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1

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

2

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

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

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

5

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

6

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

7

Protein folding and de novo protein design for biotechnological applications

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

Journal:

Trends in Biotechnology

Year:

2014

Language:

english

File:

PDF, 1.91 MB

english, 2014

8

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

9

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

10

Stochastic model reduction using a modified Hill-type kinetic rate law

Smadbeck, Patrick, Kaznessis, Yiannis

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 706 KB

english, 2012

11

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

12

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

Gorham, Ronald D., Forest, David L., Khoury, George A., Smadbeck, James, Beecher, Consuelo N., Healy, Evangeline D., Tamamis, Phanourios, Archontis, Georgios, Larive, Cynthia K., Floudas, Christodoulo

Journal:

Journal of Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 2.34 MB

english, 2015

13

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

14

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

15

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

16

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

17

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

18

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

19

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

20

Coalescent models for developmental biology and the spatio-temporal dynamics of growing tissues

Smadbeck, Patrick, Stumpf, Michael P. H.

Journal:

Journal of The Royal Society Interface

Year:

2016

Language:

english

File:

PDF, 1.27 MB

english, 2016

21

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

22

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

23

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

24

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

25

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

Murphy, Stephen J., Kosari, Farhad, Karnes, R. Jeffrey, Nasir, Aqsa, Johnson, Sarah H., Gaitatzes, Athanasios G., Smadbeck, James B., Rangel, Laureano J., Vasmatzis, George, Cheville, John C.

Journal:

Cancer Research

Year:

2017

Language:

english

File:

PDF, 1.09 MB

english, 2017

26

Genome U-Plot: A Whole Genome Visualization

Gaitatzes, Athanasios, Johnson, Sarah H, Smadbeck, James B, Vasmatzis, George

Journal:

Year:

2017

Language:

english

File:

PDF, 886 KB

english, 2017

27

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

Johnson, Sarah H., Smadbeck, James B., Smoley, Stephanie A., Gaitatzes, Athanasios, Murphy, Stephen J., Harris, Faye R., Drucker, Travis M., Zenka, Roman M., Pitel, Beth A., Rowsey, Ross A., Hoppman,

Journal:

Cancer Genetics

Year:

2018

Language:

english

File:

PDF, 4.63 MB

english, 2018

28

Copy Number Variant Analysis using Genome-Wide Mate-Pair Sequencing

Smadbeck, James B, Johnson, Sarah H., Smoley, Stephanie A., Gaitatzes, Athanasios, Drucker, Travis M., Zenka, Roman M., Kosari, Farhad, Murphy, Stephen J., Hoppman, Nicole, Aypar, Umut, Sukov, William

Journal:

Genes, Chromosomes and Cancer

Year:

2018

Language:

english

File:

PDF, 1.28 MB

english, 2018

29

De Novo Peptide Design and Experimental Validation of Histone Methyltransferase Inhibitors

Smadbeck, James, Peterson, Meghan B., Zee, Barry M., Garapaty, Shivani, Mago, Aashna, Lee, Christina, Giannis, Athanassios, Trojer, Patrick, Garcia, Benjamin A., Floudas, Christodoulos A., Sun, H. Sun

Journal:

Year:

2014

Language:

english

File:

PDF, 2.06 MB

english, 2014

30

9. Detection of fusion genes from complex rearrangements reported by genome-wide mate-pair sequencing (MPseq)

Johnson, Sarah H, Smadbeck, James, Harris, Faye, Mansfield, Aaron, Gaitatzes, Athanasios, Murphy, Stephen, Vasmatzis, George

Journal:

Cancer Genetics

Year:

2018

Language:

english

File:

PDF, 75 KB

english, 2018

31

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

32

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

33

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

34

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

Language:

english

File:

PDF, 119 KB

english, 2018

35

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

36

Use of mate-pair sequencing (MPseq) to characterize a complex cryptic BCR/ABL1 rearrangement observed in a newly diagnosed case of chronic myeloid leukemia

Peterson, Jess F., Pitel, Beth A., Smoley, Stephanie A., Smadbeck, James B., Johnson, Sarah H., Vasmatzis, George, Kearney, Hutton M., Greipp, Patricia T., Hoppman, Nicole L., Baughn, Linda B., Ketter

Journal:

Human Pathology

Year:

2018

Language:

english

File:

PDF, 1.94 MB

english, 2018

37

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

Aypar, Umut, Smoley, Stephanie A, Pitel, Beth A, Pearce, Kathryn E, Zenka, Roman M, Vasmatzis, George, Johnson, Sarah H, Smadbeck, James B, Peterson, Jess F, Geiersbach, Katherine B, Van Dyke, Daniel

Journal:

European Journal of Haematology

Year:

2018

Language:

english

File:

PDF, 922 KB

english, 2018

38

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

39

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

40

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

41

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

Vasmatzis, George, Kosari, Farhad, Murphy, Stephen J., Terra, Simone, Kovtun, Irina V., Harris, Faye R., Zarei, Shabnam, Smadbeck, James B., Johnson, Sarah H., Gaitatzes, Athanasios G., Therneau, Terr

Journal:

Mayo Clinic Proceedings

Year:

2019

Language:

english

File:

PDF, 2.11 MB

english, 2019

42

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

43

Cover Image

Aypar, Umut, Smoley, Stephanie A., Pitel, Beth A., Pearce, Kathryn E., Zenka, Roman M., Vasmatzis, George, Johnson, Sarah H., Smadbeck, James B., Peterson, Jess F., Geiersbach, Katherine B., Van Dyke,

Journal:

European Journal of Haematology

Year:

2019

File:

PDF, 872 KB

2019

44

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

Language:

english

File:

PDF, 442 KB

english, 2019

45

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

46

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

47

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

48

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

49

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

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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