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Research Output 2003 2019

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Article
2019

Clinicopathological features and outcomes of fibrolamellar hepatocellular carcinoma

Chakrabarti, S., Tella, S. H., Kommalapati, A., Huffman, B. M., Yadav, S., Riaz, I. B., Goyal, G., Mody, K., Borad, M. J., Cleary, S., Smoot, R. & Mahipal, A., Jan 1 2019, In : Journal of Gastrointestinal Oncology. 10, 3, p. 554-561 8 p.

Research output: Contribution to journalArticle

Survival
Recurrence
Fibrolamellar hepatocellular carcinoma
Cell Death
Phosphotransferases

Decline in the seroprevalence of syphilis markers among first-time blood donors in Libreville (Gabon) between 2004 and 2016

Bisseye, C., Eko Mba, J. M., Ntsame Ndong, J. M., Kosiorek, H. E., Butterfield, R. J., Mombo, L. E., M'Batchi, B., Borad, M. J., Nagalo, B. & Allain, J. P., Feb 8 2019, In : BMC Public Health. 19, 1, 167.

Research output: Contribution to journalArticle

Gabon
Seroepidemiologic Studies
Syphilis
Blood Donors
Odds Ratio

Feasibility of circulating tumor DNA testing in hepatocellular carcinoma

Mody, K., Kasi, P. M., Yang, J. D., Surapaneni, P. K., Ritter, A., Roberts, A., Nagy, R. & Borad, M. J., Jan 1 2019, In : Journal of Gastrointestinal Oncology. 10, 4, p. 745-750 6 p.

Research output: Contribution to journalArticle

Hepatocellular Carcinoma
DNA
Neoplasms
Biliary Tract Neoplasms
Genes
9 Citations (Scopus)

Gemcitabine, Cisplatin, and nab-Paclitaxel for the Treatment of Advanced Biliary Tract Cancers: A Phase 2 Clinical Trial

Shroff, R. T., Javle, M. M., Xiao, L., Kaseb, A. O., Varadhachary, G. R., Wolff, R. A., Raghav, K. P. S., Iwasaki, M., Masci, P., Ramanathan, R. K., Ahn, D., Bekaii-Saab, T. & Borad, M. J., Jan 1 2019, In : JAMA Oncology.

Research output: Contribution to journalArticle

gemcitabine
Biliary Tract Neoplasms
Nanoparticles
Cisplatin
Clinical Trials

Integration of Comprehensive Genomic Analysis and Functional Screening of Affected Molecular Pathways to Inform Cancer Therapy

Vasmatzis, G., Liu, M. C., Reganti, S., Feathers, R. W., Smadbeck, J., Johnson, S. H., Schaefer Klein, J. L., Harris, F. R., Yang, L., Kosari, F., Murphy, S. J., Borad, M. J., Thompson, E. A., Cheville, J. C. & Anastasiadis, P. Z., Jan 1 2019, (Accepted/In press) In : Mayo Clinic proceedings.

Research output: Contribution to journalArticle

Open Access
Neoplasms
Mutation
Therapeutics
Precision Medicine
Preclinical Drug Evaluations

MetaMarker: A pipeline for de novo discovery of novel metagenomic biomarkers

Koohi-Moghadam, M., Borad, M. J., Tran, N. L., Swanson, K. R., Boardman, L. A., Sun, H. & Wang, J., Oct 1 2019, In : Bioinformatics. 35, 19, p. 3812-3814 3 p.

Research output: Contribution to journalArticle

Metagenomics
Biomarkers
Colorectal Cancer
Pipelines
Metagenome
3 Citations (Scopus)

Neoadjuvant vs. adjuvant chemotherapy for cholangiocarcinoma: A propensity score matched analysis

Yadav, S., Xie, H., Bin-Riaz, I., Sharma, P., Durani, U., Goyal, G., Borah, B. J., Borad, M. J., Smoot, R., Roberts, L. R., Go, R. S., Mc Williams, R. R. & Mahipal, A., Jan 1 2019, In : European Journal of Surgical Oncology.

Research output: Contribution to journalArticle

Propensity Score
Cholangiocarcinoma
Adjuvant Chemotherapy
Drug Therapy
Survival
4 Citations (Scopus)

Preclinical In Vitro and In Vivo Evidence of an Antitumor Effect of CX-4945, a Casein Kinase II Inhibitor, in Cholangiocarcinoma

Zakharia, K., Miyabe, K., Wang, Y., Wu, D., Moser, C. D., Borad, M. J. & Roberts, L. R., Jan 1 2019, In : Translational Oncology. 12, 1, p. 143-153 11 p.

Research output: Contribution to journalArticle

Casein Kinase II
Cholangiocarcinoma
gemcitabine
Cisplatin
Heterografts

Prognostic subclass of intrahepatic cholangiocarcinoma by integrative molecular–clinical analysis and potential targeted approach

Ahn, K. S., O’Brien, D., Kang, Y. N., Mounajjed, T., Kim, Y. H., Kim, T. S., Kocher, J-P., Allotey, L. K., Borad, M. J., Roberts, L. R. & Kang, K. J., Jan 1 2019, In : Hepatology International.

Research output: Contribution to journalArticle

Cholangiocarcinoma
RNA Sequence Analysis
gemcitabine
Pathology
Cholangitis
2018
60 Citations (Scopus)

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer Cell. 33, 4, p. 690-705.e9

Research output: Contribution to journalArticle

Breast Neoplasms
Atlases
Long Noncoding RNA
Decision Trees
Genome
8 Citations (Scopus)

Adjuvant systemic therapy after resection of node positive gallbladder cancer: Time for a well-designed trial? (Results of a US-national retrospective cohort study)

Bergquist, J. R., Shah, H. N., Habermann, E. B., Hernandez, M. C., Ivanics, T., Kendrick, M. L., Smoot, R. L., Nagorney, D. M., Borad, M. J., Mc Williams, R. R. & Truty, M., Apr 1 2018, In : International Journal of Surgery. 52, p. 171-179 9 p.

Research output: Contribution to journalArticle

Gallbladder Neoplasms
Cohort Studies
Retrospective Studies
Adjuvant Chemotherapy
Gallbladder
117 Citations (Scopus)

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 400-416.e11

Research output: Contribution to journalArticle

Atlases
Genes
Genome
Survival
Neoplasms
30 Citations (Scopus)

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 386-399.e12

Research output: Contribution to journalArticle

Genes
Tumors
Neoplasms
Computational methods
Chromatin
10 Citations (Scopus)

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily

The Cancer Genome Atlas Research Network, Oct 24 2018, In : Cell Systems. 7, 4, p. 422-437.e7

Research output: Contribution to journalArticle

Transforming Growth Factors
Neoplasms
Sequence Deletion
Genes
Gastrointestinal Neoplasms
1 Citation (Scopus)

A phase I study of the safety and tolerability of VLX600, an Iron Chelator, in patients with refractory advanced solid tumors

Mody, K., Mansfield, A., Vemireddy, L., Nygren, P., Gulbo, J. & Borad, M. J., Jan 1 2018, (Accepted/In press) In : Investigational New Drugs.

Research output: Contribution to journalArticle

Chelating Agents
Iron
Safety
Maximum Tolerated Dose
Neoplasms
1 Citation (Scopus)

Association between treatment facility volume, therapy types and overall survival in patients with intrahepatic cholangiocarcinoma

Kommalapati, A., Tella, S. H., Goyal, G., Borad, M. J., Alberts, S. R., Roberts, L. R., Hubbard, J. M., Durgin, L., Cleary, S. & Mahipal, A., Jan 1 2018, (Accepted/In press) In : HPB.

Research output: Contribution to journalArticle

Cholangiocarcinoma
Survival
Liver
Therapeutics
Insurance
148 Citations (Scopus)

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

The Cancer Genome Atlas Network, Apr 5 2018, In : Cell. 173, 2, p. 291-304.e6

Research output: Contribution to journalArticle

Tumors
Tissue
Histology
Methylation
Oncology

Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples

Vasmatzis, G., Wang, X., Smadbeck, J., Murphy, S. J., Geiersbach, K. B., Johnson, S. H., Gaitatzes, A. G., Asmann, Y., Kosari, F., Borad, M. J., Serie, D. J., McLaughlin, S. A., Kachergus, J. M., Necela, B. M. & Thompson, E. A., Jul 13 2018, In : BMC Cancer. 18, 1, 738.

Research output: Contribution to journalArticle

Chromosomes, Human, Pair 8
Breast Neoplasms
Chromosomes, Human, Pair 17
Transcriptome
Genome
45 Citations (Scopus)

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer Cell. 33, 4, p. 721-735.e8

Research output: Contribution to journalArticle

Adenocarcinoma
Neoplasms
Genome
Chromosomal Instability
Rectum
50 Citations (Scopus)

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

The Cancer Genome Atlas Research Network, Aug 13 2018, In : Cancer Cell. 34, 2, p. 211-224.e6

Research output: Contribution to journalArticle

Alternative Splicing
Neoplasms
Exons
Exome
Peptides
177 Citations (Scopus)

Comprehensive Characterization of Cancer Driver Genes and Mutations

The MC3 Working Group & The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 371-385.e18

Research output: Contribution to journalArticle

Neoplasm Genes
Tumors
Genes
Mutation
Neoplasms
12 Citations (Scopus)

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer

The Cancer Genome Atlas Research Network, Oct 30 2018, In : Cell Reports. 25, 5, p. 1304-1317.e5

Research output: Contribution to journalArticle

Genes
Neoplasms
Squamous Cell Neoplasms
Tumors
Atlases
51 Citations (Scopus)

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

The Fusion Analysis Working Group & The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 227-238.e3

Research output: Contribution to journalArticle

Human Development
Phosphotransferases
Genes
Gene expression
Tumors
1 Citation (Scopus)

E6201, an intravenous MEK1 inhibitor, achieves an exceptional response in BRAF V600E-mutated metastatic malignant melanoma with brain metastases

Babiker, H. M., Byron, S. A., Hendricks, W. P. D., Elmquist, W. F., Gampa, G., Vondrak, J., Aldrich, J., Cuyugan, L., Adkins, J., De Luca, V., Tibes, R., Borad, M. J., Marceau, K., Myers, T. J., Paradiso, L. J., Liang, W. S., Korn, R. L., Cridebring, D., Von Hoff, D. D., Carpten, J. D. & 3 others, Craig, D. W., Trent, J. M. & Gordon, M. S., Jan 1 2018, (Accepted/In press) In : Investigational New Drugs.

Research output: Contribution to journalArticle

Melanoma
Neoplasm Metastasis
Brain
Blood-Brain Barrier
Exome
23 Citations (Scopus)

Evaluation of pre-analytical factors affecting plasma DNA analysis

Markus, H., Contente-Cuomo, T., Farooq, M., Liang, W. S., Borad, M. J., Sivakumar, S., Gollins, S., Tran, N., Dhruv, H. D., Berens, M. E., Bryce, A. H., Sekulic, A. D., Ribas, A., Trent, J. M., Lorusso, P. M. & Murtaza, M., Dec 1 2018, In : Scientific Reports. 8, 1, 7375.

Research output: Contribution to journalArticle

DNA
cells
sampling
droplets
blood
35 Citations (Scopus)

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 194-212.e6

Research output: Contribution to journalArticle

Squamous Cell Carcinoma
MicroRNAs
Mutation
Epithelial Cells
Squamous Cell Neoplasms
55 Citations (Scopus)

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer Cell. 33, 4, p. 676-689.e3

Research output: Contribution to journalArticle

Aneuploidy
Chromosomes
Neoplasms
Genome
Mutation Rate
83 Citations (Scopus)

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 239-254.e6

Research output: Contribution to journalArticle

DNA Repair-Deficiency Disorders
Atlases
DNA Damage
Repair
Genes

HSP90 Inhibition Drives Degradation of FGFR2 Fusion Proteins: Implications for Treatment of Cholangiocarcinoma

Lamberti, D., Cristinziano, G., Porru, M., Leonetti, C., Egan, J. B., Shi, C. X., Buglioni, S., Amoreo, C. A., Castellani, L., Borad, M. J., Alemà, S., Anastasi, S. & Segatto, O., Jan 1 2018, (Accepted/In press) In : Hepatology.

Research output: Contribution to journalArticle

Receptor, Fibroblast Growth Factor, Type 2
HSP90 Heat-Shock Proteins
Cholangiocarcinoma
Proteins
Protein-Tyrosine Kinases
13 Citations (Scopus)

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 213-226.e3

Research output: Contribution to journalArticle

Ubiquitin
Genes
Neoplasms
Tumors
Amplification
90 Citations (Scopus)

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer Cell. 33, 4, p. 706-720.e9

Research output: Contribution to journalArticle

Long Noncoding RNA
Epigenomics
Cell Cycle
Genes
Neoplasms
19 Citations (Scopus)

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 172-180.e3

Research output: Contribution to journalArticle

Atlases
Learning systems
Tumors
Genes
Chemical activation
85 Citations (Scopus)

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 338-354.e15

Research output: Contribution to journalArticle

Learning systems
Tumors
Neoplasms
Stem cells
Logistics
20 Citations (Scopus)

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 255-269.e4

Research output: Contribution to journalArticle

Tumors
Carbohydrates
Oncology
Metabolism
Vitamins
189 Citations (Scopus)

Oncogenic Signaling Pathways in The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 321-337.e10

Research output: Contribution to journalArticle

Atlases
Tumors
Genes
Genome
Neoplasms
33 Citations (Scopus)

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

The Cancer Genome Atlas Network, Mar 28 2018, In : Cell Systems. 6, 3, p. 282-300.e2

Research output: Contribution to journalArticle

Atlases
Oncogenes
Genome
Neoplasms
Neoplasm Genes
56 Citations (Scopus)

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 297-312.e12

Research output: Contribution to journalArticle

Long Noncoding RNA
Neoplasm Genes
Tumors
Genes
Neoplasms
84 Citations (Scopus)

Pathogenic Germline Variants in 10,389 Adult Cancers

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 355-370.e14

Research output: Contribution to journalArticle

Gene expression
Automatic teller machines
Tumors
Neoplasms
Genes
42 Citations (Scopus)

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 305-320.e10

Research output: Contribution to journalArticle

Genomics
Tumors
Genes
Neoplasms
Atlases
17 Citations (Scopus)

Phase 1 trials of PEGylated recombinant human hyaluronidase PH20 in patients with advanced solid tumours

Infante, J. R., Korn, R. L., Rosen, L. S., Lorusso, P., Dychter, S. S., Zhu, J., Maneval, D. C., Jiang, P., Shepard, H. M., Frost, G., Von Hoff, D. D., Borad, M. J. & Ramanathan, R. K., Jan 1 2018, In : British Journal of Cancer. 118, 2, p. 153-161 9 p.

Research output: Contribution to journalArticle

Hyaluronoglucosaminidase
Neoplasms
Hyaluronic Acid
Maximum Tolerated Dose
Myalgia
74 Citations (Scopus)

Phase II study of BGJ398 in patients with FGFR-Altered advanced cholangiocarcinoma

Javle, M., Lowery, M., Shroff, R. T., Weiss, K. H., Springfeld, C., Borad, M. J., Ramanathan, R. K., Goyal, L., Sadeghi, S., Macarulla, T., El-Khoueiry, A., Kelley, R. K., Borbath, I., Choo, S. P., Oh, D. Y., Philip, P. A., Chen, L. T., Reungwetwattana, T., Van Cutsem, E., Yeh, K. H. & 9 others, Ciombor, K., Finn, R. S., Patel, A., Sen, S., Porter, D., Isaacs, R., Zhu, A. X., Abou-Alfa, G. K. & Bekaii-Saab, T., Jan 20 2018, In : Journal of Clinical Oncology. 36, 3, p. 276-282 7 p.

Research output: Contribution to journalArticle

Receptor, Fibroblast Growth Factor, Type 2
Cholangiocarcinoma
Hyperphosphatemia
Stomatitis
gemcitabine
7 Citations (Scopus)

Pilot evaluation of PD-1 inhibition in metastatic cancer patients with a history of liver transplantation: The Mayo Clinic experience

DeLeon, T. T., Salomao, M. A., Aqel, B. A., Sonbol, M. B., Yokoda, R. T., Ali, A. H., Moss, A. A., Mathur, A., Chascsa, D. M., Rakela, J., Bryce, A. H. & Borad, M. J., Dec 1 2018, In : Journal of Gastrointestinal Oncology. 9, 6, p. 1054-1062 9 p.

Research output: Contribution to journalArticle

Liver Transplantation
Neoplasms
Proteins
Allografts
Ligands
3 Citations (Scopus)

Prevalent hepatitis B surface antigen among first-time blood donors in Gabon

Eko Mba, J. M., Bisseye, C., Ntsame Ndong, J. M., Mombo, L. E., Bengone, C., Migolet, G. M., Batchi, B. M., Kosiorek, H. E., Butterfield, R. J., Roberts, L. R., Borad, M. J. & Nagalo, B., Apr 1 2018, In : PLoS One. 13, 4, e0194285.

Research output: Contribution to journalArticle

Gabon
Seroepidemiologic Studies
Hepatitis B Surface Antigens
Blood Donors
seroprevalence
2 Citations (Scopus)

Safety, pharmacokinetics, and preliminary efficacy of E6201 in patients with advanced solid tumours, including melanoma: Results of a phase 1 study

Tibes, R., Borad, M. J., Dutcus, C. E., Reyderman, L., Feit, K., Eisen, A., Verbel, D. A. & Von Hoff, D. D., Jun 1 2018, In : British Journal of Cancer. 118, 12, p. 1580-1585 6 p.

Research output: Contribution to journalArticle

Melanoma
Pharmacokinetics
Maximum Tolerated Dose
Safety
Neoplasms
57 Citations (Scopus)

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

MC3 Working Group & The Cancer Genome Atlas Research Network, Mar 28 2018, In : Cell Systems. 6, 3, p. 271-281.e7

Research output: Contribution to journalArticle

Exome
Mutation
Atlases
Neoplasms
Genomics
41 Citations (Scopus)

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 282-296.e4

Research output: Contribution to journalArticle

Genes
Mutation
Neoplasms
Tumors
RNA
59 Citations (Scopus)

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 181-193.e7

Research output: Contribution to journalArticle

Tumor-Infiltrating Lymphocytes
Lymphocytes
Pathology
Tumors
Learning
19 Citations (Scopus)

Surveillance for hepatobiliary cancers in patients with primary sclerosing cholangitis

Ali, A. H., Tabibian, J. H., Nasser-Ghodsi, N., Lennon, R. J., DeLeon, T., Borad, M. J., Hilscher, M., Silveira, M. G., Carey, E. J. & Lindor, K. D., Jun 1 2018, In : Hepatology. 67, 6, p. 2338-2351 14 p.

Research output: Contribution to journalArticle

Sclerosing Cholangitis
Cholangiocarcinoma
Neoplasms
Gallbladder
Survival
28 Citations (Scopus)

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 270-281.e3

Research output: Contribution to journalArticle

Tumors
Mutation
Neoplasms
Bioelectric potentials
Bioinformatics
61 Citations (Scopus)

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 313-326.e5

Research output: Contribution to journalArticle

Atlases
Renal Cell Carcinoma
Genes
Cells
Genome