Publications

• Saltz J, Sharma A, Iyer G, Bremer E, Wang F, Jasniewski A, DiPrima T, Almeida JS, Gao Y, Zhao T, Saltz M, Kurc T. A Containerized software system for generation, management, and exploration of features from whole slide tissue images. Cancer Research, 2017 77:21. DOI: 10.1158/0008-5472.
  • Citation: 0
  • Journal Impact Factor: 9.211
• Spagnolo DM, Al-Kofahi Y, Zhu P, Lezon TR, Gough A, Stern AM, Lee AV, Ginty F, Sarachan B, Taylor DL, Chennubhotla, SC. Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images. Cancer Research, 2017 77:21. DOI: 10.1158/0008-5472.
  • Citation: 0
  • Journal Impact Factor: 9.211
• Saltz J, Gupta R, Hou L, Lazar AJ, Sharma A, Thorsson V. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Report 2018 23, 181-200.
  • Citation: 0
  • Journal Impact Factor: 8.282
• Savova G, Tseytlin E, Finan S,  Castine M, Miller T, Medvedeva O, Harris D, Hochheiser H, Lin C, Chavan G, Jacobson, RS. DeepPhe: A Natural language processing system for extracting cancer phenotypes from clinical records. Cancer Research 2017 77:21. DOI: 10.1158/0008-5472.
  • Citation: 0
  • Journal Impact Factor: 9.122
• Tseytlin E, Mitchell K, Legowski E, Corrigan J, Chavan G, Jacobson RS. NOBLE – Flexible concept recognition for large-scale biomedical natural language processing. BMC Bioinformatics 2016 17:32. PMID: 26763894 PMCID: PMC4712516
  • Citation: 9
  • Journal Impact Factor: 2.435

• Jacobson RS, Becich MJ, Bollag RJ, Chavan G, Corrigan J, Dhir R, et al. A federated network for translational cancer research using clinical data and biospecimens. Cancer Res. 2015 December 15;75(24):5194-201. PMCID: PMC4683415
  • Citation: 5
  • Journal Impact Factor: 9.239

• Crowley RS, Castine M, Mitchell KJ, Chavan G, McSherry T, Feldman M. caTIES
  A Grid Based System for Coding and Retrieval of Surgical Pathology Reports and Tissue Specimens In Support Of Translational Research. J Am Med Inform Assoc. 2010 May 1;17(3):253-64. PMID: 20442142
  • Citation: 55
  • Journal Impact Factor: 3.428

• Mitchell KJ, Becich MJ, Berman, JJ, Chapman WW, Gilbertson J, Gupta D, Harrison J, Legowski E, and Crowley RS.
  Implementation and Evaluation of a Negation Tagger in a Pipeline-based System for Information Extraction from Pathology Reports. Proc MEDINFO 2004; 11(Pt 1): 663-67. PMID:15360896
  • Citation: 50
  • Journal Impact Factor: 5.175

• Liu K, Mitchell KJ, Chapman WW, and Crowley RS.
  Automating tissue bank annotation from pathology reports – comparison to a gold standard expert annotation set.
  Proc AMIA Symp, 2005 460-464, PMCID: PMC1560700
  • Citation: 18
  • Journal Impact Factor: 5.175

• Tobias J, Chilukuri R, Komatsoulis GA, Mohanty S, Sioutos N, Warzel DB, Wright LW, Crowley RS.
  The CAP cancer protocols – a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid. BMC Med Inform Decis Mak. 2006 Jun 20; 6:25, PMCID: PMC1524939
  • Citation: 37
  • Journal Impact Factor: 2.86

• Drake TA, Braun J, Marchevsky A, Kohane IS, Fletcher C, Chueh H, Beckwith B, Berkowicz D, Kuo F, Zeng QT, Balis U, Holzbach A, McMurry A, Gee CE, McDonald CJ, Schadow G, Davis M, Hattab EM, Blevins L, Hook J, Becich M, Crowley RS, Taube SE, Berman J;
  A system for sharing routine surgical pathology specimens across institutions: the Shared Pathology Informatics Network.
  Hum Pathol. 2007 Aug; 38(8): 1212-25 PMID:17490722
  • Citation: 29
  • Journal Impact Factor: 2.769

• Liu K, Chapman W, Hwa R, Crowley RS.
  Heuristic sample selection to minimize reference standard training set for a part-of-speech tagger.J Am Med Inform Assoc. 2007 Sep-Oct; 14 (5):641-50. PMCID: PMC1975798
  • Citation: 28
  • Journal Impact Factor: 3.428

• Mohanty SK, Parwani AV, Crowley RS, Winters S, Becich MJ.
  The Importance of Pathology Informatics in Translational Research.Adv Anat Pathol. 2007 Sep;14(5):320-22 PMID:17717431
  • Citation: 13
  • Journal Impact Factor: 2.57

• Piwowar H, Becich MJ, Bilofsky H, Crowley RS.
  Towards a data sharing culture: Recommendations for leadership from Academic Health Centers.
  PLoS Med. 2008 Sep 2;5(9):e183, PMCID: PMC2528049
  • Citation: 96
  • Journal Impact Factor: 13.585

• Manion FJ, Robbins RJ, Weems WA, Crowley RS.
  Security and privacy requirements for a multi-institutional cancer research data grid: an interview-based study.
  BMC Med Inform Decis Mak. 2009 Jun 15;9(1):31. PMCID: PMC270961
  • Citation: 39
  • Journal Impact Factor: 2.86

• Lui K, Hogan WR, Crowley RS.
  Natural Language Processing Methods and Systems for Biomedical Ontology Learning.
  J Biomed Inform. 2011 Feb;44(1):163-79. PMCID: PMC2990796
  • Citation: 81
  • Journal Impact Factor: 2.131

• Liu K, Chapman WW, Savova G, Chute CG, Sioutos N, Crowley RS.
  Effectiveness of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents.
  Methods Inf Med. Oct 17, 2011;50(5):397-407. PMCID: PMC3125434
  • Citation: 17
  • Journal Impact Factor: 1.8

• Savova GK, Chapman WW, Zheng J, Crowley RS.
  Anaphoric relations in the clinical narrative: corpus creation.
  J Am Med Inform Assoc. 2011 Jul 1;18(4):459-65. PMCID:PMC3128403
  • Citation: 45
  • Journal Impact Factor: 3.428

• Chapman WW, Savova GK, Zheng J, Tharp M, Crowley R.
  Anaphoric Reference in Clinical Reports: Characteristics of an Annotated Corpus.
  J Biomed Inform. 2012 Jun;45(3):507-21. doi: 10.1016/j.jbi.2012.01.010. Epub 2012 Feb 9. PMID: 22343015
  • Citation: 11
  • Journal Impact Factor: 3.428

• Liu K, Mitchell KJ, Chapman WW, Savova GK, Sioutos N, Ruben DL, Crowley RS.
  Formative Evaluation of Ontology Learning Methods by Using Existing Ontologies as Reference Standards.
  Methods of Information in Medicine, 2013 May 13;52(4). PMID: 23666409
  • Citation: 7
  • Journal Impact Factor: 1.8

• Chennubhotla C, Clarke LP, Fedorov A, Foran D, Harris G, Helton E. An Assessment of Imaging Informatics for Precision Medicine in Cancer. IMIA Yearbook of Medical Informatics 2017: 26(01): 110-119. DOI: 10.15265/IY-2017-041
  • Citation: 0
  • Journal Impact Factor: 1.58
• Xie F, Lee J, Munoz-Plaza CE, Hahn EE, and Chen W. Application of text information extraction system for real-time cancer case identification in an integrated healthcare organization. J Pathol Inform 2017. 8:48.
  • Citation: 0
  • Journal Impact Factor: N/A
• Castro SM, Tseytlin E, Medvedeva O, Mitchell K, Visweswaran S, Bekhuis T, Jacobson RS. Automated annotation and classification of BI-RADS assessment from radiology reports. Journal of Biomedical Informatics 2017: 69. DOI: 10.1016/j.jbi.2017.04.011
  • Citation: 0
  • Journal Impact Factor: 2.131
• Khoury, T, Gaudioso, C, Fang, YV, Jacobson, R. The Role of Skin Ulceration in Breast Carcinoma Staging and Outcome. Breast Journal, 2017 June DOI: 10.1111 PMID:28597587
  • Citation: 0
  • Journal Impact Factor: 2.381
• Youngwoo, K., Furlan, A., Borhani, A.A., Bae, K.T. Computer aided diagnosis program for classifying the risk of hepatocellular carcinoma on MR images following liver imagining reporting and data system (LI-RADS) Magn. Reson. Imaging, 2017. DOI:10.1002/jmri.25772
  • Citation: 2
  • Journal Impact Factor: 3.083
• Uttam, S., Pham, H., LaFace, J., Leibowitz, B., Yu, J., Brand, R.E., Hartman, D.J., Liu, Y. Early prediction of cancer progression by depth-resolved nanoscale mapping of nuclear architecture from unstained tissue specimens. American Association for Cancer Research, 2015. DOI: 10.1158
  • Citation: 14
  • Journal Impact Factor: 20.011

NMVB Team Publications

The National Mesothelioma Virtual Bank (NMVB) collects and distributes tumor tissue and blood samples to the research community from consented patients. The specimens are stored with de-identified clinical data and that is made available for research. Investigators can search the study database to identify and request these materials via the NMVB website. NMVB is the largest and most accessible resource for biospecimens donated by mesothelioma patients.

Publications by CDC NIOSH funded network site investigators (bolded)

• Amin W, Srinivasan M, Song S, Parwani AV, Becich MJ. Use of Automated Image Analysis in Evaluation of Mesothelioma Tissue Microarray (TMA) from National Mesothelioma Virtual Bank. Pathology Research and Practice. 2014 February, 210(2) 79–82 PMID: 24359722
  • Citation: 1
  • Journal Impact Factor: 1.13
• Amin W, Parwani AV, Melamed J, Raja F, Pennathur A, Valdevieso F, Whelan NB, Landreneau R, Luketich J, Feldman M, Pass HI, Becich MJ. National Mesothelioma Virtual Bank: A Platform for Collaborative Research and Mesothelioma Biobanking Resource to Support Translational Research, Lung Cancer International, vol. 2013, Article ID 765748, 9 pages, 2013. doi:10.1155/2013/765748. PMCID: PMC4437393
  • Citation: 1
  • Journal Impact Factor: 0.70
• Schaub NP, Alimchandani M, Quezado M, Kalina P, Eberhardt JS, Hughes MS, Beresnev T, Hassan R, Bartlett DL, Libutti SK, Pingpank JF, Royal RE, Kammula US, Pandalai P, Phan GQ, Stojadinovic A, Rudloff U, Alexander HR, Avital I. A Novel Nomogram for Peritoneal Mesothelioma Predicts Survival. Ann Surg Oncol. 2012 Dec 12. PMID:23233234
  • Citation: 19
  • Journal Impact Factor: 3.930
• Wilson RA, Chapman WW, Defries SJ, Becich MJ, Chapman BE. Automated ancillary cancer history classification for mesothelioma patients from free-text clinical reports. J Pathol Inform. 2010 Oct 11;1:24. PMID: 21031012 PMCID: PMC2956176
  • Citation: 13
  • Journal Impact Factor:
• Kang HP, Borromeo CD, Berman JJ, Becich MJ. The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data. J Pathol Inform. 2010 Jul 13;1. pii: 9. PMID:20805954 PMCID: PMC2929536
  • Citation: 3
  • Journal Impact Factor:
• Amin W, Singh H, Pople AK, Winters S, Dhir R, Parwani AV, Becich MJ. A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research. J Pathol Inform. 2010 Aug 10;1. pii: 12. PMID: 20922029 PMCID: PMC2941965
  • Citation: 11
  • Journal Impact Factor:
• Amin W, Parwani AV, Schmandt L, Mohanty SK, Farhat G, Pople AK, Winters SB, Whelan NB, Schneider AM, Milnes JT, Valdivieso FA, Feldman M, Pass HI, Dhir R, Melamed J, Becich MJ. National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research. BMC Cancer. 2008 Aug 13;8(1):236. PMID:18700971 PMCID: PMC2533341
  • Citation: 35
  • Journal Impact Factor: 3.362
• Mohanty SK, Mistry AT, Amin W, Parwani AV, Pople AK, Schmandt L, Winters SB, Milliken E, Kim P, Whelan NB, Farhat G, Melamed J, Taioli E, Dhir R, Pass HI, and Becich MJ. The development and deployment of Common Data Elements for tissue banks for translational research in cancer – an emerging standard based approach for the Mesothelioma Virtual Tissue Bank. BMC Cancer. 2008 Apr 8;8:91. PMID: 18397527 PMCID: PMC2329649
  • Citation: 45
  • Journal Impact Factor: 3.362
• Dhir R, Patel AA, Winters S, Bisceglia M, Swanson D, Aamodt R, Becich MJ. A multidisciplinary approach to honest broker services for tissue banks and clinical data: a pragmatic and practical model. Cancer. 2008 Aug 5. PMID: 18683217 PMCID: PMC2745185
  • Citation: 55
  • Journal Impact Factor: 5.649

Publications by Research Teams who Received Biospecimens from NMVB

2009:

• Crisanti MC, Wallace AF, Kapoor V, Vandermeers F, Dowling ML, Pereira LP, Coleman K, Campling BG, Fridlender ZG, Kao GD,Albelda SM. The HDAC inhibitor panobinostat (LBH589) inhibits mesothelioma and lung cancer cells in vitro and in vivo with particular efficacy for small cell lung cancer. Mol Cancer Ther. 2009 Aug;8(8):2221-31. doi: 10.1158/1535-7163.MCT-09-0138. Epub 2009 Aug 11. PMID: 19671764 PMCID: PMC3605895
  Citation: 54
  Journal Impact Factor: 453
• Cao X, Littlejohn J, Rodarte C, Zhang L, Martino B, Rascoe P, Hamid K, Jupiter D, Smythe WR.Up-regulation of Bcl-xl by hepatocyte growth factor in human mesothelioma cells involves ETS transcription factors. Am J Pathol. 2009 Nov;175(5):2207-16. doi: 10.2353/ajpath.2009.090070. Epub 2009 Oct 15. PMID: 19834061
  Citation: 17
  Journal Impact Factor: 514

2010:

• Vassiliki Saloura, Liang-Chuan S. Wang, Zvi G. Fridlender, Jing Sun, Guanjun Cheng, Veena Kapoor, Daniel H. Sterman, Ronald N. Harty, Atsushi Okumura, Glen N. Barber, Richard G. Vile, Mark J. Federspiel, Stephen J. Russell, Leslie Litzky, andSteven M. Albelda. Evaluation of an Attenuated Vesicular Stomatitis Virus Vector Expressing Interferon-β for Use in Malignant Pleural Mesothelioma: Heterogeneity in Interferon Responsiveness Defines Potential Efficacy. Human Gene Therapy. January 2010, 21(1): 51-64. PMID: 19715403 PMCID: PMC2829454
  Citation: 41
  Journal Impact Factor: 436
• Bhatia K, Modali R,Goedert JJ. Merkel cell polyomavirus is not detected in mesotheliomas. J Clin Virol. 2010 Feb;47(2):196-8. Epub 2009 Dec 16. PMID: 20006539 PMC2818524
  Citation: 11
  Journal Impact Factor: 016
• Chaturvedi AK, Caporaso NE, Katki HA, Wong HL, Chatterjee N, Pine SR, Chanock SJ,Goedert JJ, Engels EA. C-reactive protein and risk of lung cancer. J Clin Oncol. 2010 Jun 1;28(16):2719-26. doi: 10.1200/JCO.2009.27.0454. Epub 2010 Apr 26. PMID: 20421535 PMCID: PMC2881850.
  Citation: 81
  Journal Impact Factor: 428
• Gretchen V. Gee, Devin C. Koestler, Brock C. Christensen, David J. Sugarbaker, Donatella Ugolini, Giovanni P. Ivaldi, Murray B. Resnick, E. Andres Houseman, Karl T. Kelsey,Carmen J. Marsit Downregulated MicroRNAs in the Differential Diagnosis of Malignant Pleural Mesothelioma. Int J Cancer. Author manuscript; Published in final edited form as: Int J Cancer. 2010 December 15; 127(12): 2859–2869. doi: 10.1002/ijc.25285. PMCID: PMC2911512
  Citation: 67
  Journal Impact Factor: 085

2013:

• Xu Y, Zheng M, Merritt RE, Shrager JB, Wakelee H, Kratzke RA,Hoang CD. miR-1 induces growth arrest and apoptosis in malignant mesothelioma.  2013 Nov;144(5):1632-43. doi: 10.1378/chest.12-2770.
  Citation: 13
  Journal Impact Factor: 7.132
• Zhang X, Shen W, Dong X, Fan J, Liu L, Gao X, Kernstine KH,Zhong L. Identification of novel autoantibodies for detection of malignant mesothelioma. PLoS One. 2013 Aug 19;8(8):e72458. doi: 10.1371/journal.pone.0072458. PMID: 23977302 PMCID: PMC3747111
  Citation: 2
  Journal Impact Factor: 234
• Song JY, Siegfried JM, Diergaarde B, Land SR, Bowser R, Stabile LP, Dacic S,Dhir R, Nukui T, Romkes M, Weissfeld JL.Genetic variation in ESR2 and estrogen receptor-beta expression in lung tumors. Cancer Epidemiol. 2013 Aug;37(4):518-22. doi: 10.1016/j.canep.2013.03.020. Epub 2013 Apr 23.201
  Citation: 3
  Journal Impact Factor: 711

2014:

• Dabir S, Kluge A, Kresak A, Yang M, Fu P, Groner B, Wildey G,Dowlati A. Low PIAS3 expression in malignant mesothelioma is associated with increased STAT3 activation and poor patient survival. Clin Cancer Res. 2014 Oct 1;20(19):5124-32. doi: 10.1158/1078-0432.CCR-14-1233. Epub 2014 Aug 14.PMID: 25124686.
  Citation: 8
  Journal Impact Factor: 72

2015:

• Snehal Dabir, Adam Kresak, Michael Yang, Pingfu Fu, Gary Wildey,Afshin Dowlati. CD30 is a potential therapeutic target in malignant mesothelioma. Mol Cancer Ther. Author manuscript; available in PMC 2016 March 1. Published in final edited form as: Mol Cancer Ther. 2015 March; 14(3): 740–746. Published online 2015 January 14. doi: 10.1158/1535-7163.MCT-14-0972.PMID: 25589494 PMCID: PMC4456236.
  Citation: 1
  Journal Impact Factor: 085
• Nasu M, Emi M, Pastorino S, Tanji M, Powers A, Baumann F, Zhang YA, Gazdar A, Kanodia S, Tiirikainen M, Flores E, Gaudino G, Becich MJ, Pass HI,Yang H, Carbone M. High Incidence of Somatic BAP1 Alterations in Sporadic Malignant Mesothelioma. J Thorac Oncol. 2015 Jan 30. PMID: 25658628.
  Citation: 0
  Journal Impact Factor: 282

2017:

• De Rienzo A, Cook RW, Wilkinson J, Gustafson CE, Richards WG, Amin W, Johnson CE, Oelschlager KM, Maetzold DJ, Stone JF, Feldman FD, Becich MJ, Yeap BY,Bueno R, Gene Expression-Ratio Test Validation in Formalin-Fixed, Paraffin-Embedded Mesothelioma Tissues. Journal of Molecular Diagnostics. 2017 Jan 31;19(1):65-71.

• Towards a Pathology Imaging Data Commons for Discovery and Precision Oncology – April 2018