Smadbeck, J. B.: search on Z-Library

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1

Solution of chemical master equations for nonlinear stochastic reaction networks

Smadbeck, Patrick, Kaznessis, Yiannis N

Journal:

Current Opinion in Chemical Engineering

Year:

2014

Language:

english

File:

PDF, 690 KB

english, 2014

2

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Smadbeck, James, Peterson, Meghan B., Khoury, George A., Taylor, Martin S., Floudas, Christodoulos A.

Journal:

Journal of Visualized Experiments

Year:

2013

Language:

english

File:

PDF, 2.47 MB

english, 2013

3

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

Mansfield, A. S., Murphy, S. J., Harris, F. R., Robinson, S. I., Marks, R. S., Johnson, S. H., Smadbeck, J. B., Halling, G. C., Yi, E. S., Wigle, D., Vasmatzis, G., Jen, J.

Journal:

Annals of Oncology

Year:

2016

Language:

english

File:

PDF, 1.28 MB

english, 2016

4

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

Khoury, George A., Thompson, Jeff P., Smadbeck, James, Kieslich, Chris A., Floudas, Christodoulos A.

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 15.25 MB

english, 2013

5

13. Clinical utility of mate pair sequencing to detect diagnostic and prognostic chromosomal rearrangements and copy number changes in patients with acute myeloid leukemia

Baughn, Linda B., Smoley, Stephanie A., Aypar, Umut, Pitel, Beth A., Vasmatzis, George, Johnson, Sarah H., Smadbeck, James B., Peterson, Jess F., Geiersbach, Katherine B., Van Dyke, Daniel L., Thorlan

Journal:

Cancer Genetics

Year:

2018

Language:

english

File:

PDF, 46 KB

english, 2018

6

1. Clinical utility of mate pair sequencing to detect diagnostic and prognostic chromosomal rearrangements and copy number changes in patients with acute myeloid leukemia

Baughn, Linda, Smoley, Stephanie, Pitel, Beth, Vasmatzis, George, Johnson, Sarah, Smadbeck, James, Peterson, Jess, Van Dyke, Daniel, Ketterling, Rhett, Jenkins, Robert, Hoppman, Nicole, Kearney, Hutto

Journal:

Cancer Genetics

Year:

2018

File:

PDF, 119 KB

2018

7

Whole genome mate-pair sequencing of plasma cell neoplasm as a novel diagnostic strategy: a case of unrecognized t(2;11) structural variation

Peterson, Jess F., Meyer, Reid G., Smoley, Stephanie A., Webley, Matthew, Smadbeck, James B., Vasmatzis, George, Pearce, Kathryn, Greipp, Patricia T., Ketterling, Rhett P., Craig, Fiona E., Stewart, A

Journal:

Clinical Lymphoma Myeloma and Leukemia

Year:

2019

File:

PDF, 2.08 MB

2019

8

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

Smadbeck, James, Peterson, Jess F., Pearce, Kathryn E., Pitel, Beth A., Figueroa, Andrea Lebron, Timm, Michael, Jevremovic, A. Dragan, Shi, Min, Stewart, A. Keith, Braggio, Esteban, Riggs, Daniel L.,

Journal:

Blood Cancer Journal

Year:

2019

File:

PDF, 1.34 MB

2019

9

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

Halai, Reena, Bellows-Peterson, Meghan L, Branchett, Will, Smadbeck, James, Kieslich, Chris A, Croker, Daniel E, Cooper, Matthew A, Morikis, Dimitrios, Woodruff, Trent M, Floudas, Christodoulos A, Mon

Journal:

European Journal of Pharmacology

Year:

2014

Language:

english

File:

PDF, 746 KB

english, 2014

10

Mo1348 AN EARLY INSIGHT INTO GENOMIC STRUCTURAL VARIATION IN TREATMENT NAIVE PANCREATIC DUCTAL ADENOCARCINOMA

Murphy, Stephen J., Levy, Michael J., James, Smadbeck B., Karagouga, Giannoula, Udell, Julia B., Johnson, Sarah H., Kipp, Benjamin R., Vasmatzis, George, Gleeson, Ferga C.

Journal:

Gastroenterology

Year:

2020

File:

PDF, 828 KB

2020

11

Modeling stochasticity in biochemical reaction networks

Constantino, P H, Vlysidis, M, Smadbeck, P, Kaznessis, Y N

Journal:

Journal of Physics D Applied Physics

Year:

2016

Language:

english

File:

PDF, 506 KB

english, 2016

12

Genomic rearrangements in sporadic lymphangioleiomyomatosis: an evolving genetic story

Murphy, Stephen J, Terra, Simone B, Harris, Faye R, Nasir, Aqsa, Voss, Jesse S, Smadbeck, James B, Johnson, Sarah H, Serla, Vishnu, Ryu, Jay H, Yi, Eunhee S, Kipp, Benjamin R, Vasmatzis, George, Carmo

Journal:

Modern Pathology

Year:

2017

Language:

english

File:

PDF, 2.50 MB

english, 2017

13

Mate pair sequencing outperforms fluorescence in situ hybridization and improves diagnostic yield in the genomic characterization of multiple myeloma

Baughn, Linda, James, Smadbeck, Kathryn, Pearce, Pitel, Beth, Timm, Michael, Bergsagel, Leif, Jevremovic, Dragan, Shi, Min, Stewart, Keith, Braggio, Esteban, Riggs, Daniel, George, Vasmatzis, Kearney,

Journal:

Clinical Lymphoma Myeloma and Leukemia

Year:

2019

File:

PDF, 60 KB

2019

14

On a theory of stability for nonlinear stochastic chemical reaction networks

Smadbeck, Patrick, Kaznessis, Yiannis N.

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 2.78 MB

english, 2015

15

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

Bryce, Alan H., Egan, Jan B., Smadbeck, James B., Johnson, Sarah H., Murphy, Stephen J., Harris, Faye R., Halling, Geoffrey C., Terra, Simone B. S. P., Cheville, John, Pagliaro, Lance, Leibovich, Brad

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 3.05 MB

english, 2019

16

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

Peterson, Jess F., He, Rui R., Nayer, Hassan, Cuevo, Raymund S., Smadbeck, James B., Vasmatzis, George, Greipp, Patricia T., Ketterling, Rhett P., Hoppman, Nicole L., Baughn, Linda B.

Journal:

Cancer Genetics

Year:

2019

File:

PDF, 2.18 MB

2019

17

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

Khoury, George A., Smadbeck, James, Kieslich, Chris A., Koskosidis, Alexandra J., Guzman, Yannis A., Tamamis, Phanourios, Floudas, Christodoulos A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 4.30 MB

english, 2017

18

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

Vasmatzis, George, Wang, Xue, Smadbeck, James B., Murphy, Stephen J., Geiersbach, Katherine B., Johnson, Sarah H., Gaitatzes, Athanasios G., Asmann, Yan W., Kosari, Farhad, Borad, Mitesh J., Serie, Da

Journal:

Year:

2018

Language:

english

File:

PDF, 1.28 MB

english, 2018

19

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

Peterson, Jess F., Sukov, William R., Pitel, Beth A., Smoley, Stephanie A., Pearce, Kathryn E., Meyer, Reid G., Williamson, Cynthia M., Smadbeck, James B., Vasmatzis, George, Hoppman, Nicole L., Greip

Journal:

Genes, Chromosomes and Cancer

Year:

2019

Language:

english

File:

PDF, 1.17 MB

english, 2019

20

Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma

Mansfield, Aaron S., Peikert, Tobias, Smadbeck, James B., Udell, Julia B.M., Garcia-Rivera, Enrique, Elsbernd, Laura, Erskine, Courtney L., Van Keulen, Virginia P., Kosari, Farhad, Murphy, Stephen J.,

Journal:

Journal of Thoracic Oncology

Year:

2018

Language:

english

File:

PDF, 1.62 MB

english, 2018

21

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

Khoury, George A., Smadbeck, James, Tamamis, Phanourios, Vandris, Andrew C., Kieslich, Chris A., Floudas, Christodoulos A.

Journal:

ACS Synthetic Biology

Year:

2014

Language:

english

File:

PDF, 2.10 MB

english, 2014

22

Integrated genomic analysis of pancreatic ductal adenocarcinomas reveals genomic rearrangement events as significant drivers of disease.

Murphy, S. J., Hart, S. N., Halling, G., Johnson, S. H., Smadbeck, J. B., Drucker, T., Felipe Lima, J., Rakhshan Rohakhtar, F., Harris, F. R., Kosari, F., Subramanian, S., Petersen, G. M., Wiltshire,

Journal:

Cancer Research

Year:

2015

Language:

english

File:

PDF, 4.55 MB

english, 2015

23

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

Kieslich, Chris A., Smadbeck, James, Khoury, George A., Floudas, Christodoulos A.

Journal:

Journal of Chemical Information and Modeling

Year:

2016

Language:

english

File:

PDF, 2.38 MB

english, 2016

24

Next Generation Sequencing of Sporadic Vestibular Schwannoma

Carlson, Matthew L., Smadbeck, James B., Link, Michael J., Klee, Eric W., Vasmatzis, George, Schimmenti, Lisa A.

Journal:

Otology & Neurotology

Year:

2018

Language:

english

File:

PDF, 371 KB

english, 2018

25

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

Rusheen, Aaron, Smadbeck, James, Schimmenti, Lisa, Klee, Eric, Link, Michael, Vasmatzis, George, Carlson, Matthew

Journal:

Journal of Neurological Surgery Part B Skull Base

Year:

2019

File:

PDF, 442 KB

2019

26

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

Leiting, Jennifer L., Murphy, Stephen J., Bergquist, John R., Hernandez, Matthew C., Ivanics, Tommy, Abdelrahman, Amro M., Yang, Lin, Lynch, Isaac, Smadbeck, James B., Cleary, Sean P., Nagorney, David

Journal:

Year:

2020

Language:

english

File:

PDF, 3.31 MB

english, 2020

27

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

Misener, Ruth, Smadbeck, James B., Floudas, Christodoulos A.

Journal:

Optimization Methods and Software

Year:

2015

Language:

english

File:

PDF, 1.05 MB

english, 2015

28

Characterization of a t(1;2)(p36;p21) involving the PRDM16 gene region by mate-pair sequencing (MPseq) in a patient with newly diagnosed acute myeloid leukemia with myelodysplasia-related changes

Muppa, Prasuna, Van Dyke, Daniel L., Bianco, Michelle K., Pitel, Beth A., Smoley, Stephanie A., Vasmatzis, George, Smadbeck, James B., Sukov, William R., Greipp, Patricia T., Ketterling, Rhett P., Bau

Journal:

Journal of Hematopathology

Year:

2019

Language:

english

File:

PDF, 984 KB

english, 2019

29

Identification of a Novel ZBTB20-JAK2 Fusion by Mate-Pair Sequencing in a Young Adult With B-Lymphoblastic Leukemia/Lymphoma

Peterson, Jess F., Blackburn, Patrick R., Webley, Matthew R., Pearce, Kathryn E., Williamson, Cynthia M., Vasmatzis, George, Smadbeck, James B., Bieliauskas, Shannon L., Reichard, Kaaren K., Ketterlin

Journal:

Mayo Clinic Proceedings

Year:

2019

Language:

english

File:

PDF, 1023 KB

english, 2019

30

Secondary acquisition of BCR-ABL1 fusion in de novo GATA2-MECOM positive acute myeloid leukemia with subsequent emergence of a rare KMT2A-ASXL2 fusion

Blackburn, Patrick R., Huang, Li, Dalovisio, Andrew, Pitel, Beth A., Chen, Dong, Oliveira, Jennifer L., Wood, Adam J., Smadbeck, James B., Johnson, Sarah H., Vasmatzis, George, Haferlach, Claudia, Gre

Journal:

Cancer Genetics

Year:

2019

File:

PDF, 930 KB

2019

31

Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines

Khoury, George A., Tamamis, Phanourios, Pinnaduwage, Neesha, Smadbeck, James, Kieslich, Chris A., Floudas, Christodoulos A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.10 MB

english, 2014

32

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

Peterson, Jess F., Pitel, Beth A., Smoley, Stephanie A., Smadbeck, James B., Johnson, Sarah H., Vasmatzis, George, Koon, Sarah J., Webley, Matthew R., McGrath, Mary, Bayerl, Michael G., Baughn, Linda

Journal:

Molecular Case Studies

Year:

2019

Language:

english

File:

PDF, 8.44 MB

english, 2019

33

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

Vasmatzis, George, Liu, Minetta C., Reganti, Sowjanya, Feathers, Ryan W., Smadbeck, James, Johnson, Sarah H., Schaefer Klein, Janet L., Harris, Faye R., Yang, Lin, Kosari, Farhad, Murphy, Stephen J.,

Journal:

Mayo Clinic Proceedings

Year:

2019

Language:

english

File:

PDF, 3.09 MB

english, 2019

34

Efficient moment matrix generation for arbitrary chemical networks

P. Smadbeck, Y.N. Kaznessis

Journal:

Chemical Engineering Science

Year:

2012

Language:

english

File:

PDF, 357 KB

english, 2012

35

De novo protein design of agonists and antagonists of C5a receptors

Peter N. Monk, Meghan L. Bellows-Peterson, James Smadbeck, Christodoulos A. Floudas, Christopher A. Kieslich, Dimitrios Morikis, Trent M. Woodruff

Journal:

Year:

2012

Language:

english

File:

PDF, 82 KB

english, 2012

36

False-negative Rates for MYC FISH Probes in B-cell Neoplasms

King, Rebecca L., McPhail, Ellen D., Meyer, Reid G., Vasmatzis, George, Pearce, Kathryn, Smadbeck, James B., Ketterling, Rhett P., Smoley, Stephanie A., Greipp, Patricia T., Hoppman, Nicole L., Peters

Journal:

Year:

2018

Language:

english

File:

PDF, 1.43 MB

english, 2018

37

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

Peterson, Jess F., Smoley, Stephanie A., Luoma, Ivy M., Pitel, Beth A., Rice, Christopher S., Benevides Demasi, Jonna C., Vasmatzis, George, Smadbeck, James B., Yang, Tong, Greipp, Patricia T., Ketter

Journal:

Journal of Hematopathology

Year:

2019

Language:

english

File:

PDF, 1.38 MB

english, 2019

38

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

Rowsey, Ross A., Smoley, Stephanie A., Williamson, Cynthia M., Vasmatzis, George, Smadbeck, James B., Ning, Yi, Greipp, Patricia T., Hoppman, Nicole L., Baughn, Linda B., Ketterling, Rhett P., Peterso

Journal:

Blood Cancer Journal

Year:

2019

Language:

english

File:

PDF, 957 KB

english, 2019

39

Cryptic and atypical KMT2AâUSP2 and KMT2AâUSP8 rearrangements identified by mate pair sequencing in infant and childhood leukemia

Blackburn, Patrick R., Smadbeck, James B., Znoyko, Iya, Webley, Matthew R., Pitel, Beth A., Vasmatzis, George, Xu, Xinjie, Greipp, Patricia T., Hoppman, Nicole L., Ketterling, Rhett P., Baughn, Linda

Journal:

Genes, Chromosomes and Cancer

Year:

2020

File:

PDF, 1.68 MB

2020

40

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

Parney, Ian F, Gustafson, Michael P, Solseth, Mary, Bulur, Peggy, Peterson, Timothy E, Smadbeck, James B, Johnson, Sarah H, Murphy, Stephen J, Vasmatzis, George, Dietz, Allan B

Journal:

Neuro-Oncology Advances

Year:

2020

File:

PDF, 1.49 MB

2020

41

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

Smadbeck, James, Chan, Kiat Hwa, Khoury, George A., Xue, Bo, Robinson, Robert C., Hauser, Charlotte A. E., Floudas, Christodoulos A., Levitt, Michael

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.00 MB

english, 2014

42

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

Harris, Faye R., Kovtun, Irina V., Smadbeck, James, Multinu, Francesco, Jatoi, Aminah, Kosari, Farhad, Kalli, Kimberly R., Murphy, Stephen J., Halling, Geoffrey C., Johnson, Sarah H., Liu, Minetta C.,

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.46 MB

english, 2016

43

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

Peterson, Jess F., Pitel, Beth A., Smoley, Stephanie A., Smadbeck, James B., Johnson, Sarah H., Vasmatzis, George, Pearce, Kathryn E., He, Rong, Kelemen, Katalin, Al-Mondhiry, Hamid A.B., Lamparella,

Journal:

Cancer Genetics

Year:

2018

Language:

english

File:

PDF, 2.88 MB

english, 2018

44

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

Berg, Holly E., Blackburn, Patrick R., Baughn, Linda B., Ketterling, Rhett P., Xu, Xinjie, Greipp, Patricia T., Hoppman, Nicole L., Smadbeck, James B., Vasmatzis, George, Shi, Min, Reichard, Kaaren K.

Journal:

Genes, Chromosomes and Cancer

Year:

2020

File:

PDF, 1.87 MB

2020

45

A closure scheme for chemical master equations

Smadbeck, P., Kaznessis, Y. N.

Journal:

Proceedings of the National Academy of Sciences

Year:

2013

Language:

english

File:

PDF, 659 KB

english, 2013

46

Identification of a Novel ZBTB20-JAK2 Fusion by Mate-Pair Sequencing in a Young Adult With B-Lymphoblastic Leukemia/Lymphoma

Peterson, Jess F., Blackburn, Patrick R., Webley, Matthew R., Pearce, Kathryn E., Williamson, Cynthia M., Vasmatzis, George, Smadbeck, James B., Bieliauskas, Shannon L., Reichard, Kaaren K., Ketterlin

Journal:

Mayo Clinic Proceedings

Year:

2019

File:

PDF, 1023 KB

2019

47

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

Polonis, Katarzyna, Schultz, Matthew J., Olteanu, Horatiu, Smadbeck, James B., Johnson, Sarah H., Vasmatzis, George, Xu, Xinjie, Greipp, Patricia T., Ketterling, Rhett P., Hoppman, Nicole L., Baughn,

Journal:

Annals of Diagnostic Pathology

Year:

2020

File:

PDF, 1.68 MB

2020

48

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

Peterson, Jess F., Baughn, Linda B., Ketterling, Rhett P., Pitel, Beth A., Smoley, Stephanie A., Vasmatzis, George, Smadbeck, James B., Greipp, Patricia T., Mangaonkar, Abhishek A., Thompson, Carrie A

Journal:

Year:

2019

File:

PDF, 1.44 MB

2019

49

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

Boddicker, R. L., Razidlo, G. L., Dasari, S., Zeng, Y., Hu, G., Knudson, R. A., Greipp, P. T., Davila, J. I., Johnson, S. H., Porcher, J. C., Smadbeck, J. B., Eckloff, B. W., Billadeau, D. D., Kurtin,

Journal:

Year:

2016

Language:

english

File:

PDF, 1.76 MB

english, 2016

50

Whole genome mate-pair sequencing of plasma cell neoplasm as a novel diagnostic strategy: a case of unrecognized t(2;11) structural variation

Peterson, Jess F., Meyer, Reid G., Smoley, Stephanie A., Webley, Matthew, Smadbeck, James B., Vasmatzis, George, Pearce, Kathryn, Greipp, Patricia T., Ketterling, Rhett P., Craig, Fiona E., Stewart, A

Journal:

Clinical Lymphoma Myeloma and Leukemia

Year:

2019

Language:

english

File:

PDF, 2.08 MB

english, 2019

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