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1

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

Zhang, Bin, Gaiteri, Chris, Bodea, Liviu-Gabriel, Wang, Zhi, McElwee, Joshua, Podtelezhnikov, Alexei A., Zhang, Chunsheng, Xie, Tao, Tran, Linh, Dobrin, Radu, Fluder, Eugene, Clurman, Bruce, Melquist,

Journal:

Year:

2013

Language:

english

File:

PDF, 1.96 MB

english, 2013

2

Modeling HIV-1 integrase complexes based on their hydrodynamic properties

Alexei A. Podtelezhnikov, Kui Gao, Frederic D. Bushman, J. Andrew McCammon

Journal:

Year:

2003

Language:

english

File:

PDF, 706 KB

english, 2003

3

Testing the quality of electron microscope mapping data for DNA molecules with sequence-specific ligands

Alexey A. Podtelezhnikov, Alexey V. Kurakin, Alexander V. Vologodskii, Dmitry I. Cherny

Journal:

Year:

1994

Language:

english

File:

PDF, 795 KB

english, 1994

4

CRANKITE: A fast polypeptide backbone conformation sampler

Alexei A Podtelezhnikov, David L Wild

Journal:

Source Code for Biology and Medicine

Year:

2008

Language:

english

File:

PDF, 439 KB

english, 2008

5

Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds

Alexei A. Podtelezhnikov, David L. Wild

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 249 KB

english, 2005

6

Learning about protein hydrogen bonding by minimizing contrastive divergence

Alexei A. Podtelezhnikov, Zoubin Ghahramani, David L. Wild

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 371 KB

english, 2007

7

Induction of Alzheimer’s-like changes in brain of mice expressing mutant APP fed excess methionine

Alexander McCampbell, Keith Wessner, Michael W. Marlatt, Carrie Wolffe, Dawn Toolan, Alexei Podtelezhnikov, Suzie Yeh, Rena Zhang, Peter Szczerba, Keith Q. Tanis, John Majercak, William J. Ray, Mary S

Journal:

Journal of Neurochemistry

Year:

2011

Language:

english

File:

PDF, 990 KB

english, 2011

8

Large-scale effects of transcriptional DNA supercoiling in Vivo

Andrey S. Krasilnikov, Alexei Podtelezhnikov, Alexander Vologodskii, Sergei M. Mirkin

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 487 KB

english, 1999

9

Transcriptional Architecture of the Primate Neocortex

Amy Bernard, Laura S. Lubbers, Keith Q. Tanis, Rui Luo, Alexei A. Podtelezhnikov, Eva M. Finney, Mollie M.E. McWhorter, Kyle Serikawa, Tracy Lemon, Rebecca Morgan, Catherine Copeland, Kimberly Smith,

Journal:

Year:

2012

Language:

english

File:

PDF, 4.86 MB

english, 2012

10

High methionine diet induces beta-amyloid–related transcriptional changes in mouse brain

Alexander McCampbell, Keith Wessner, Dawn Toolan, Alexei Podtelezhnikov, John Majercak, Keith Q. Tanis, William J. Ray, Mary J. Savage

Journal:

Alzheimer's & Dementia

Year:

2010

Language:

english

File:

PDF, 40 KB

english, 2010

11

Multimerization-Cyclization of DNA Fragments as a Method of Conformational Analysis

Podtelezhnikov, Alexei A., Mao, Chengde, Seeman, Nadrian C., Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2000

Language:

english

File:

PDF, 343 KB

english, 2000

12

Reconstruction and Stability of Secondary Structure Elements in the Context of Protein Structure Prediction

Podtelezhnikov, Alexei A., Wild, David L.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 794 KB

english, 2009

13

Bayesian Segmental Models with Multiple Sequence Alignment Profiles for Protein Secondary Structure and Contact Map Prediction

Wei Chu,, Ghahramani, Z., Podtelezhnikov, A., Wild, D.L.

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.72 MB

english, 2006

14

Accelerated Aging and Metabolic Disruption in the Brain Provide the Basis for Alzheimer's Disease Progression Modeling

Podtelezhnikov, Alexei A., Tanis, Keith Q., Stone, David J., Loboda, Andrey P.

Journal:

Alzheimer's & Dementia

Year:

2010

Language:

english

File:

PDF, 42 KB

english, 2010

15

Equilibrium Distributions of Topological States in Circular DNA: Interplay of Supercoiling and Knotting

Alexei A. Podtelezhnikov, Nicholas R. Cozzarelli and Alexander V. Vologodskii

Journal:

Proceedings of the National Academy of Sciences

Year:

1999

Language:

english

File:

PDF, 1.43 MB

english, 1999

16

Dynamics of Small Loops in DNA Molecules

Podtelezhnikov, Alexei A., Vologodskii, Alexander V.

Journal:

Year:

2000

Language:

english

File:

PDF, 59 KB

english, 2000

17

Simulations of Polymer Cyclization by Brownian Dynamics

Podtelezhnikov, Alexei, Vologodskii, Alexander

Journal:

Year:

1997

Language:

english

File:

PDF, 145 KB

english, 1997

18

Equilibrium distributions of topological states in circular DNA: Interplay of supercoiling and knotting

Podtelezhnikov, A. A., Cozzarelli, N. R., Vologodskii, A. V.

Journal:

Proceedings of the National Academy of Sciences

Year:

1999

Language:

english

File:

PDF, 306 KB

english, 1999

19

Mechanism of topology simplification by type II DNA topoisomerases

Vologodskii, A. V., Zhang, W., Rybenkov, V. V., Podtelezhnikov, A. A., Subramanian, D., Griffith, J. D., Cozzarelli, N. R.

Journal:

Proceedings of the National Academy of Sciences

Year:

2001

Language:

english

File:

PDF, 824 KB

english, 2001

20

Phase I Pharmacologic and Pharmacodynamic Study of the Gamma Secretase (Notch) Inhibitor MK-0752 in Adult Patients With Advanced Solid Tumors

Krop, I., Demuth, T., Guthrie, T., Wen, P. Y., Mason, W. P., Chinnaiyan, P., Butowski, N., Groves, M. D., Kesari, S., Freedman, S. J., Blackman, S., Watters, J., Loboda, A., Podtelezhnikov, A., Luncef

Journal:

Journal of Clinical Oncology

Year:

2012

Language:

english

File:

PDF, 144 KB

english, 2012

21

Comment on “Efficient Monte Carlo trial moves for polypeptide simulations” [J. Chem. Phys. 123, 174905 (2005)]

Podtelezhnikov, Alexei A., Wild, David L.

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 377 KB

english, 2008

22

Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA)

Zhang, R., Podtelezhnikov, A. A., Hogenesch, J. B., Anafi, R. C.

Journal:

Journal of Biological Rhythms

Year:

2016

Language:

english

File:

PDF, 1.13 MB

english, 2016

23

Toxicogenomics in drug development: a match made in heaven?

Qin, Chunhua, Tanis, Keith Q., Podtelezhnikov, Alexei A., Glaab, Warren E., Sistare, Frank D., DeGeorge, Joseph J.

Journal:

Expert Opinion on Drug Metabolism & Toxicology

Year:

2016

Language:

english

File:

PDF, 544 KB

english, 2016

24

Effects of Long-Term Odanacatib Treatment on Bone Gene Expression in Ovariectomized Adult Rhesus Monkeys: Differentiation From Alendronate

Muise, Eric S, Podtelezhnikov, Alexei A, Pickarski, Maureen, Loboda, Andrey, Tan, Yejun, Hu, Guanghui, Thomspon, John R, Duong, Le T

Journal:

Journal of Bone and Mineral Research

Year:

2016

Language:

english

File:

PDF, 1.04 MB

english, 2016

25

An accessible pharmacodynamic transcriptional biomarker for notch target engagement

Tanis, KQ, Podtelezhnikov, AA, Blackman, SC, Hing, J, Railkar, RA, Lunceford, J, Klappenbach, JA, Wei, B, Harman, A, Camargo, LM, Shah, S, Finney, EM, Hardwick, JS, Loboda, A, Watters, J, Bergstrom, D

Journal:

Clinical Pharmacology & Therapeutics

Year:

2016

Language:

english

File:

PDF, 978 KB

english, 2016

26

Transcriptional profiling of cholinergic neurons from basal forebrain identifies changes in expression of genes between sleep and wake

Nikonova, Elena V., Gilliland, Jason DA, Tanis, Keith Q., Podtelezhnikov, Alexei A., Rigby, Alison M, Galante, Raymond J., Finney, Eva M, Stone, David J., Renger, John J., Pack, Allan I., Winrow, Chri

Journal:

Year:

2017

Language:

english

File:

PDF, 1.24 MB

english, 2017

27

The Transcriptomic Signature Of Disease Development And Progression Of Nonalcoholic Fatty Liver Disease

Cazanave, Sophie, Podtelezhnikov, Alexei, Jensen, Kristian, Seneshaw, Mulugeta, Kumar, Divya P., Min, Hae-Ki, Santhekadur, Prasanna K., Banini, Bubu, Mauro, Adolfo Gabriele, M. Oseini, Abdul, Vincent,

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 4.00 MB

english, 2017

28

Blood-Gene Expression Reveals Reduced Circadian Rhythmicity in Individuals Resistant to Sleep Deprivation

Arnardottir, Erna S., Nikonova, Elena V., Shockley, Keith R., Podtelezhnikov, Alexei A., Anafi, Ron C., Tanis, Keith Q., Maislin, Greg, Stone, David J., Renger, John J., Winrow, Christopher J., Pack,

Journal:

Year:

2014

Language:

english

File:

PDF, 1.24 MB

english, 2014

29

Molecular Insights into the Pathogenesis of Alzheimer's Disease and Its Relationship to Normal Aging

Podtelezhnikov, Alexei A., Tanis, Keith Q., Nebozhyn, Michael, Ray, William J., Stone, David J., Loboda, Andrey P., Deli, Maria A.

Journal:

Year:

2011

Language:

english

File:

PDF, 1.57 MB

english, 2011

30

Comparative transcriptomics of choroid plexus in Alzheimer’s disease, frontotemporal dementia and Huntington’s disease: implications for CSF homeostasis

Stopa, Edward G., Tanis, Keith Q., Miller, Miles C., Nikonova, Elena V., Podtelezhnikov, Alexei A., Finney, Eva M., Stone, David J., Camargo, Luiz M., Parker, Lisan, Verma, Ajay, Baird, Andrew, Donahu

Journal:

Fluids and Barriers of the CNS

Year:

2018

Language:

english

File:

PDF, 2.59 MB

english, 2018

31

AhR Activation in Pharmaceutical Development: Applying Liver Gene Expression Biomarker Thresholds to Identify Doses Associated with Tumorigenic Risks in Rats

Qin, Chunhua, Aslamkhan, Amy G, Pearson, Kara, Tanis, Keith Q, Podtelezhnikov, Alexei, Frank, Erika, Pacchione, Stephen, Pippert, Todd, Glaab, Warren E, Sistare, Frank D

Journal:

Toxicological Sciences

Year:

2019

Language:

english

File:

PDF, 1016 KB

english, 2019

32

Quantitative Transcriptional Biomarkers of Xenobiotic Receptor Activation in Rat Liver for The Early Assessment of Drug Safety Liabilities

Podtelezhnikov, Alexei A, Monroe, James J, Aslamkhan, Amy G, Pearson, Kara, Qin, Chunhua, Tamburino, Alex M, Loboda, Andrey P, Glaab, Warren E, Sistare, Frank D, Tanis, Keith Q

Journal:

Toxicological Sciences

Year:

2020

File:

PDF, 3.00 MB

2020

33

Application of a Rat Liver Drug Bioactivation Transcriptional Response Assay Early in Drug Development that informs Chemically Reactive Metabolite formation and Potential for Drug Induced Liver Injury

Monroe, James J, Tanis, Keith Q, Podtelezhnikov, Alexei A, Nguyen, Truyen, Mahotka, Sam, Lynch, Donna, Evers, Raymond, Palamanda, Jairam, Miller, Randy, Pippert, Todd, Cabalu, Tammie, Johnson, Timothy

Journal:

Toxicological Sciences

Year:

2020

File:

PDF, 2.80 MB

2020

34

Development and Application of a Transcriptomic Signature of Bioactivation in an Advanced In Vitro Liver Model to Reduce Drug-induced Liver Injury Risk Early in the Pharmaceutical Pipeline

Kang, Wen, Podtelezhnikov, Alexei A, Tanis, Keith Q, Pacchione, Stephen, Su, Ming, Bleicher, Kimberly B, Wang, Zhibin, Laws, George M, Griffiths, Thomas G, Kuhls, Matthew C, Chen, Qing, Knemeyer, Ian,

Journal:

Toxicological Sciences

Year:

2020

File:

PDF, 2.01 MB

2020

35

Author Correction: The Transcriptomic Signature Of Disease Development And Progression Of Nonalcoholic Fatty Liver Disease

Cazanave, Sophie, Podtelezhnikov, Alexei, Jensen, Kristian, Seneshaw, Mulugeta, Kumar, Divya P., Min, Hae-Ki, Santhekadur, Prasanna K., Banini, Bubu, Mauro, Adolfo Gabriele, Oseini, Abdul M., Vincent,

Journal:

Scientific Reports

Year:

2020

File:

PDF, 619 KB

2020