Journals

[accepted] [2022] [2020] [2019] [2018] [2017] [2016] [2015] [2014] [2013] [2012] [2011] [2009]

*These authors contributed equally to the respective work.

accepted

2022
[J43]Carver, J.C., Weber, N., Ram, K., Gesing, S., Katz, D.S.. (2022).
A survey of the state of the practice for research software in the United States
PeerJ Computer Science 8:e963, https://doi.org/10.7717/peerj-cs.963
[J42]Pierantoni, G., Kiss, T., Bolotov, A., Kagialis, D., Deslauriers, J., Ullah, A., Chen, H., Chan You Fee, D., Dang, H., Kovacs, J., Belehaki, A., Herekakis, T., Tsagouri, I. and Gesing, S. (2022)
Towards a Reference Architecture based Science Gateway Framework with Embedded E-Learning Support
Concurrency and Computation: Practice & Experience, January 2022

2020
[J41]Austin CC, Bernier A, Bezuidenhout L, Bicarregui J, Biro T, Cambon-Thomsen A, Carroll SR, Cournia Z, Dabrowski PW, Diallo G, Duflot T, Garcia L, Gesing, S., Gonzalez-Beltran A, Gururaj A, Harrower N, Lin D, Medeiros C, Méndez E, Meyers N, Mietchen D, Nagrani R, Nilsonne G, Parker S, Pickering B, Pienta A, Polydoratou P, Psomopoulos F, Rennes S, Rowe R, Sansone SA, Shanahan H, Sitz L, Stocks J, Tovani-Palone MR, Uhlmansiek M (2020)
Research Data Alliance. Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group.
Wellcome Open Res. 2020 Nov 9;5:267. doi: 10.12688/wellcomeopenres.16378.1. PMID: 33501381; PMCID: PMC7808050.
[J40]Calyam, P., Wilkins-Diehr, N., Miller, M. Brookes, E., Arora, R., Chourasia, A., Jennewein, D., Nandigam, V., Lamar, M. D., Cleveland, S., Newman, G., Wang, S., Zaslavsky, I., Cianfrocco, M., Ellett, K., Tarboton, D., Jeffery, K., Zhao, Z., González-Aranda, J., Perri, M., Tucker, G., Candela, L., Kiss, T. and Gesing, S. (2020)
Measuring Success for a Future Vision: Defining Impact in Science Gateways/Virtual Research Environments
Concurrency and Computation, 2020;e6099. doi. https://doi.org/10.1002/cpe.6099
[J39]Jay, C., Haines, R., Katz, D.S., Carver, J., Gesing, S., Brandt, S.R., Howison, J., Dubey, A., Phillips, J.C., Wan, H., and Turk, M. (2020)
The Challenges of Theory-Software Translation
F1000Research 2020, 9:1192, doi: https://doi.org/10.12688/f1000research.25561.1
[J38]Brower, D., Gesing, S., Johnson, R., Meyers, N., Meyerson, J. and Narlock, M. (2020)
ATG Special Report - On Institutional Repositories, “Beyond the Repository Services,” their Content, Maintainers, and Stakeholders
Against the Grain, April 2020
[J37]Saxena, A., Joshi, R., Darbari, H., Mazurek, C., Bhat, A., Srivastava, A., Wojkovich, K., Buetow, K. and Gesing, S. (2020)
The ICTBioMed NCIP Hub: Cancer research in a science gateway consortium
Future Generation Computer Systems. Volume 105, April 2020, pp. 27-32

2019
[J36]Gesing, S., Dahan, M., Zentner, M., Wilkins-Diehr, N. and Lawrence, K. (2019)
The Science Gateways Community Institute: Collaborations and efforts on international scale
Future Generation Computer Systems, Volume 101, December 2019, Pages 951-958
[J35]Stirm, C., Zink, R., Gesing, S., Zentner, M., and Junk, D.. (2019)
REMEDI central - expanding and sustaining a medical device community
Future Generation Computer Systems, Volume 101, December 2019, Pages 372-380
[J34]Barker, M., Olabarriaga, S., Wilkins-Diehr, N., Gesing, S., Katz, D.S., Shahand, S., Henwood, S., Glatard, T., Jeffery, K., Corrie, B., Glaves, H., Wyborn, L., Hong, N.C., and Costa, A. (2019)
The Global Impact of Science Gateways, Virtual Research Environments and Virtual Laboratories
Future Generation Computer Systems
[J33]Gesing, S., Lawrence, K., Dahan, M., Pierce, M.E., Wilkins-Diehr, N. and Zentner, M. (2019)
Science gateways: Sustainability via on-campus teams
Future Generation Computer Systems, volume 94, pages 97-102, May 2019.
[J32]Banegas-Luna, A.J., Imbernon, B., Llanes Castro, A., Perez-Garrido, A., Ceron-Carrasco, J.P., Gesing, S., Merelli, I., D’Agostino, D. and Perez-Sanchez, Horacio (2019)
Advances in distributed computing with modern drug discovery
Expert Opinion on Drug Discovery, 14(1):9-22, 2019, doi:10.1080/17460441.2019.1552936

2018
[J31]Katz, D. S., McInnes, L.C., Bernholdt, D.E., Mayes, A.C., Hong, N.P.C, Duckles, J., Gesing, S., Heroux, M.A., Hettrick, S., Jimenez, R.C., Pierce, M., Weaver, B. and Wilkins-Diehr, N. (2018)
Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained
Computing in Science & Engineering, doi: 10.1109/MCSE.2018.2883051
[J30]Carver, J., Gesing, S., Katz, D.S., Ram, K. and Weber, N. (2018)
Conceptualization of a US Research Software Sustainability Institute (URSSI)
IEEE Computing in Science & Engineering, Volume: 20, Issue: 3, pp. 4-9, 2018, DOI: 10.1109/MCSE.2018.03221924
[J29]Katz, D.S., Niemeyer, K., Gesing, S., Hwang, L., Bangerth, W., Hettrick, S., Idaszak, R., Salac, J., Chue Hong, N., Nunez-Corrales, S., Allen,A., Geiger, R.S., Miller, J., Chen, E., Dubey, A., Lago, P (2018)
Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)
Journal of Open Research Software, 6(1), p.10. DOI: http://doi.org/10.5334/jors.184

2017
[J28]Gesing, S., Dooley, R., Pierce, M., Krüger, J., Grunzke, R., Herres-Pawlis, S. and Hoffmann, A. (2017)
Gathering Requirements for Advancing Simulations in HPC Infrastructures via Science Gateways
Future Generation Computer Systems, https://doi.org/10.1016/j.future.2017.02.042
[J27]Atkinson, M.,Gesing, S., Montagnat, J. and Taylor, I. (2017)
Scientific Workflows: Past, Present and Future
Future Generation Computer Systems, volume 75, pages 216-227, 2017
[J26]Gesing, S., Carretero, J., Garcia Blas, J. and Montagnat, J. (2017)
Boosting Analyses in the Life Sciences via Clusters, Grids and Clouds
Future Generation Computer Systems, volume 67, pages 325-328, 2017

2016
[J25]Gesing, S., Wilkins-Diehr, N., Barker, M. and Pierantoni, G. (2016)
Science Gateway Workshops 2015 Special Issue Conference Publications
Journal of Grid Computing, 14(4):495-498, 2016, doi:10.1007/s10723-016-9389-4
[J24]Gesing, S., Krüger, J., Grunzke, R., Herres-Pawlis, S. and Hoffmann, A. (2016)
Using Science Gateways for Bridging the Differences between Research Infrastructures
Journal of Grid Computing, 14(4):545-557, 2016, doi:10.1007/s10723-016-9385-8
[J23]Arshad, J., Hoffmann, A., Gesing, S., Grunzke, R., Krüger, J., Kiss, T., Herres-Pawlis, S., Terstyanszky, G. (2016)
Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry
Journal of Cheminformatics (2016) 8: 58. doi:10.1186/s13321-016-0169-8
[J22]Katz, D S, Choi, S-C T , Niemeyer, K E, Hetherington, J, Löffler, F, Gunter, D, Idaszak, R, Brandt, S R, Miller, M A, Gesing, S, Jones, N D, Weber, N, Marru, S, Allen, G, Penzenstadler, B, Venters, C C, Davis, E, Hwang, L, Todorov, I, Patra, A and de Val-Borro, M (2016)
Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)
Journal of Open Research Software, 4: e37, DOI: http://dx.doi.org/10.5334/jors.118
[J21]Krüger, J., Thiel, P., Merelli, I., Grunzke, R., and Gesing, S. (2016)
Portals and Web-based Resources for Virtual Screening
Current Drug Targets, volume 17, issue 14, pages 1649-1660, year 2016, doi: 10.2174/1389450117666160201105806
[J20]Perez-Sanchez, H., Gesing, S. and Merelli, I. (2016)
Editorial: High Performance Computing in Drug Discovery
Current Drug Targets, volume 17, issue 14, pages 1578-1579, year 2016, doi: 10.2174/138945011714160930230542
[J19]Perez-Sanchez, H., Rezaei, V., Mezhuyev, V., Man, D., Pena-Garcia, J., den-Haan, H. and Gesing, S. (2016)
Developing Science Gateways for Drug Discovery in a Grid Environment
SpringerPlus 2016, 5(1):1-9, doi: 10.1186/s40064-016-2914-x
[J18]de la Garza, L., Veit, J., Szolek, A., Röttig, M., Aiche, S., Gesing, S., Reinert, K., and Kohlbacher, O (2016)
From the Desktop to the Grid: scalable Bioinformatics via Workflow Conversion
BMC Bioinformatics 2016, 17(1):127, DOI: 10.1186/s12859-016-0978-9

2015
[J17]Gesing, S. and Wilkins-Diehr, N. (2015)
Science gateway workshops 2014 special issue conference publications
Concurrency Computation: Practice and Experience, 27(16):4247–4251, doi: 10.1002/cpe.3615
[J16]Carretero, J., Garcia-Blas, J., and Gesing, S. (2015)
Introduction to the Special Issue on Cloud for Health
Scalable Computing: Practice and Experience, Vol. 16, No 1 (2015)
[J15]Wilkins-Diehr, N., Gesing, S., and Kiss, T. (2015)
Science gateway workshops 2013 special issue conference publications
Concurrency Computation: Practice and Experience, 27(2):253–257, doi: 10.1002/cpe.3362
[J14]Herres-Pawlis, S., Hoffmann, A., Balasko, A., Birkenheuer, G., Brinkmann, A., Gesing, S., Grunzke, R., Kacsuk, P., Krüger, J., Terstyansky, G., and Weingarten, N. (2015)
Quantum chemical metaworkflows in MoSGrid
Concurrency and Computation: Practice and Experience, 27(2):344–357, doi: 10.1002/cpe.3292

2014
[J13]Giraldo-Calderon, G., Emrich, S., MacCallum, R., Maslen, G., Dialynas, E., Topalis, P., Ho, N., Gesing, S., the VectorBase Consortium, Madey, G., Collins, F., and Lawson, D. (2014)
VectorBase: an updated bioinformatics resource for invertebrate vectors of human pathogens
Nucleic Acids Research, doi:10.1093/nar/gku1117
[J12]Merelli, I., Pérez-Sánchez, H., Gesing, S. and D'Agostino, D. (2014)
Managing, Analysing and Integrating Big Data in Medical Bioinformatics: Open Problems and Future Perspectives
BioMed Research International, Volume 2014 (2014), Article ID 134023, 13 pages,
doi:10.1155/2014/134023
[J11]Krüger, J., Grunzke, R., Herres-Pawlis, S., Hoffmann, A., de la Garza, L., Kohlbacher, O., Nagel, W.E., and Gesing, S. (2014)
Performance Studies on Distributed Virtual Screening
BioMed Research International, vol. 2014, Article ID 624024, 7 pages, doi:10.1155/2014/624024
[J10]Merelli, I., Pérez-Sánchez, H., Gesing, S., and D'Agostino, D. (2014)
Latest advances in distributed, parallel, and graphic processing unit accelerated approaches to computational biology
Concurrency and Computation: Practice and Experience, 26(10): 1699–1704.
[J9]Grunzke, R., Breuers, S., Gesing, S., Herres-Pawlis, S., Kruse, M., Blunk, D., de la Garza, L., Packschies, L., Schäfer, P., Schärfe, C., Schlemmer, T., Steinke, T., Schuller, B., Müller-Pfefferkorn, R., Nagel, W., Atkinson, M., and Krüger, J. (2014)
Standards-based Metadata Management for Molecular Simulations
Concurrency and Computation: Practice and Experience, 26(10): 1744–1759.
[J8]Krüger, J.*, Grunzke, R.*, Gesing, S.*, Breuers, S., Brinkmann, A., de la Garza, L., Kohlbacher, O., Kruse, M., Nagel, W.E., Packschies, L., Müller-Pfefferkorn, R., Schäfer, P., Schärfe, C., Steinke, T., Schlemmer, T., Warzecha, K., Zink, A., and Herres-Pawlis, S. (2014)
The MoSGrid Science Gateway – A Complete Solution for Molecular Simulations
Journal of Chemical Theory and Computation, 10(6): 2232–2245, DOI: 10.1021/ct500159h

2013
[J7]Packschies, L., Birkenheuer, G., Blunk, D., Breuers, S., Brinkmann, A., de la Garza, L., dos Santos Vieira, I., Fels, G., Gesing, S., Grunzke, R., Herres-Pawlis, S., Kohlbacher, O., Krüger, J., Kruse, M., Lang, U., Müller-Pfefferkorn, R., Schäfer, P., Schlemmer, T., Schärfe, C., Steinke, T., Warzecha, K., and Zink, A. (2013)
The MoSGrid-e-Science Gateway: Molecular Simulations in a Distributed Computing Environment
Journal of Cheminformatics 2013, 5(Suppl 1):O3, doi:10.1186/1758-2946-5-S1-O3

2012
[J6]Gesing, S.*, Grunzke, R.*, Krüger, J., Birkenheuer, G., Wewior, M., Schäfer, P., Schuller, B., Schuster, J., Herres-Pawlis, S., Breuers, S., Balasko, A., Kozlovszky, M., Szikszay Fabri, A., Packschies, L., Kacsuk, P., Blunk, D., Steinke, T., Brinkmann, A., Fels, G., Müller-Pfefferkorn, R., Jäkel, R., and Kohlbacher, O. (2012)
A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics
Journal of Grid Computing, 10(4):769-790.
[J5]Birkenheuer, G., Blunk, D., Breuers, S., Brinkmann, A., dos Santos Vieira, I., Fels, G., Gesing, S., Grunzke, R., Herres-Pawlis, S., Kohlbacher, O., Krüger, J., Lang, U., Packschies, L., Müller-Pfefferkorn, R., Schäfer, P., Steinke, T., Warzecha K., and Wewior, M. (2012).
MoSGrid: Efficient Data Management and a Standardized Data Exchange Format for Molecular Simulations in a Grid Environment
Journal of Cheminformatics 2012, 4(Suppl 1):P21, doi:10.1186/1758-2946-4-S1-P21

2011
[J4]Gesing, S., Hemert, J. v., Kacsuk, P. and Kohlbacher, O. (2011)
Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools.
Concurrency and Computation: Practice and Experience, 23: 223–234. DOI: http://dx.doi.org/10.1002/cpe.1687
[J3]Krüger, J., Birkenheuer, G., Blunk, D., Breuers, S., Brinkmann, A., Fels, G., Gesing, S., Grunzke, R., Kohlbacher, O., Kruber, N., Lang, U., Packschies, L., Müller-Pfefferkorn, R., Herres-Pawlis, S., Schäfer, P., Schmalz, H., Steinke, T., Warzecha, K., and Wewior, M. (2011).
Molecular simulation grid.
Journal of Cheminformatics 2011, 3(Suppl 1):O17, doi:10.1186/1758-2946-3-S1-O17
[J2]Birkenheuer, G., Blunk, D., Breuers, S., Brinkmann, A., dos Santos Vieira, I., Fels, G., Gesing, S., Grunzke, R., Herres-Pawlis, S., Kohlbacher, O., Krüger, J., Lang, U., Packschies, L., Müller-Pfefferkorn, R., Schäfer, P., Schmalz, H., Steinke, T., Warzecha, K., and Wewior, M. (2011).
A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science.
Journal of Cheminformatics 2011, 3(Suppl 1):P14, doi:10.1186/1758-2946-3-S1-P14

2009
[J1]Schneeberger, K.*, Hagmann, J.*, Ossowski, S.*, Warthmann, N., Gesing, S., Kohlbacher, O., and Weigel, D. (2009).
Simultaneous alignment of short reads against multiple genomes
Genome Biology, 10(9):R98.

[accepted] [2022] [2020] [2019] [2018] [2017] [2016] [2015] [2014] [2013] [2012] [2011] [2009]