2025 | |
| Ismael Kherroubi Garcia ,Christopher Erdmann,Sandra Gesing,Michael Barton,Lauren Cadwallader, Geerten Hengeveld,Christine R. Kirkpatrick,Kathryn Knight,Carsten Lemmen,Rebecca Ringuette,Qing Zhan,Melissa Harrison,Feilim Mac Gabhann,Natalie Meyers,Cailean Osborne,Charlotte Till,Paul Brenner,Matt Buys,Min Chen,Allen Lee,Jason Papin,Yuhan Rao (2025 Ten simple rules for good model-sharing practices PLOS Computational Biology 21(1): e1012702. https://doi.org/10.1371/journal.pcbi.1012702 |
2024 | |
| Wilmer Contreras-Sepúlveda, Braulio Misael Villegas-Martínez, Sandra Gesing, José Javier Sánchez-Mondragón, Juan Carlos Sánchez-Pérez, Claudia Andrea Vidales-Basurto, J. Jesús Escobedo-Alatorre, Angel David Torres-Palencia, Omar Palillero-Sandoval, Jacob Licea-Rodriguez, Néstor Lozano-Crisóstomo, Julio César García-Melgarejo, Eddie Nelson Palacios-Perez (2024) Unleashing quantum algorithms with Qinterpreter: bridging the gap between theory and practice across leading quantum computing platforms PeerJ Computer Science 10:e2318, https://doi.org/10.7717/peerj-cs.2318 |
2023 | |
| Gesing, S., Stirm, C., Klimeck, G., Zentner, L., Wang, S., Villegas Martinez, B., Moya-Cessa, H. M., Diaz Eaton, C., Donovan, S., Song, C., Zhao, L., Kim, I. L., Strachan, A., Zentner, M., Kalyanam, R. (2023) Hubzero: Community Growth for Four Science Gateways Supporting Open Science IEEE Computing in Science and Engineering | |
| Kee, K., Hayes, C., Gesing, S., Rugg, A., Bradley, S., Brandt, S. R., Meyers, N., Johnson, R. P., Dombrowski, Q. (2023) Science Gateways and the Humanities: An Exploratory Study of their Rare Partnership IEEE Computing in Science and Engineering | |
| Sandra Gesing, Ewa Deelman, Michael Hildreth, Ramandeep Makhija, Mary Ann McDowell, Natalie K. Meyers, Douglas Thain (2023) VisDict: Improving Communication via a Visual Dictionary in a Science Gateway IEEE Computing in Science and Engineering | |
| Frédéric Labbé, Maha Abdeladhim, Jenica Abrudan, Alejandra Saori Araki, Ricardo N. Araujo, Peter Arensburger, Joshua B. Benoit, Reginaldo Pecanha Brazil, Rafaela V. Bruno, Gustavo Bueno da Silva Rivas, Vinicius Carvalho de Abreu, Jason Charamis, Iliano V. Coutinho-Abreu, Samara G. da Costa-Latgé, Alistair Darby, Viv M. Dillon, Scott J. Emrich, Daniela Fernandez-Medina, Nelder Figueiredo Gontijo, Catherine M. Flanley, Derek Gatherer, Fernando A. Genta, Sandra Gesing, Gloria I. Giraldo-Calderón, Bruno Gomes, Eric Roberto Guimaraes Rocha Aguiar, James G. C. Hamilton, Omar Hamarsheh, Mallory Hawksworth, Jacob M. Hendershot, Paul V. Hickner, Jean-Luc Imler, Panagiotis Ioannidis, Emily C. Jennings, Shaden Kamhawi, Charikleia Karageorgiou, Ryan C. Kennedy, Andreas Krueger, José M. Latorre-Estivalis, Petros Ligoxygakis, Antonio Carlos A. Meireles-Filho , Patrick Minx , Jose Carlos Miranda , Michael J. Montague , Ronald J. Nowling , Fabiano Oliveira , João Ortigão-Farias , Marcio G. Pavan , Marcos Horacio Pereira , Andre Nobrega Pitaluga , Roenick Proveti Olmo , Marcelo Ramalho-Ortigao , José M. C. Ribeiro , Andrew J. Rosendale , Mauricio R.V.Sant’Anna , Steven E.Scherer , Nágila F.C.Secundino , Douglas A.Shoue , Caroline da Silva Moraes , João Silveira Moledo Gesto , Nataly Araujo Souza , Zainulabueddin Syed , Samuel Tadros , Rayane Teles-de-Freitas , Erich L.Telleria , Chad Tomlinson , Yara M.Traub-Csekö , João Trindade Marques , Zhijian Tu , Maria F.Unger , Jesus Valenzuela , Flávia V.Ferreira , Karla P.V.de Oliveira , Felipe M.Vigoder , John Vontas , Lihui Wang , Gareth D. Weedall , Elyes Zhioua , Stephen Richards , Wesley C. Warren , Robert M. Waterhouse , Rod J. Dillon , Mary Ann McDowell (2023) Genomic analysis of two phlebotomine sand fly vectors of leishmania from the new and old World PLOS Neglected Tropical Diseases, 17:4, 2023, https://doi.org/10.1371/journal.pntd.0010862 |
2022 | |
| 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 | |
| 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. Gesing S.(2022) Towards a Reference Architecture based Science Gateway Framework with Embedded E-Learning Support Concurrency and Computation: Practice & Experience |
2020 | |
| 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. | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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. | |
| 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:https://doi.org/10.1080/17460441.2019.1552936 |
2018 | |
| Katz, D. S., McInnes, L.C., Bernholdt, D.E., Mayes, A.C., Hong, Neil P. Chue, 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| Gesing, S., Wilkins-Diehr, N., Barker, M. and Pierantoni, G. (2016) Science Gateway Workshops 2015 Special Issue Conference Publications Journal of Grid Computing (2016), doi:10.1007/s10723-016-9389-4 | |
| 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 (2016), doi:10.1007/s10723-016-9385-8 | |
| 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 | |
| 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 | |
| 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 | |
| Perez-Sanchez, H., Gesing, S. and Merelli, I. (2016) Special Issue: High Performance Computing in Drug Discovery Current Drug Targets, volume 17, issue 14, pages 1578-1703, year 2016 | |
| 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 | |
| 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 | |
| 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 | |
| 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) | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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. | |
| 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. | |
| 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 | |
| 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 | |
| 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. | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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. |