Paul A. Rejto: search on Z-Library

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1

Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma

Wang, Kai, Lim, Ho Yeong, Shi, Stephanie, Lee, Jeeyun, Deng, Shibing, Xie, Tao, Zhu, Zhou, Wang, Yuli, Pocalyko, David, Yang, Wei Jennifer, Rejto, Paul A., Mao, Mao, Park, Cheol-Keun, Xu, Jiangchun

Journal:

Year:

2013

Language:

english

File:

PDF, 7.43 MB

english, 2013

2

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Kohala Coast, Hawaii, USA (4 – 8 January 2015)] Biocomputing 2015 - CELL INDEX DATABASE (CELLX): A WEB TOOL FOR CANCER PRECISION MEDICINE

CHING, KEITH A., WANG, KAI, KAN, ZHENGYAN, FERNANDEZ, JULIO, ZHONG, WENYAN, KOSTROWICKI, JAREK, XIE, TAO, ZHU, ZHOU, MARTINI, JEAN-FRANCOIS, KOEHLER, MARIA, ARNDT, KIM, REJTO, PAUL

Language:

english

File:

PDF, 2.26 MB

english

3

A Novel SND1-BRAF Fusion Confers Resistance to c-Met Inhibitor PF-04217903 in GTL16 Cells though MAPK Activation

Lee, Nathan V., Lira, Maruja E., Pavlicek, Adam, Ye, Jingjing, Buckman, Dana, Bagrodia, Shubha, Srinivasa, Sreesha P., Zhao, Yongjun, Aparicio, Samuel, Rejto, Paul A., Christensen, James G., Ching, Ke

Journal:

Year:

2012

Language:

english

File:

PDF, 935 KB

english, 2012

4

Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: Structural analysis of the peptide complexes with SH2 domains

Gennady M. Verkhivker, Djamal Bouzida, Daniel K. Gehlhaar, Paul A. Rejto, Lana Schaffer, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Veda Larson, Brock A. Luty, Tami Marrone, Peter W. Rose

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 1.29 MB

english, 2001

5

Assay optimization and kinetic profile of the human and the rabbit isoforms of 11β-HSD1

Arturo Castro, Jeff X. Zhu, Gordon R. Alton, Paul Rejto, Jacques Ermolieff

Journal:

Biochemical and Biophysical Research Communications

Year:

2007

Language:

english

File:

PDF, 247 KB

english, 2007

6

Combining CDK4/6 inhibition with taxanes enhances anti-tumor efficacy by sustained impairment of pRB-E2F pathways in squamous cell lung cancer

Cao, Joan, Zhu, Zhou, Wang, Hui, Nichols, Timothy C., Lui, Goldie Y. L., Deng, Shibing, Rejto, Paul A., VanArsdale, Todd, Hardwick, James S., Weinrich, Scott L., Wei, Ping

Journal:

Year:

2019

Language:

english

File:

PDF, 3.86 MB

english, 2019

7

Identification and characterization of a novel and functional murine Pin1 isoform

Jeff X. Zhu, Eleanor Dagostino, Paul A. Rejto, Barbara Mroczkowski, Brion Murray

Journal:

Biochemical and Biophysical Research Communications

Year:

2007

Language:

english

File:

PDF, 961 KB

english, 2007

8

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Mauna Lani, Hawaii, USA (4 – 9 January 1999)] Biocomputing '99 - Thermodynamics and kinetics of ligand—protein binding studied with the weighted histogram analysis method and simulated annealing

Bouzida, Djamal, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Gehlhaar, Daniel K., Larson, Veda, Luty, Brock A., Rejto, Paul A., Rose, Peter W., Verkhivker, Gennady M.

Year:

1998

Language:

english

File:

PDF, 870 KB

english, 1998

9

Inhibition of 11β-Hydroxysteroid Dehydrogenase Type 1 Activity in Vivo Limits Glucocorticoid Exposure to Human Adipose Tissue and Decreases Lipolysis

Tomlinson, Jeremy W., Sherlock, Mark, Hughes, Beverley, Hughes, Susan V., Kilvington, Fiona, Bartlett, William, Courtney, Rachel, Rejto, Paul, Carley, William, Stewart, Paul M.

Journal:

Journal of Clinical Endocrinology & Metabolism

Year:

2007

Language:

english

File:

PDF, 266 KB

english, 2007

10

A reactive-flux theory of chemical surface diffusion

Rejto, Paul A., Andersen, Hans C.

Journal:

The Journal of Chemical Physics

Year:

1990

Language:

english

File:

PDF, 861 KB

english, 1990

11

Parallel simulated tempering dynamics of ligand–protein binding with ensembles of protein conformations

Gennady M. Verkhivker, Paul A. Rejto, Djamal Bouzida, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Daniel K. Gehlhaar, Veda Larson, Brock A. Luty, Tami Marrone, Peter W. Rose

Journal:

Chemical Physics Letters

Year:

2001

Language:

english

File:

PDF, 351 KB

english, 2001

12

Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma

Fernandez-Banet, Julio, Lee, Nikki P., Chan, Kin Tak, Gao, Huan, Liu, Xiao, Sung, Wing-Kin, Tan, Winnie, Fan, Sheung Tat, Poon, Ronnie T., Li, Shiyong, Ching, Keith, Rejto, Paul A., Mao, Mao, Kan, Zhe

Journal:

Year:

2014

Language:

english

File:

PDF, 2.70 MB

english, 2014

13

Mean field analysis of FKBP12 complexes with FK506 and rapamycin: Implications for a role of crystallographic water molecules in molecular recognition and specificity

Paul A. Rejto, Gennady M. Verkhivker

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 226 KB

english, 1997

14

Monte Carlo study of ligand–protein binding energy landscapes with the weighted histogram analysis method

Djamal Bouzida, Paul A. Rejto, Gennady M. Verkhivker

Journal:

International Journal of Quantum Chemistry

Year:

1999

Language:

english

File:

PDF, 235 KB

english, 1999

15

Crystal Structure of Human ABAD/HSD10 with a Bound Inhibitor: Implications for Design of Alzheimer's Disease Therapeutics

Charles R. Kissinger, Paul A. Rejto, Laura A. Pelletier, James A. Thomson, Richard E. Showalter, Melwyn A. Abreo, Charles S. Agree, Stephen Margosiak, Jerry J. Meng, Robert M. Aust, Darin Vanderpool,

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 606 KB

english, 2004

16

Patterns of somatic alterations between matched primary and metastatic colorectal tumors characterized by whole-genome sequencing

Xie, Tao, Cho, Yong Beom, Wang, Kai, Huang, Donghui, Hong, Hye Kyung, Choi, Yoon-La, Ko, Young Hyeh, Nam, Do-Hyun, Jin, Juyoun, Yang, Heekyoung, Fernandez, Julio, Deng, Shibing, Rejto, Paul A., Lee, W

Journal:

Year:

2014

Language:

english

File:

PDF, 2.06 MB

english, 2014

17

[IEEE 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - San Diego, CA, USA (2019.11.18-2019.11.21)] 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Detecting somatic mutations with high accuracy in plasma cell-free DNA with TNER2

Deng, Shibing, Hsu, Joy, Bienkowska, Jadwiga, Rejto, Paul A., Xie, Tao

Year:

2019

File:

PDF, 3.26 MB

2019

18

Protein conformational substates from X-ray crystallography

Paul A. Rejto, Stephan T. Freer

Journal:

Progress in Biophysics and Molecular Biology

Year:

1996

Language:

english

File:

PDF, 2.32 MB

english, 1996

19

Antisense inhibition of 11βhydroxysteroid dehydrogenase type 1 improves diabetes in a novel cortisone-induced diabetic KK mouse model

B. Ganesh Bhat, Husam Younis, Jocelyn Herrera, Kimbie Palacio, Bernadette Pascual, George Hur, Bart Jessen, Kathleen M. Ogilvie, Paul A. Rejto

Journal:

Biochemical and Biophysical Research Communications

Year:

2008

Language:

english

File:

PDF, 209 KB

english, 2008

20

A Mean Field Model of Ligand-Protein Interactions: Implications for the Structural Assessment of Human Immunodeficiency Virus Type 1 Protease Complexes and Receptor-Specific Binding

Gennady M. Verkhivker and Paul A. Rejto

Journal:

Proceedings of the National Academy of Sciences

Year:

1996

Language:

english

File:

PDF, 257 KB

english, 1996

21

Visualization of fast energy flow and solvent caging in unimolecular dynamics

Rejto, Paul A., Bindewald, Eckart, Chandler, David

Journal:

Year:

1995

File:

PDF, 469 KB

1995

22

Deciphering common failures in molecular docking of ligand-protein complexes

Gennady M. Verkhivker, Djamal Bouzida, Daniel K. Gehlhaar, Paul A. Rejto, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Veda Larson, Brock A. Luty, Tami Marrone, Peter W. Rose

Journal:

Journal of Computer-Aided Molecular Design

Year:

2000

Language:

english

File:

PDF, 405 KB

english, 2000

23

Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes

Gennady M. Verkhivker, Paul A. Rejto, Daniel K. Gehlhaar, Stephan T. Freer

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1996

Language:

english

File:

PDF, 1011 KB

english, 1996

24

Dose-dependent effects of small-molecule antagonists on the genomic landscape of androgen receptor binding

Zhu, Zhou, Shi, Manli, Hu, Wenyue, Estrella, Heather, Engebretsen, Jon, Nichols, Tim, Briere, David, Hosea, Natilie, Los, Gerrit, Rejto, Paul A, Fanjul, Andrea

Journal:

Year:

2012

Language:

english

File:

PDF, 929 KB

english, 2012

25

[ACM Press the 17th ACM SIGKDD international conference - San Diego, California, USA (2011.08.21-2011.08.24)] Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '11 - Knowledge discovery and data mining in pharmaceutical cancer research

Year:

2011

Language:

english

File:

PDF, 346 KB

english, 2011

26

Examining ligand-protein interactions with binding-energy landscapes

Paul A. Rejto, Djamal Bouzida, Gennady M. Verkhivker

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

1999

Language:

english

File:

PDF, 225 KB

english, 1999

27

Statistical method on nonrandom clustering with application to somatic mutations in cancer

Jingjing Ye, Adam Pavlicek, Elizabeth A Lunney, Paul A Rejto, Chi-Hse Teng

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 447 KB

english, 2010

28

P-cadherin expression as a prognostic biomarker in a 3992 case tissue microarray series of breast cancer

Turashvili, Gulisa, McKinney, Steven E, Goktepe, Ozge, Leung, Samuel C, Huntsman, David G, Gelmon, Karen A, Los, Gerrit, Rejto, Paul A, Aparicio, Samuel A J R

Journal:

Modern Pathology

Year:

2011

Language:

english

File:

PDF, 1.59 MB

english, 2011

29

Structural consensus in ligand-protein docking identifies recognition peptide motifs that bind streptavidin

Nirav K. Shah, Paul A. Rejto, Gennady M. Verkhivker

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 287 KB

english, 1997

30

Hierarchy of Simulation Models in Predicting Structure and Energetics of the Src SH2 Domain Binding to Tyrosyl Phosphopeptides

Verkhivker, Gennady M., Bouzida, Djamal, Gehlhaar, Daniel K., Rejto, Paul A., Schaffer, Lana, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Larson, Veda, Luty, Brock A., Marrone, Tami, Rose,

Journal:

Journal of Medicinal Chemistry

Year:

2002

Language:

english

File:

PDF, 553 KB

english, 2002

31

Interatomic potentials and the phase diagram of Xe/Pt(111)

Rejto, Paul A., Andersen, Hans C.

Journal:

The Journal of Chemical Physics

Year:

1993

Language:

english

File:

PDF, 1.32 MB

english, 1993

32

Outlier analysis of functional genomic profiles enriches for oncology targets and enables precision medicine

Zhu, Zhou, Ihle, Nathan T., Rejto, Paul A., Zarrinkar, Patrick P.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.13 MB

english, 2016

33

Complexity and simplicity of ligand–macromolecule interactions: the energy landscape perspective

Gennady M Verkhivker, Djamal Bouzida, Daniel K Gehlhaar, Paul A Rejto, Stephan T Freer, Peter W Rose

Journal:

Current Opinion in Structural Biology

Year:

2002

Language:

english

File:

PDF, 64 KB

english, 2002

34

Energy Flow during Isomerization Reactions in Liquids

Rejto, Paul A., Chandler, David

Journal:

Journal of Physical Chemistry

Year:

1994

Language:

english

File:

PDF, 513 KB

english, 1994

35

Computer simulations of ligand–protein binding with ensembles of protein conformations: A Monte Carlo study of HIV-1 protease binding energy landscapes

Djamal Bouzida, Paul A. Rejto, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Daniel K. Gehlhaar, Veda Larson, Brock A. Luty, Peter W. Rose, Gennady M. Verkhivker

Journal:

International Journal of Quantum Chemistry

Year:

1999

Language:

english

File:

PDF, 470 KB

english, 1999

36

Unraveling Principles of Lead Discovery: From Unfrustrated Energy Landscapes to Novel Molecular Anchors

Paul A. Rejto and Gennady M. Verkhivker

Journal:

Proceedings of the National Academy of Sciences

Year:

1996

Language:

english

File:

PDF, 1.09 MB

english, 1996

37

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

Daniel K. Gehlhaar, Gennady M. Verkhivker, Paul A. Rejto, Christopher J. Sherman, David R. Fogel, Lawrence J. Fogel, Stephan T. Freer

Journal:

Chemistry & Biology

Year:

1995

Language:

english

File:

PDF, 1.01 MB

english, 1995

38

Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: The energy landscape analysis of a hot spot at the intermolecular interface

Gennady M. Verkhivker, Djamal Bouzida, Daniel K. Gehlhaar, Paul A. Rejto, Stephan T. Freer, Peter W. Rose

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2002

Language:

english

File:

PDF, 1.32 MB

english, 2002

39

TNER: a novel background error suppression method for mutation detection in circulating tumor DNA

Deng, Shibing, Lira, Maruja, Huang, Donghui, Wang, Kai, Valdez, Crystal, Kinong, Jennifer, Rejto, Paul A., Bienkowska, Jadwiga, Hardwick, James, Xie, Tao

Journal:

BMC Bioinformatics

Year:

2018

Language:

english

File:

PDF, 856 KB

english, 2018

40

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand–protein interactions

Gennady M. Verkhivker, Paul A. Rejto, Djamal Bouzida, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Daniel K. Gehlhaar, Veda Larson, Brock A. Luty, Tami Marrone, Peter W. Rose

Journal:

Journal of Molecular Recognition

Year:

1999

Language:

english

File:

PDF, 1.14 MB

english, 1999

41

Navigating ligand–protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

Gennady M. Verkhivker, Paul A. Rejto, Djamal Bouzida, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Daniel K. Gehlhaar, Veda Larson, Brock A. Luty, Tami Marrone, Peter W. Rose

Journal:

Chemical Physics Letters

Year:

2001

Language:

english

File:

PDF, 243 KB

english, 2001

42

Computational detection of the binding-site hot spot at the remodeled human growth hormone–receptor interface

Gennady M. Verkhivker, Djamal Bouzida, Daniel K. Gehlhaar, Paul A. Rejto, Stephan T. Freer, Peter W. Rose

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 767 KB

english, 2003

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