. doi: 10.15171/apb.2015.091. Epub 2015 Dec 31.

22.

Identification of Novel Single Chain Fragment Variable Antibodies Against TNF-α Using Phage Display Technology.

Alizadeh AA, Hamzeh-Mivehroud M, Dastmalchi S.

Adv Pharm Bull. 2015 Dec;5(Suppl 1):661-6. doi: 10.15171/apb.2015.090. Epub 2015 Dec 31.

23.

Corrigendum: Organocatalytic removal of formaldehyde adducts from RNA and DNA bases.

Karmakar S, Harcourt EM, Hewings DS, Scherer F, Lovejoy AF, Kurtz DM, Ehrenschwender T, Barandun LJ, Roost C, Alizadeh AA, Kool ET.

Nat Chem. 2015 Dec;7(12):1033. doi: 10.1038/nchem.2401. No abstract available.

PMID:
26587722
24.

Predicting Radiotherapy Responses and Treatment Outcomes Through Analysis of Circulating Tumor DNA.

Chaudhuri AA, Binkley MS, Osmundson EC, Alizadeh AA, Diehn M.

Semin Radiat Oncol. 2015 Oct;25(4):305-12. doi: 10.1016/j.semradonc.2015.05.001. Epub 2015 May 15. Review.

25.

Organocatalytic removal of formaldehyde adducts from RNA and DNA bases.

Karmakar S, Harcourt EM, Hewings DS, Scherer F, Lovejoy AF, Kurtz DM, Ehrenschwender T, Barandun LJ, Roost C, Alizadeh AA, Kool ET.

Nat Chem. 2015 Sep;7(9):752-8. doi: 10.1038/nchem.2307. Epub 2015 Aug 3. Erratum in: Nat Chem. 2015 Dec;7(12):1033.

26.

Integrating Tumor and Stromal Gene Expression Signatures With Clinical Indices for Survival Stratification of Early-Stage Non-Small Cell Lung Cancer.

Gentles AJ, Bratman SV, Lee LJ, Harris JP, Feng W, Nair RV, Shultz DB, Nair VS, Hoang CD, West RB, Plevritis SK, Alizadeh AA, Diehn M.

J Natl Cancer Inst. 2015 Aug 18;107(10). pii: djv211. doi: 10.1093/jnci/djv211. Print 2015 Oct.

PMID:
26286589
27.

Toward understanding and exploiting tumor heterogeneity.

Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel JO, Lichter P, Mason CE, Navin N, Pe'er D, Polyak K, Roberts CW, Siu L, Snyder A, Stower H, Swanton C, Verhaak RG, Zenklusen JC, Zuber J, Zucman-Rossi J.

Nat Med. 2015 Aug;21(8):846-53. doi: 10.1038/nm.3915.

28.

Large-Scale and Comprehensive Immune Profiling and Functional Analysis of Normal Human Aging.

Whiting CC, Siebert J, Newman AM, Du HW, Alizadeh AA, Goronzy J, Weyand CM, Krishnan E, Fathman CG, Maecker HT.

PLoS One. 2015 Jul 21;10(7):e0133627. doi: 10.1371/journal.pone.0133627. eCollection 2015.

29.

The prognostic landscape of genes and infiltrating immune cells across human cancers.

Gentles AJ, Newman AM, Liu CL, Bratman SV, Feng W, Kim D, Nair VS, Xu Y, Khuong A, Hoang CD, Diehn M, West RB, Plevritis SK, Alizadeh AA.

Nat Med. 2015 Aug;21(8):938-945. doi: 10.1038/nm.3909. Epub 2015 Jul 20.

30.

A Simple and Rapid Method for Expression and Purification of Functional TNF-α Using GST Fusion System.

Alizadeh AA, Hamzeh-Mivehroud M, Farajzadeh M, Moosavi-Movahedi AA, Dastmalchi S.

Curr Pharm Biotechnol. 2015;16(8):707-15.

PMID:
26044863
31.

Noninvasive monitoring of diffuse large B-cell lymphoma by immunoglobulin high-throughput sequencing.

Kurtz DM, Green MR, Bratman SV, Scherer F, Liu CL, Kunder CA, Takahashi K, Glover C, Keane C, Kihira S, Visser B, Callahan J, Kong KA, Faham M, Corbelli KS, Miklos D, Advani RH, Levy R, Hicks RJ, Hertzberg M, Ohgami RS, Gandhi MK, Diehn M, Alizadeh AA.

Blood. 2015 Jun 11;125(24):3679-87. doi: 10.1182/blood-2015-03-635169. Epub 2015 Apr 17.

32.

Robust enumeration of cell subsets from tissue expression profiles.

Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA.

Nat Methods. 2015 May;12(5):453-7. doi: 10.1038/nmeth.3337. Epub 2015 Mar 30.

33.

Potential clinical utility of ultrasensitive circulating tumor DNA detection with CAPP-Seq.

Bratman SV, Newman AM, Alizadeh AA, Diehn M.

Expert Rev Mol Diagn. 2015 Jun;15(6):715-9. doi: 10.1586/14737159.2015.1019476. Epub 2015 Mar 16. Review.

34.

A Simple Method for Estimating Interactions between a Treatment and a Large Number of Covariates.

Tian L, Alizadeh AA, Gentles AJ, Tibshirani R.

J Am Stat Assoc. 2014 Oct;109(508):1517-1532.

35.

Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation.

Green MR, Kihira S, Liu CL, Nair RV, Salari R, Gentles AJ, Irish J, Stehr H, Vicente-Dueñas C, Romero-Camarero I, Sanchez-Garcia I, Plevritis SK, Arber DA, Batzoglou S, Levy R, Alizadeh AA.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1116-25. doi: 10.1073/pnas.1501199112. Epub 2015 Feb 23.

36.

In-silico Investigation of Tubulin Binding Modes of a Series of Novel Antiproliferative Spiroisoxazoline Compounds Using Docking Studies.

Abolhasani H, Zarghi A, Hamzeh-Mivehroud M, Alizadeh AA, Shahbazi Mojarrad J, Dastmalchi S.

Iran J Pharm Res. 2015 Winter;14(1):141-7.

37.

FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution.

Newman AM, Bratman SV, Stehr H, Lee LJ, Liu CL, Diehn M, Alizadeh AA.

Bioinformatics. 2014 Dec 1;30(23):3390-3. doi: 10.1093/bioinformatics/btu549. Epub 2014 Aug 20.

38.

Transient expression of Bcl6 is sufficient for oncogenic function and induction of mature B-cell lymphoma.

Green MR, Vicente-Dueñas C, Romero-Camarero I, Long Liu C, Dai B, González-Herrero I, García-Ramírez I, Alonso-Escudero E, Iqbal J, Chan WC, Campos-Sanchez E, Orfao A, Pintado B, Flores T, Blanco O, Jiménez R, Martínez-Climent JA, Criado FJ, Cenador MB, Zhao S, Natkunam Y, Lossos IS, Majeti R, Melnick A, Cobaleda C, Alizadeh AA, Sánchez-García I.

Nat Commun. 2014 Jun 2;5:3904. doi: 10.1038/ncomms4904.

39.

Hit-and-run lymphomagenesis by the Bcl6 oncogene.

Green MR, Vicente-Dueñas C, Alizadeh AA, Sánchez-García I.

Cell Cycle. 2014;13(12):1831-2. doi: 10.4161/cc.29326. Epub 2014 May 27. No abstract available.

40.

Common progenitor cells in mature B-cell malignancies: implications for therapy.

Green MR, Alizadeh AA.

Curr Opin Hematol. 2014 Jul;21(4):333-40. doi: 10.1097/MOH.0000000000000049. Review.

PMID:
24811163
41.

Active idiotypic vaccination versus control immunotherapy for follicular lymphoma.

Levy R, Ganjoo KN, Leonard JP, Vose JM, Flinn IW, Ambinder RF, Connors JM, Berinstein NL, Belch AR, Bartlett NL, Nichols C, Emmanouilides CE, Timmerman JM, Gregory SA, Link BK, Inwards DJ, Freedman AS, Matous JV, Robertson MJ, Kunkel LA, Ingolia DE, Gentles AJ, Liu CL, Tibshirani R, Alizadeh AA, Denney DW Jr.

J Clin Oncol. 2014 Jun 10;32(17):1797-803. doi: 10.1200/JCO.2012.43.9273. Epub 2014 May 5.

42.

Tumor antigen discovery through translation of the cancer genome.

Khodadoust MS, Alizadeh AA.

Immunol Res. 2014 May;58(2-3):292-9. doi: 10.1007/s12026-014-8505-4. Review.

PMID:
24718952
43.

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage.

Newman AM, Bratman SV, To J, Wynne JF, Eclov NC, Modlin LA, Liu CL, Neal JW, Wakelee HA, Merritt RE, Shrager JB, Loo BW Jr, Alizadeh AA, Diehn M.

Nat Med. 2014 May;20(5):548-54. doi: 10.1038/nm.3519. Epub 2014 Apr 6.

44.

Phage display as a technology delivering on the promise of peptide drug discovery.

Hamzeh-Mivehroud M, Alizadeh AA, Morris MB, Church WB, Dastmalchi S.

Drug Discov Today. 2013 Dec;18(23-24):1144-57. doi: 10.1016/j.drudis.2013.09.001. Epub 2013 Sep 17. Review.

PMID:
24051398
45.

Identification of gene microarray expression profiles in patients with chronic graft-versus-host disease following allogeneic hematopoietic cell transplantation.

Kohrt HE, Tian L, Li L, Alizadeh AA, Hsieh S, Tibshirani RJ, Strober S, Sarwal M, Lowsky R.

Clin Immunol. 2013 Jul;148(1):124-35. doi: 10.1016/j.clim.2013.04.013. Epub 2013 May 1.

PMID:
23685278
46.

Utility in prognostic value added by molecular profiles for diffuse large B-cell lymphoma.

Gentles AJ, Alizadeh AA.

Blood. 2013 Apr 11;121(15):3052-4. doi: 10.1182/blood-2013-01-477521. No abstract available.

47.

Germinal centre protein HGAL promotes lymphoid hyperplasia and amyloidosis via BCR-mediated Syk activation.

Romero-Camarero I, Jiang X, Natkunam Y, Lu X, Vicente-Dueñas C, Gonzalez-Herrero I, Flores T, Garcia JL, McNamara G, Kunder C, Zhao S, Segura V, Fontan L, Martínez-Climent JA, García-Criado FJ, Theis JD, Dogan A, Campos-Sánchez E, Green MR, Alizadeh AA, Cobaleda C, Sánchez-García I, Lossos IS.

Nat Commun. 2013;4:1338. doi: 10.1038/ncomms2334.

48.

High PD-1 expression and suppressed cytokine signaling distinguish T cells infiltrating follicular lymphoma tumors from peripheral T cells.

Myklebust JH, Irish JM, Brody J, Czerwinski DK, Houot R, Kohrt HE, Timmerman J, Said J, Green MR, Delabie J, Kolstad A, Alizadeh AA, Levy R.

Blood. 2013 Feb 21;121(8):1367-76. doi: 10.1182/blood-2012-04-421826. Epub 2013 Jan 7.

49.

Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma.

Green MR, Gentles AJ, Nair RV, Irish JM, Kihira S, Liu CL, Kela I, Hopmans ES, Myklebust JH, Ji H, Plevritis SK, Levy R, Alizadeh AA.

Blood. 2013 Feb 28;121(9):1604-11. doi: 10.1182/blood-2012-09-457283. Epub 2013 Jan 7.

50.

Role of Smad proteins in resistance to BMP-induced growth inhibition in B-cell lymphoma.

Huse K, Bakkebø M, Wälchli S, Oksvold MP, Hilden VI, Forfang L, Bredahl ML, Liestøl K, Alizadeh AA, Smeland EB, Myklebust JH.

PLoS One. 2012;7(10):e46117. doi: 10.1371/journal.pone.0046117. Epub 2012 Oct 1.

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