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Items: 1 to 50 of 125

1.

Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ.

Foley JW, Zhu C, Jolivet P, Zhu SX, Lu P, Meaney MJ, West RB.

Genome Res. 2019 Sep 13. pii: gr.234807.118. doi: 10.1101/gr.234807.118. [Epub ahead of print]

2.

Cell cycle progression in confining microenvironments is regulated by a growth-responsive TRPV4-PI3K/Akt-p27Kip1 signaling axis.

Nam S, Gupta VK, Lee HP, Lee JY, Wisdom KM, Varma S, Flaum EM, Davis C, West RB, Chaudhuri O.

Sci Adv. 2019 Aug 7;5(8):eaaw6171. doi: 10.1126/sciadv.aaw6171. eCollection 2019 Aug.

3.

Genomic landscape of ductal carcinoma in situ and association with progression.

Lin CY, Vennam S, Purington N, Lin E, Varma S, Han S, Desa M, Seto T, Wang NJ, Stehr H, Troxell ML, Kurian AW, West RB.

Breast Cancer Res Treat. 2019 Nov;178(2):307-316. doi: 10.1007/s10549-019-05401-x. Epub 2019 Aug 17.

PMID:
31420779
4.

Blood transcriptome and clonal T cell correlates of response and nonresponse to eltrombopag therapy in a cohort of patients with chronic immune thrombocytopenia.

Zhang H, Zhang BM, Guo X, Xu L, You X, West RB, Bussel JB, Zehnder JL.

Haematologica. 2019 Jul 11. pii: haematol.2019.226688. doi: 10.3324/haematol.2019.226688. [Epub ahead of print]

5.

Genomic analysis of benign prostatic hyperplasia implicates cellular re-landscaping in disease pathogenesis.

Middleton LW, Shen Z, Varma S, Pollack AS, Gong X, Zhu S, Zhu C, Foley JW, Vennam S, Sweeney RT, Tu K, Biscocho J, Eminaga O, Nolley R, Tibshirani R, Brooks JD, West RB, Pollack JR.

JCI Insight. 2019 May 16;5. pii: 129749. doi: 10.1172/jci.insight.129749.

6.

YAP-independent mechanotransduction drives breast cancer progression.

Lee JY, Chang JK, Dominguez AA, Lee HP, Nam S, Chang J, Varma S, Qi LS, West RB, Chaudhuri O.

Nat Commun. 2019 Apr 23;10(1):1848. doi: 10.1038/s41467-019-09755-0.

7.

Increased Galectin-1 Expression in Thymic Epithelial Tumors.

Riess JW, Kong CS, West RB, Padda SK, Neal JW, Wakelee HA, Le QT.

Clin Lung Cancer. 2019 May;20(3):e356-e361. doi: 10.1016/j.cllc.2018.12.005. Epub 2018 Dec 21.

PMID:
30773448
8.

Most canine ameloblastomas harbor HRAS mutations, providing a novel large-animal model of RAS-driven cancer.

Saffari PS, Vapniarsky N, Pollack AS, Gong X, Vennam S, Pollack AJ, Verstraete FJM, West RB, Arzi B, Pollack JR.

Oncogenesis. 2019 Feb 11;8(2):11. doi: 10.1038/s41389-019-0119-1.

9.

The HTN3-MSANTD3 Fusion Gene Defines a Subset of Acinic Cell Carcinoma of the Salivary Gland.

Andreasen S, Varma S, Barasch N, Thompson LDR, Miettinen M, Rooper L, Stelow EB, Agander TK, Seethala RR, Chiosea SI, Homøe P, Wessel I, Larsen SR, Erentaite D, Bishop JA, Ulhøi BP, Kiss K, Melchior LC, Pollack JR, West RB.

Am J Surg Pathol. 2019 Apr;43(4):489-496. doi: 10.1097/PAS.0000000000001200.

PMID:
30520817
10.

Matrix mechanical plasticity regulates cancer cell migration through confining microenvironments.

Wisdom KM, Adebowale K, Chang J, Lee JY, Nam S, Desai R, Rossen NS, Rafat M, West RB, Hodgson L, Chaudhuri O.

Nat Commun. 2018 Oct 8;9(1):4144. doi: 10.1038/s41467-018-06641-z.

11.

GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma.

Zhang W, Bouchard G, Yu A, Shafiq M, Jamali M, Shrager JB, Ayers K, Bakr S, Gentles AJ, Diehn M, Quon A, West RB, Nair V, van de Rijn M, Napel S, Plevritis SK.

Cancer Res. 2018 Jul 1;78(13):3445-3457. doi: 10.1158/0008-5472.CAN-17-2928. Epub 2018 May 14.

12.

Higher Absolute Lymphocyte Counts Predict Lower Mortality from Early-Stage Triple-Negative Breast Cancer.

Afghahi A, Purington N, Han SS, Desai M, Pierson E, Mathur MB, Seto T, Thompson CA, Rigdon J, Telli ML, Badve SS, Curtis CN, West RB, Horst K, Gomez SL, Ford JM, Sledge GW, Kurian AW.

Clin Cancer Res. 2018 Jun 15;24(12):2851-2858. doi: 10.1158/1078-0432.CCR-17-1323. Epub 2018 Mar 26.

13.

Local estrogen axis in the human bone microenvironment regulates estrogen receptor-positive breast cancer cells.

Amanatullah DF, Tamaresis JS, Chu P, Bachmann MH, Hoang NM, Collyar D, Mayer AT, West RB, Maloney WJ, Contag CH, King BL.

Breast Cancer Res. 2017 Nov 15;19(1):121. doi: 10.1186/s13058-017-0910-x.

14.

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.

15.

Genome-wide reconstruction of complex structural variants using read clouds.

Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A.

Nat Methods. 2017 Sep;14(9):915-920. doi: 10.1038/nmeth.4366. Epub 2017 Jul 17.

16.

Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma.

Barasch N, Gong X, Kwei KA, Varma S, Biscocho J, Qu K, Xiao N, Lipsick JS, Pelham RJ, West RB, Pollack JR.

PLoS One. 2017 Feb 17;12(2):e0171265. doi: 10.1371/journal.pone.0171265. eCollection 2017.

17.

'Non-classical' HER2 FISH results in breast cancer: a multi-institutional study.

Ballard M, Jalikis F, Krings G, Schmidt RA, Chen YY, Rendi MH, Dintzis SM, Jensen KC, West RB, Sibley RK, Troxell ML, Allison KH.

Mod Pathol. 2017 Feb;30(2):227-235. doi: 10.1038/modpathol.2016.175. Epub 2016 Oct 14.

18.

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.

19.

BRAF inhibitor therapy of primary ameloblastoma.

Tan S, Pollack JR, Kaplan MJ, Colevas AD, West RB.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2016 Oct;122(4):518-9. doi: 10.1016/j.oooo.2016.05.017. Epub 2016 Jul 5. No abstract available.

PMID:
27651290
20.

Loss of Expression of AZGP1 Is Associated With Worse Clinical Outcomes in a Multi-Institutional Radical Prostatectomy Cohort.

Brooks JD, Wei W, Pollack JR, West RB, Shin JH, Sunwoo JB, Hawley SJ, Auman H, Newcomb LF, Simko J, Hurtado-Coll A, Troyer DA, Carroll PR, Gleave ME, Lin DW, Nelson PS, Thompson IM, True LD, McKenney JK, Feng Z, Fazli L.

Prostate. 2016 Nov;76(15):1409-19. doi: 10.1002/pros.23225. Epub 2016 Jun 21.

21.

BRAF inhibitor treatment of primary BRAF-mutant ameloblastoma with pathologic assessment of response.

Tan S, Pollack JR, Kaplan MJ, Colevas AD, West RB.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2016 Jul;122(1):e5-7. doi: 10.1016/j.oooo.2015.12.016. Epub 2016 Feb 23.

PMID:
27209484
22.

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.

23.

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.

24.

Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer.

Afghahi A, Forgó E, Mitani AA, Desai M, Varma S, Seto T, Rigdon J, Jensen KC, Troxell ML, Gomez SL, Das AK, Beck AH, Kurian AW, West RB.

Breast Cancer Res. 2015 Aug 13;17:108. doi: 10.1186/s13058-015-0623-y.

25.

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.

26.

Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling.

Riordan DP, Varma S, West RB, Brown PO.

PLoS One. 2015 Jul 15;10(7):e0128975. doi: 10.1371/journal.pone.0128975. eCollection 2015.

27.

Fast and scalable inference of multi-sample cancer lineages.

Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S.

Genome Biol. 2015 May 6;16:91. doi: 10.1186/s13059-015-0647-8.

28.

Ameloblastoma: a clinical review and trends in management.

McClary AC, West RB, McClary AC, Pollack JR, Fischbein NJ, Holsinger CF, Sunwoo J, Colevas AD, Sirjani D.

Eur Arch Otorhinolaryngol. 2016 Jul;273(7):1649-61. doi: 10.1007/s00405-015-3631-8. Epub 2015 Apr 30. Review.

PMID:
25926124
29.

Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia.

Weng Z, Spies N, Zhu SX, Newburger DE, Kashef-Haghighi D, Batzoglou S, Sidow A, West RB.

Genome Med. 2015 Apr 9;7(1):28. doi: 10.1186/s13073-015-0146-2. eCollection 2015.

30.

Clinically Relevant Molecular Subtypes in Leiomyosarcoma.

Guo X, Jo VY, Mills AM, Zhu SX, Lee CH, Espinosa I, Nucci MR, Varma S, Forgó E, Hastie T, Anderson S, Ganjoo K, Beck AH, West RB, Fletcher CD, van de Rijn M.

Clin Cancer Res. 2015 Aug 1;21(15):3501-11. doi: 10.1158/1078-0432.CCR-14-3141. Epub 2015 Apr 20.

31.

Novel mutations in neuroendocrine carcinoma of the breast: possible therapeutic targets.

Ang D, Ballard M, Beadling C, Warrick A, Schilling A, O'Gara R, Pukay M, Neff TL, West RB, Corless CL, Troxell ML.

Appl Immunohistochem Mol Morphol. 2015 Feb;23(2):97-103. doi: 10.1097/PDM.0b013e3182a40fd1.

PMID:
25679062
32.

Pemetrexed in patients with thymic malignancies previously treated with chemotherapy.

Liang Y, Padda SK, Riess JW, West RB, Neal JW, Wakelee HA.

Lung Cancer. 2015 Jan;87(1):34-8. doi: 10.1016/j.lungcan.2014.11.006. Epub 2014 Nov 15.

PMID:
25443273
33.

Diffuse high intensity PD-L1 staining in thymic epithelial tumors.

Padda SK, Riess JW, Schwartz EJ, Tian L, Kohrt HE, Neal JW, West RB, Wakelee HA.

J Thorac Oncol. 2015 Mar;10(3):500-8. doi: 10.1097/JTO.0000000000000429.

34.

Fingerprints of Epstein-Barr virus in nasopharyngeal carcinoma.

West RB.

Nat Genet. 2014 Aug;46(8):809-10. doi: 10.1038/ng.3038. No abstract available.

PMID:
25070800
35.

A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions.

Brunner AL, Li J, Guo X, Sweeney RT, Varma S, Zhu SX, Li R, Tibshirani R, West RB.

Genome Biol. 2014 May 23;15(5):R71. doi: 10.1186/gb-2014-15-5-r71.

36.

Identification of recurrent SMO and BRAF mutations in ameloblastomas.

Sweeney RT, McClary AC, Myers BR, Biscocho J, Neahring L, Kwei KA, Qu K, Gong X, Ng T, Jones CD, Varma S, Odegaard JI, Sugiyama T, Koyota S, Rubin BP, Troxell ML, Pelham RJ, Zehnder JL, Beachy PA, Pollack JR, West RB.

Nat Genet. 2014 Jul;46(7):722-5. doi: 10.1038/ng.2986. Epub 2014 May 25. Erratum in: Nat Genet. 2015 Jan;47(1):97.

37.

Stromal responses among carcinomas--response.

West RB, van de Rijn M, Chen JL.

Clin Cancer Res. 2014 Mar 1;20(5):1397. doi: 10.1158/1078-0432.CCR-13-3238. No abstract available.

38.

Next generation sequencing-based expression profiling identifies signatures from benign stromal proliferations that define stromal components of breast cancer.

Guo X, Zhu SX, Brunner AL, van de Rijn M, West RB.

Breast Cancer Res. 2013 Dec 17;15(6):R117. doi: 10.1186/bcr3586.

39.

Stromal signatures in endometrioid endometrial carcinomas.

Espinosa I, Catasus L, D' Angelo E, Mozos A, Pedrola N, Bértolo C, Ferrer I, Zannoni GF, West RB, van de Rijn M, Matias-Guiu X, Prat J.

Mod Pathol. 2014 Apr;27(4):631-9. doi: 10.1038/modpathol.2013.131. Epub 2013 Nov 22.

40.

Discovery of recurrent structural variants in nasopharyngeal carcinoma.

Valouev A, Weng Z, Sweeney RT, Varma S, Le QT, Kong C, Sidow A, West RB.

Genome Res. 2014 Feb;24(2):300-9. doi: 10.1101/gr.156224.113. Epub 2013 Nov 8.

41.

Inference of tumor phylogenies with improved somatic mutation discovery.

Salari R, Saleh SS, Kashef-Haghighi D, Khavari D, Newburger DE, West RB, Sidow A, Batzoglou S.

J Comput Biol. 2013 Nov;20(11):933-44. doi: 10.1089/cmb.2013.0106.

42.

Neuregulin autocrine signaling promotes self-renewal of breast tumor-initiating cells by triggering HER2/HER3 activation.

Lee CY, Lin Y, Bratman SV, Feng W, Kuo AH, Scheeren FA, Engreitz JM, Varma S, West RB, Diehn M.

Cancer Res. 2014 Jan 1;74(1):341-52. doi: 10.1158/0008-5472.CAN-13-1055. Epub 2013 Oct 31.

43.

MAST2 and NOTCH1 translocations in breast carcinoma and associated pre-invasive lesions.

Clay MR, Varma S, West RB.

Hum Pathol. 2013 Dec;44(12):2837-44. doi: 10.1016/j.humpath.2013.08.001. Epub 2013 Oct 18.

PMID:
24140425
44.

Molecular pathological analysis of sarcomas using paraffin-embedded tissue: current limitations and future possibilities.

van de Rijn M, Guo X, Sweeney RT, Beck AH, West RB.

Histopathology. 2014 Jan;64(1):163-70. doi: 10.1111/his.12290. Epub 2013 Nov 25. Review.

45.

Integrative bioinformatics links HNF1B with clear cell carcinoma and tumor-associated thrombosis.

Cuff J, Salari K, Clarke N, Esheba GE, Forster AD, Huang S, West RB, Higgins JP, Longacre TA, Pollack JR.

PLoS One. 2013 Sep 9;8(9):e74562. doi: 10.1371/journal.pone.0074562. eCollection 2013.

46.

Stromal responses among common carcinomas correlated with clinicopathologic features.

Chen JL, Espinosa I, Lin AY, Liao OY, van de Rijn M, West RB.

Clin Cancer Res. 2013 Sep 15;19(18):5127-35. doi: 10.1158/1078-0432.CCR-12-3127. Epub 2013 Jun 26.

47.

Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types.

Giacomini CP, Sun S, Varma S, Shain AH, Giacomini MM, Balagtas J, Sweeney RT, Lai E, Del Vecchio CA, Forster AD, Clarke N, Montgomery KD, Zhu S, Wong AJ, van de Rijn M, West RB, Pollack JR.

PLoS Genet. 2013 Apr;9(4):e1003464. doi: 10.1371/journal.pgen.1003464. Epub 2013 Apr 25.

48.

Human papillomavirus 16 detected in nasopharyngeal carcinomas in white Americans but not in endemic Southern Chinese patients.

Lin Z, Khong B, Kwok S, Cao H, West RB, Le QT, Kong CS.

Head Neck. 2014 May;36(5):709-14. doi: 10.1002/hed.23362. Epub 2013 Oct 26.

49.

Desktop transcriptome sequencing from archival tissue to identify clinically relevant translocations.

Sweeney RT, Zhang B, Zhu SX, Varma S, Smith KS, Montgomery SB, van de Rijn M, Zehnder J, West RB.

Am J Surg Pathol. 2013 Jun;37(6):796-803. doi: 10.1097/PAS.0b013e31827ad9b2.

50.

Genome evolution during progression to breast cancer.

Newburger DE, Kashef-Haghighi D, Weng Z, Salari R, Sweeney RT, Brunner AL, Zhu SX, Guo X, Varma S, Troxell ML, West RB, Batzoglou S, Sidow A.

Genome Res. 2013 Jul;23(7):1097-108. doi: 10.1101/gr.151670.112. Epub 2013 Apr 8.

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