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1

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Abraham, Mark James, Murtola, Teemu, Schulz, Roland, Páll, Szilárd, Smith, Jeremy C., Hess, Berk, Lindahl, Erik

Journal:

Year:

2015

Language:

english

File:

PDF, 872 KB

english, 2015

2

GROMACS 3.0: a package for molecular simulation and trajectory analysis

Erik Lindahl, Berk Hess, David van der Spoel

Journal:

Journal of Molecular Modeling

Year:

2001

Language:

english

File:

PDF, 109 KB

english, 2001

3

GROMACS: Fast, flexible, and free

David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 338 KB

english, 2005

4

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

Hess, Berk, Kutzner, Carsten, van der Spoel, David, Lindahl, Erik

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 383 KB

english, 2008

5

Extended megadroughts in the southwestern United States during Pleistocene interglacials

Fawcett, Peter J., Werne, Josef P., Anderson, R. Scott, Heikoop, Jeffrey M., Brown, Erik T., Berke, Melissa A., Smith, Susan J., Goff, Fraser, Donohoo-Hurley, Linda, Cisneros-Dozal, Luz M.

Journal:

Year:

2011

Language:

english

File:

PDF, 527 KB

english, 2011

6

Extended megadroughts in the southwestern United States during Pleistocene interglacials

Fawcett, Peter J., Werne, Josef P., Anderson, R. Scott, Heikoop, Jeffrey M., Brown, Erik T., Berke, Melissa A., Smith, Susan J., Goff, Fraser, Donohoo-Hurley, Linda, Cisneros-Dozal, Luz M.

Journal:

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

7

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

Bjelkmar, Pär, Larsson, Per, Cuendet, Michel A., Hess, Berk, Lindahl, Erik

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 203 KB

english, 2010

8

Atmospheric circulation patterns during late Pleistocene climate changes at Lake Malawi, Africa

Bronwen L. Konecky, James M. Russell, Thomas C. Johnson, Erik T. Brown, Melissa A. Berke, Josef P. Werne, Yongsong Huang

Journal:

Earth and Planetary Science Letters

Year:

2011

Language:

english

File:

PDF, 1.75 MB

english, 2011

9

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties

Wennberg, Christian L., Murtola, Teemu, Hess, Berk, Lindahl, Erik

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 1.93 MB

english, 2013

10

Prenatally Diagnosed Fetal Brain Injuries with Known Antenatal Etiologies

G&aacute, vai, M&aacute, rta, Hargitai, Be&aacute, ta, V&aacute, radi, Val&eacute, ria, Belics, Zoran, Csap&oacute, , Zsolt, Hajd&uacute, , J&uacute, lia, Hauzman, Erik, Berkes, Enik&otilde, , Papp, Zolt&aacut

Journal:

Fetal Diagnosis and Therapy

Year:

2008

Language:

english

File:

PDF, 321 KB

english, 2008

11

Direct-Space Corrections Enable Fast Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation

Wennberg, Christian L, Murtola, Teemu, Pall, Szilard, Abraham, Mark J., Hess, Berk, Lindahl, Erik

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 355 KB

english, 2015

12

Tracking the development of co-management: using network analysis in a case from the Canadian Arctic

Kocho-Schellenberg, John-Erik, Berkes, Fikret

Journal:

Year:

2015

Language:

english

File:

PDF, 306 KB

english, 2015

13

Characteristics and treatment of new-onset arthritis after checkpoint inhibitor therapy

Leipe, Jan, Christ, Lisa A, Arnoldi, Andreas P, Mille, Erik, Berger, Frank, Heppt, Markus, Goldscheider, Ilana, Kauffmann-Guerrero, Diego, Huber, Rudolf M, Dechant, Claudia, Berking, Carola, Schulze-K

Journal:

Year:

2018

Language:

english

File:

PDF, 235 KB

english, 2018

14

Panel 2: Critical physics issues of aneutronic migma reactor

Russell Kulsrud, Herbert Berk, Constantino Ferro-Fontan, Erik Karlsson, Fred Mills

Journal:

Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment

Year:

1988

Language:

english

File:

PDF, 456 KB

english, 1988

15

Functional complexity of the twin-arginine translocase TatC component revealed by site-directed mutagenesis

Grant Buchanan, Erik de Leeuw, Nicola R. Stanley, Margaret Wexler, Ben C. Berks, Frank Sargent, Tracy Palmer

Journal:

Molecular Microbiology

Year:

2002

Language:

english

File:

PDF, 1.61 MB

english, 2002

16

Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure

Frank Sargent, Ulrich Gohlke, Erik de Leeuw, Nicola R. Stanley, Tracy Palmer, Helen R. Saibil, Ben C. Berks

Journal:

Year:

2001

Language:

english

File:

PDF, 429 KB

english, 2001

17

Tumor-selective Correction of the Chemokine Production in Colorectal Cancer to Enhance the Recruitment of Effector T Cells and Counteract Treg Infiltration

Ravikumar Muthuswamy, Beth Junecko, Erik Berk, The Minh Luong, Jim Schlesselmann, Herbert Zeh, Todd Reinhart, David Bartlett, Pawel Kalinski

Journal:

Clinical Immunology

Year:

2010

Language:

english

File:

PDF, 46 KB

english, 2010

18

Effect of flow on endothelial endocytosis of nanocarriers targeted to ICAM-1

Tridib Bhowmick, Erik Berk, Xiumin Cui, Vladimir R. Muzykantov, Silvia Muro

Journal:

Journal of Controlled Release

Year:

2012

Language:

english

File:

PDF, 1.09 MB

english, 2012

19

Towards 21st century toxicology: In vivo imaging and gene expression in organotin-exposed rats

Didima de Groot, Maria Berk, Mark Bogaard, Vincent Jeroen de Groot, Rudi Dierckx, Frieke Kuper, Arend Heerschap, Rianne Nederlof, Rob Stierum, Andor Veltien, Erik de Vries, Aren van Waarde, André Wolt

Journal:

Reproductive Toxicology

Year:

2010

Language:

english

File:

PDF, 68 KB

english, 2010

20

Lymphocyte-polarized dendritic cells are highly effective in inducing tumor-specific CTLs

Erik Berk, Ravikumar Muthuswamy, Pawel Kalinski

Journal:

Year:

2012

Language:

english

File:

PDF, 935 KB

english, 2012

21

Co-management and the co-production of knowledge: Learning to adapt in Canada's Arctic

Derek Armitage, Fikret Berkes, Aaron Dale, Erik Kocho-Schellenberg, Eva Patton

Journal:

Global Environmental Change

Year:

2011

Language:

english

File:

PDF, 717 KB

english, 2011

22

The Noxa/Mcl-1 Axis Regulates Susceptibility to Apoptosis under Glucose Limitation in Dividing T Cells

Nuno L. Alves, Ingrid A.M. Derks, Erik Berk, René Spijker, René A.W. van Lier, Eric Eldering

Journal:

Year:

2006

Language:

english

File:

PDF, 738 KB

english, 2006

23

A novel protein transport system involved in the biogenesis of bacterial electron transfer chains

Ben C. Berks, Frank Sargent, Erik De Leeuw, Andrew P. Hinsley, Nicola R. Stanley, Rachael L. Jack, Grant Buchanan, Tracy Palmer

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2000

Language:

english

File:

PDF, 247 KB

english, 2000

24

Membrane interactions and self-association of the TatA and TatB components of the twin-arginine translocation pathway

Erik De Leeuw, Ida Porcelli, Frank Sargent, Tracy Palmer, Ben C. Berks

Journal:

Year:

2001

Language:

english

File:

PDF, 268 KB

english, 2001

25

The Escherichia coli twin-arginine translocase: conserved residues of TatA and TatB family components involved in protein transport

Matthew G Hicks, Erik de Leeuw, Ida Porcelli, Grant Buchanan, Ben C Berks, Tracy Palmer

Journal:

Year:

2003

Language:

english

File:

PDF, 598 KB

english, 2003

26

Targeting signals for a bacterial Sec-independent export system direct plant thylakoid import by the ΔpH pathway

Margaret Wexler, Erik G. Bogsch, Ralf Bernd Klösgen, Tracy Palmer, Colin Robinson, Ben C. Berks

Journal:

Year:

1998

Language:

english

File:

PDF, 145 KB

english, 1998

27

Oligomeric Properties and Signal Peptide Binding by Escherichia coli Tat Protein Transport Complexes

Erik de Leeuw, Thierry Granjon, Ida Porcelli, Meriem Alami, Stephen B. Carr, Matthias Müller, Frank Sargent, Tracy Palmer, Ben C. Berks

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 566 KB

english, 2002

28

Algorithm improvements for molecular dynamics simulations

Per Larsson, Berk Hess, Erik Lindahl

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2011

Language:

english

File:

PDF, 540 KB

english, 2011

29

310-Helix Conformation Facilitates the Transition of a Voltage Sensor S4 Segment toward the Down State

Schwaiger, Christine S., Bjelkmar, Pär, Hess, Berk, Lindahl, Erik

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 1.21 MB

english, 2011

30

Phe233 in the Voltage-Sensor is Rate Limiting for Channel Closure but not for the Opening

Schwaiger, Christine S., Börjesson, Sara I., Hess, Berk, Elinder, Fredrik, Lindahl, Erik

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 39 KB

english, 2012

31

Molecular dynamics study of dislocation nucleation from a crack tip

Hess, Berk, Thijsse, Barend J., Van der Giessen, Erik

Journal:

Physical Review B

Year:

2005

Language:

english

File:

PDF, 1.53 MB

english, 2005

32

Dendritic cell-based therapeutic cancer vaccines: what we have and what we need

Kalinski, Pawel, Urban, Julie, Narang, Rahul, Berk, Erik, Wieckowski, Ewa, Muthuswamy, Ravikumar

Journal:

Future Oncology

Year:

2009

Language:

english

File:

PDF, 763 KB

english, 2009

33

[ACM Press the 2011 companion - Seattle, Washington, USA (2011.11.12-2011.11.18)] Proceedings of the 2011 companion on High Performance Computing Networking, Storage and Analysis Companion - SC '11 Companion - Poster

Páll, Szilárd, Hess, Berk, Lindahl, Erik

Year:

2011

Language:

english

File:

PDF, 285 KB

english, 2011

34

Characterization of a Series of Isotype Switch Variants of a New CD20 Monoclonal Antibody

HOOIJBERG, ERIK, SEIN, JOHAN J., van den BERK, PAUL C.M., HEKMAN, ANNEMARIE

Journal:

Year:

1996

Language:

english

File:

PDF, 1.37 MB

english, 1996

35

Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions

Kasson, Peter M., Hess, Berk, Lindahl, Erik

Journal:

Chemistry and Physics of Lipids

Year:

2013

Language:

english

File:

PDF, 931 KB

english, 2013

36

Structural Transition from Alpha- to 3_10-Helix Reduces the Free Energy Required for S4 Translation in Kv1.2/2.1 Voltage Sensors, and F233 Appears to Responsible for the Gating Barrier

Schwaiger, Christine S., Bjelkmar, Pär, Hess, Berk, Lindahl, Erik

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

37

Calcium ionophore pre-treatment induces type-1 polarized DCs with enhanced T cell stimulatory function and IL-12 production

Erik Berk,Shuwen Xu,Min Xu,Julia Terhune…

Journal:

Journal for ImmunoTherapy of Cancer

Year:

2013

Language:

english

File:

PDF, 74 KB

english, 2013

38

Characterization and Membrane Assembly of the TatA Component of the Escherichia coli Twin-Arginine Protein Transport System †

Porcelli, Ida, de Leeuw, Erik, Wallis, Russell, van den Brink-van der Laan, Els, de Kruijff, Ben, Wallace, B. A., Palmer, Tracy, Berks, Ben C.

Journal:

Year:

2002

Language:

english

File:

PDF, 157 KB

english, 2002

39

[ACM Press 2011 International Conference for High Performance Computing, Networking, Storage and Analysis - Seattle, Washington (2011.11.12-2011.11.18)] Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '11 - Copernicus

Pronk, Sander, Lindahl, Erik, Larsson, Per, Pouya, Iman, Bowman, Gregory R., Haque, Imran S., Beauchamp, Kyle, Hess, Berk, Pande, Vijay S., Kasson, Peter M.

Year:

2011

Language:

english

File:

PDF, 1.68 MB

english, 2011

40

Dendritic cells matured in the presence of TLR ligands overcome the immunosuppressive functions of regulatory T cells

Berk, Erik, Xu, Shuwen, Czerniecki, Brian J

Journal:

Year:

2014

Language:

english

File:

PDF, 277 KB

english, 2014

41

Treatment and survival of patients with EGFR-mutated non-small cell lung cancer and leptomeningeal metastasis: A retrospective cohort analysis

Kuiper, Justine L., Hendriks, Lizza E., van der Wekken, Anthonie J., de Langen, Adrianus J., Bahce, Idris, Thunnissen, Erik, Heideman, Daniëlle A.M., Berk, Yvonne, Buijs, Ed J.M., Speel, Ernst-Jan M.,

Journal:

Year:

2015

Language:

english

File:

PDF, 1.04 MB

english, 2015

42

Repurposing Diflunisal for Familial Amyloid Polyneuropathy

Berk, John L., Suhr, Ole B., Obici, Laura, Sekijima, Yoshiki, Zeldenrust, Steven R., Yamashita, Taro, Heneghan, Michael A., Gorevic, Peter D., Litchy, William J., Wiesman, Janice F., Nordh, Erik, Cora

Journal:

JAMA The Journal of the American Medical Association

Year:

2013

Language:

english

File:

PDF, 257 KB

english, 2013

43

Progressive loss of anti-HER2 CD4 + T-helper type 1 response in breast tumorigenesis and the potential for immune restoration

Datta, Jashodeep, Rosemblit, Cinthia, Berk, Erik, Showalter, Lori, Namjoshi, Prachi, Mick, Rosemarie, Lee, Kathreen P, Brod, Andrew M, Yang, Rachel L, Kelz, Rachel R, Fitzpatrick, Elizabeth, Hoyt, Cli

Journal:

Year:

2015

Language:

english

File:

PDF, 2.18 MB

english, 2015

44

Lymphocyte-polarized DC1s

Berk, Erik, Kalinski, Pawel

Journal:

Year:

2012

Language:

english

File:

PDF, 501 KB

english, 2012

45

Research Highlights

Berk, Erik, Muthuswamy, Ravikumar

Journal:

Year:

2011

Language:

english

File:

PDF, 504 KB

english, 2011

46

Association of Depressed Anti-HER2 T-Helper Type 1 Response With Recurrence in Patients With Completely Treated HER2-Positive Breast Cancer

Datta, Jashodeep, Fracol, Megan, McMillan, Matthew T., Berk, Erik, Xu, Shuwen, Goodman, Noah, Lewis, David A., DeMichele, Angela, Czerniecki, Brian J.

Journal:

Year:

2015

Language:

english

File:

PDF, 288 KB

english, 2015

47

Cross-reactivity between darunavir and trimethoprim-sulfamethoxazole in HIV-infected patients

Buijs, Bianca S., van den Berk, Guido E., Boateng, Charlotte P., Hoepelman, Andy I., van Maarseveen, Erik M., Arends, Joop E.

Journal:

Year:

2015

Language:

english

File:

PDF, 294 KB

english, 2015

48

Anti-HER2 CD4+ T-helper type 1 response is a novel immune correlate to pathologic response following neoadjuvant therapy in HER2-positive breast cancer

Datta, Jashodeep, Berk, Erik, Xu, Shuwen, Fitzpatrick, Elizabeth, Rosemblit, Cinthia, Lowenfeld, Lea, Goodman, Noah, Lewis, David A, Zhang, Paul J, Fisher, Carla, Roses, Robert E, DeMichele, Angela, C

Journal:

Breast Cancer Research

Year:

2015

Language:

english

File:

PDF, 2.70 MB

english, 2015

49

A Lyα-only Active Galactic Nucleus from the Sloan Digital Sky Survey

Hall, Patrick B., Hoversten, Erik A., Tremonti, Christy A., Vanden Berk, Daniel E., Schneider, Donald P., Strauss, Michael A., Knapp, Gillian R., York, Donald G., Hutsemékers, Damien, Newman, P. R., B

Journal:

The Astronomical Journal

Year:

2004

Language:

english

File:

PDF, 265 KB

english, 2004

50

Lysis of Syngeneic Tumor B Cells by Autoreactive Cytotoxic T Lymphocytes Specific for a CD 19 Antigen-Derived Synthetic Peptide

Hooijberg, Erik, Visseren, Marjan J W, van den Berk, Paul C M, Jellema, P, Romeijn, Petra, Sein, Johan J, van der Voort, Ellen I H, Hekman, Annemarie, Ossendorp, Ferry, Melief, Cornelis J M

Journal:

Journal of Immunotherapy

Year:

1996

File:

PDF, 906 KB

1996