J. Smadbeck

发表

WeFold: A coopetition for protein structure prediction

Adam Liwo, Yi He, David Baker, 2014, Proteins.

Protein folding and de novo protein design for biotechnological applications.

George A. Khoury, C. Floudas, J. Smadbeck, 2014, Trends in biotechnology.

Protein WISDOM: a workbench for in silico de novo design of biomolecules.

Christodoulos A Floudas, George A. Khoury, Martin S. Taylor, 2013, Journal of visualized experiments : JoVE.

Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications.

George A. Khoury, C. Floudas, J. Smadbeck, 2013, Journal of chemical theory and computation.

Forcefield_NCAA: Ab Initio Charge Parameters to Aid in the Discovery and Design of Therapeutic Proteins and Peptides with Unnatural Amino Acids and Their Application to Complement Inhibitors of the Compstatin Family

George A. Khoury, C. Floudas, J. Smadbeck, 2014, ACS synthetic biology.

Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma

Sarah H. Johnson, J. Cheville, A. Mansfield, 2019, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

YAP-associated chromosomal instability and cholangiocarcinoma in mice

G. Gores, Sumera H Rizvi, J. Smadbeck, 2017, Oncotarget.

Family history of plasma cell disorders is associated with improved survival in MGUS, multiple myeloma, and systemic AL amyloidosis

C. Vachon, D. Dingli, J. Smadbeck, 2021, Leukemia.

Characterization of a cryptic PML-RARA fusion by mate-pair sequencing in a case of acute promyelocytic leukemia with a normal karyotype and negative RARA FISH studies

Sarah H. Johnson, J. Smadbeck, P. Blackburn, 2019, Leukemia & lymphoma.

Shared and unique genomic structural variants of different histological components within testicular germ cell tumours identified with mate pair sequencing

Sarah H. Johnson, J. Cheville, B. Leibovich, 2019, Scientific Reports.

Mate pair sequencing improves detection of genomic abnormalities in acute myeloid leukemia

Sarah H. Johnson, Roman M. Ženka, E. Thorland, 2018, European journal of haematology.

Proposal for Modification of Cahan's Criteria Utilizing Molecular Genetic Analyses for Cases without Baseline Histopathology: A Unique Method Applicable to Primary Radiosurgery

J. Smadbeck, M. Carlson, G. Vasmatzis, 2018, Journal of Neurological Surgery Part B: Skull Base.

Genomic rearrangements in sporadic lymphangioleiomyomatosis: an evolving genetic story

Sarah H. Johnson, Jesse S. Voss, J. Smadbeck, 2017, Modern Pathology.

Clinical utility of next generation sequencing to detect IGH/IL3 rearrangements [t(5;14)(q31.1;q32.1)] in B-lymphoblastic leukemia/lymphoma.

J. Smadbeck, G. Vasmatzis, R. Ketterling, 2021, Annals of diagnostic pathology.

Characterization of a cryptic IGH/CCND1 rearrangement in a case of mantle cell lymphoma with negative CCND1 FISH studies.

J. Smadbeck, G. Vasmatzis, B. Pitel, 2019, Blood advances.

Mate-pair sequencing identifies a cryptic BMPR2 mutation in hereditary pulmonary arterial hypertension

J. Smadbeck, G. Vasmatzis, R. Frantz, 2020, Pulmonary circulation.

Biliary tract cancer patient-derived xenografts: Surgeon impact on individualized medicine

G. Gores, D. Nagorney, L. Roberts, 2020, JHEP reports : innovation in hepatology.

Copy number variant analysis using genome‐wide mate‐pair sequencing

Travis M. Drucker, Sarah H. Johnson, Roman M. Ženka, 2018, Genes, chromosomes & cancer.

SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq).

Travis M. Drucker, Sarah H. Johnson, Roman M. Ženka, 2018, Cancer genetics.

Detection of cryptic CCND1 rearrangements in mantle cell lymphoma by next generation sequencing.

Sarah H. Johnson, J. Smadbeck, M. Schultz, 2020, Annals of diagnostic pathology.

Detection of a cryptic NUP214/ABL1 gene fusion by mate-pair sequencing (MPseq) in a newly diagnosed case of pediatric T-lymphoblastic leukemia

Sarah H. Johnson, J. Smadbeck, G. Vasmatzis, 2019, Cold Spring Harbor molecular case studies.

New Compstatin Peptides Containing N-Terminal Extensions and Non-Natural Amino Acids Exhibit Potent Complement Inhibition and Improved Solubility Characteristics

Christodoulos A. Floudas, George A. Khoury, Phanourios Tamamis, 2014, Journal of medicinal chemistry.

Characterizing false-positive fluorescence in situ hybridization results by mate-pair sequencing in a patient with chronic myeloid leukemia and progression to myeloid blast crisis.

Sarah H. Johnson, J. Smadbeck, G. Vasmatzis, 2020, Cancer genetics.

Dual Primary IGH Translocations in Multiple Myeloma: A Novel Finding.

J. Smadbeck, Shaji K. Kumar, R. Ketterling, 2021, Clinical lymphoma, myeloma & leukemia.

Novel strategy for manufacturing autologous dendritic cell/allogeneic tumor lysate vaccines for glioblastoma

Sarah H. Johnson, A. Dietz, J. Smadbeck, 2020, Neuro-oncology advances.

Mate pair sequencing outperforms fluorescence in situ hybridization in the genomic characterization of multiple myeloma

P. L. Bergsagel, H. Kearney, J. Smadbeck, 2019, Blood Cancer Journal.

Retention of Interstitial Genes between TMPRSS2 and ERG Is Associated with Low-Risk Prostate Cancer.

Sarah H. Johnson, J. Cheville, R. Karnes, 2017, Cancer research.

Large Chromosomal Rearrangements Yield Biomarkers to Distinguish Low‐Risk From Intermediate‐ and High‐Risk Prostate Cancer

Sarah H. Johnson, I. V. Kovtun, T. Therneau, 2019, Mayo Clinic proceedings.

Integrated mate-pair and RNA sequencing identifies novel, targetable gene fusions in peripheral T-cell lymphoma.

Sarah H. Johnson, J. Cerhan, Y. Asmann, 2016, Blood.

Optimizing clinical cytology touch preparations for next generation sequencing.

Sarah H. Johnson, A. Mansfield, D. Wigle, 2020, Genomics.

Integrated Genomic Analysis of Pancreatic Ductal Adenocarcinomas Reveals Genomic Rearrangement Events as Significant Drivers of Disease.

Travis M. Drucker, Fergus J Couch, Steven N Hart, 2016, Cancer research.

Using genomics to differentiate multiple primaries from metastatic lung cancer.

Sarah H. Johnson, A. Mansfield, D. Wigle, 2019, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

Assessment of isochromosome 12p and 12p abnormalities in germ cell tumors using fluorescence in situ hybridization, single-nucleotide polymorphism arrays, and next-generation sequencing/mate-pair sequencing

J. Cheville, R. Thompson, S. Boorjian, 2021, Human Pathology.

Apparent coexistence of ETV6::RUNX1 and KMT2A::MLLT3 fusions due to a nonproductive KMT2A rearrangement in B-ALL

J. Smadbeck, P. Blackburn, Y. Akkari, 2022, Leukemia & lymphoma.

The Prognostic Role of MYC Structural Variants Identified by NGS and FISH in Multiple Myeloma

Y. Asmann, P. L. Bergsagel, J. Smadbeck, 2021, Clinical Cancer Research.

Chromosomal Junction Detection from Whole Genome Sequencing on Formalin-fixed, Paraffin-embedded Tumors.

Sarah H. Johnson, Jesse S. Voss, J. Cheville, 2020, The Journal of molecular diagnostics : JMD.

Biology and grading of pleomorphic xanthoastrocytoma—what have we learned about it?

J. Smadbeck, C. Kramm, G. Vasmatzis, 2020, Brain pathology.

Constitutional chromosome rearrangements that mimic the 2017 world health organization "acute myeloid leukemia with recurrent genetic abnormalities": A study of three cases and review of the literature.

Sarah H. Johnson, H. Kearney, J. Smadbeck, 2019, Cancer genetics.

Characterization of TCF3 rearrangements in pediatric B-lymphoblastic leukemia/lymphoma by mate-pair sequencing (MPseq) identifies complex genomic rearrangements and a novel TCF3/TEF gene fusion

Y. Ning, J. Smadbeck, G. Vasmatzis, 2019, Blood Cancer Journal.

Advances in Protein Design: Conformational Switch, Multimeric, and Protein-DNA Design

James Smadbeck, J. Smadbeck, 2015 .

De Novo Peptide Design and Experimental Validation of Histone Methyltransferase Inhibitors

Christodoulos A. Floudas, Benjamin A. Garcia, Athanassios Giannis, 2014, PloS one.

Quantification of Somatic Chromosomal Rearrangements in Circulating Cell-Free DNA from Ovarian Cancers

Sarah H. Johnson, I. V. Kovtun, Minetta C. Liu, 2016, Scientific Reports.

Chromoplectic TPM3–ALK rearrangement in a patient with inflammatory myofibroblastic tumor who responded to ceritinib after progression on crizotinib

A. Mansfield, R. Marks, D. Wigle, 2016, Annals of oncology : official journal of the European Society for Medical Oncology.

Genome U‐Plot: a whole genome visualization

Athanasios Gaitatzes, Sarah H. Johnson, George Vasmatzis, 2018, Bioinform..

Characterization of a rarely reported STAT5B/RARA gene fusion in a young adult with newly diagnosed acute promyelocytic leukemia with resistance to ATRA therapy.

J. Smadbeck, G. Vasmatzis, R. Ketterling, 2019, Cancer genetics.

Next Generation Sequencing of Sporadic Vestibular Schwannoma: Necessity of Biallelic NF2 Inactivation and Implications of Accessory Non-NF2 Variants.

J. Smadbeck, M. Carlson, G. Vasmatzis, 2018, Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology.

Whole Genome Mate-pair Sequencing of Plasma Cell Neoplasm as a Novel Diagnostic Strategy: A Case of Unrecognized t(2;11) Structural Variation.

J. Smadbeck, G. Vasmatzis, A. Stewart, 2019, Clinical lymphoma, myeloma & leukemia.

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

Sarah H. Johnson, D. Serie, Y. Asmann, 2018, BMC Cancer.

False-negative rates for MYC fluorescence in situ hybridization probes in B-cell neoplasms

J. Smadbeck, G. Vasmatzis, R. Ketterling, 2018, Haematologica.

Dynamically generated cutting planes for mixed-integer quadratically constrained quadratic programs and their incorporation into GloMIQO 2

Christodoulos A. Floudas, Ruth Misener, James B. Smadbeck, 2015, Optim. Methods Softw..

Increased complexity of t(11;14) rearrangements in plasma cell neoplasms compared with mantle cell lymphoma

J. Smadbeck, Shaji K. Kumar, R. Ketterling, 2021, Genes, chromosomes & cancer.

Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double‐blind predictions during the CASP11 experiment

Christodoulos A Floudas, Yannis A. Guzman, George A. Khoury, 2017, Proteins.

conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure

Christodoulos A. Floudas, George A. Khoury, Chris A. Kieslich, 2016, J. Chem. Inf. Model..

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides

Christodoulos A. Floudas, George A. Khoury, Bo Xue, 2014, PLoS Comput. Biol..

Acute leukemias harboring KMT2A/MLLT10 fusion: a 10‐year experience from a single genomics laboratory

J. Smadbeck, G. Vasmatzis, B. Pitel, 2019, Genes, chromosomes & cancer.

Characterization of a cryptic KMT2A/AFF1 gene fusion by mate-pair sequencing (MPseq) in a young adult with newly diagnosed B-lymphoblastic leukemia

J. Smadbeck, G. Vasmatzis, B. Pitel, 2019, Journal of Hematopathology.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

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

Sarah H. Johnson, J. Cheville, Minetta C. Liu, 2019, Mayo Clinic proceedings.

Detection of a Cryptic EP300/ZNF384 Gene Fusion by Chromosomal Microarray and Next-Generation Sequencing Studies in a Pediatric Patient with B-Lymphoblastic Leukemia.

Sarah H. Johnson, J. Smadbeck, P. Blackburn, 2020, Laboratory medicine.

Identification of EWSR1 rearrangements in patients with immature hematopoietic neoplasms: A case series and review of literature.

J. Smadbeck, G. Vasmatzis, R. Ketterling, 2022, Annals of diagnostic pathology.

Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines

Christodoulos A Floudas, George A. Khoury, George A Khoury, 2014, Proteins.

Tumor junction burden and antigen presentation as predictors of survival in mesothelioma treated with immune checkpoint inhibitors.

Sarah H. Johnson, J. Cheville, A. Mansfield, 2021, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

Characterization of unusual iAMP21 B‐lymphoblastic leukemia (iAMP21‐ALL) from the Mayo Clinic and Children's Oncology Group

M. Shago, J. Smadbeck, K. Tsuchiya, 2022, Genes, chromosomes & cancer.

Identification of a novel KMT2A/GIMAP8 gene fusion in a pediatric patient with acute undifferentiated leukemia

J. Smadbeck, P. Blackburn, G. Vasmatzis, 2020, Genes, chromosomes & cancer.

Cryptic and atypical KMT2A‐USP2 and KMT2A‐USP8 rearrangements identified by mate pair sequencing in infant and childhood leukemia

J. Smadbeck, P. Blackburn, G. Vasmatzis, 2020, Genes, chromosomes & cancer.

Derivation of ligands for the complement C3a receptor from the C-terminus of C5a

Christodoulos A Floudas, Chris A Kieslich, Dimitrios Morikis, 2014, European journal of pharmacology.

Immunopharmacology and in fl ammation Derivation of ligands for the complement C 3 a receptor from the C-terminus of C 5 a

C. Floudas, P. Monk, J. Smadbeck, 2014 .

Theragnostic chromosomal rearrangements in treatment‐naive pancreatic ductal adenocarcinomas obtained via endoscopic ultrasound

Sarah H. Johnson, J. Cheville, J. Smadbeck, 2021, Journal of cellular and molecular medicine.