HITS Publications

2025

• Ruiter AJ, Seitenzahl IR (2025). Type Ia supernova progenitors: a contemporary view of a long-standing puzzle, Astron Astrophys Rev 33(1),1 2052
• Knirsch L, Morel B, Stamatakis A (2025). Distanzbasierte Inferenz von Genbäumen unter Berücksichtigung ihres Speziesbaumes (Bachelor's Thesis) 1915
• Athanasiou C, Cabezudo AC, Tsengenes A, Wade RC (2025). Simulation of Neurotrophin Receptor Transmembrane Helix Interactions Reveals Active States and Distinct Signaling Mechanisms, JACS Au,jacsau.5c00174 2063
• Ferraz MV, Adan WCS, Lima TE, Santos AJ, Paula SOd, Dhalia R, Wallau GL, Wade RC, Viana IF, Lins RD (2025). Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning, PLoS Comput Biol 21(4):e1012921 2062
• Muñiz‐Chicharro A (2025). Prediction of drug-protein binding kinetics (Doctoral Thesis), Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 2057
• Amaro RE, Aqvist J, Bahar I, Battistini F, Bellaiche A, Beltran D, Biggin PC, Bonomi M, Bowman GR, Bryce RA, Bussi G, Carloni P, Case DA, Cavalli A, Chang CA, Cheatham TE3, Cheung MS, Chipot C, Chong LT, Choudhary P, Cisneros GA, Clementi C, Collepardo-Guevara R, Coveney P, Covino R, Crawford TD, Peraro MD, Groot BLd, Delemotte L, Vivo MD, Essex JW, Fraternali F, Gao J, Gelpi JL, Gervasio FL, Gonzalez-Nilo FD, Grubmuller H, Guenza MG, Guzman HV, Harris S, Head-Gordon T, Hernandez R, Hospital A, Huang N, Huang X, Hummer G, Iglesias-Fernandez J, Jensen JH, Jha S, Jiao W, Jorgensen WL, Kamerlin SCL, Khalid S, Laughton C, Levitt M, Limongelli V, Lindahl E, Lindorff-Larsen K, Loverde S, Lundborg M, Luo YL, Luque FJ, Lynch CI, MacKerell ADJ, Magistrato A, Marrink SJ, Martin H, McCammon JA, Merz K, Moliner V, Mulholland AJ, Murad S, Naganathan AN, Nangia S, Noe F, Noy A, Olah J, O'Mara ML, Ondrechen MJ, Onuchic JN, Onufriev A, Osuna S, Palermo G, Panchenko AR, Pantano S, Parish C, Parrinello M, Perez A, Perez-Acle T, Perilla JR, Pettitt BM, Pietropaolo A, Piquemal JP, Poma AB, Praprotnik M, Ramos MJ, Ren P, Reuter N, Roitberg A, Rosta E, Rovira C, Roux B, Rothlisberger U, Sanbonmatsu KY, Schlick T, Shaytan AK, Simmerling C, Smith JC, Sugita Y, Swiderek K, Taiji M, Tao P, Tieleman DP, Tikhonova IG, Tirado-Rives J, Tunon I, Kamp MWvd, Spoel Dvd, Velankar S, Voth GA, Wade R, Warshel A, Welborn VV, Wetmore SD, Wheeler TJ, Wong CF, Yang LW, Zacharias M, Orozco M (2025). The need to implement FAIR principles in biomolecular simulations., Nat Methods. 2025 Apr 2. doi: 10.1038/s41592-025-02635-0. 2049
• Mertová L, Polreich S, Lewkovski O, Müller W (2025). The BeeProject: Advanced Digitisation and Creation of a Dataset for the Monitoring of Beehives, Lukrécia Mertová, Severin Polreich, Oleg Lewkowski, and Wolfgang Müller. 2024. The BeeProject: Advanced Digitisation and Creation of a Dataset for the Monitoring of Beehives. In The 2024 ACM/IEEE Joint Conference on Digital Libraries (JCDL ’24), December 16–20, 2024, Hong Kong, China. ACM, New York, NY, USA, 11 pages. https://doi.org/10.1145/3677389.3702599 2017
• Amaral AVR, Wolffram D, Moraga P, Bracher J (2025). Post-processing and weighted combination of infectious disease nowcasts, PLOS Computational Biology, 21(3):e1012836 2048
• Pinsonneault MH, Zinn JC, Tayar J, Serenelli A, García RA, Mathur S, Vrard M, Elsworth YP, Mosser B, Stello D, Bell KJ, Bugnet L, Corsaro E, Gaulme P, Hekker S, Hon M, Huber D, Kallinger T, Cao K, Johnson JA, Liagre B, Patton RA, Santos ÂRG, Basu S, Beck PG, Beers TC, Chaplin WJ, Cunha K, Frinchaboy PM, Girardi L, Godoy-Rivera D, Holtzman JA, Jönsson H, Mészáros S, Reyes C, Rix H, Shetrone M, Smith VV, Spoo T, Stassun KG, Wang J (2025). APOKASC-3: The Third Joint Spectroscopic and Asteroseismic Catalog for Evolved Stars in the Kepler Fields, ApJS 276(2):69 2053
• Beier S, Arend D, Bauer D, Brandizi M, Brilhaus D, Chadwick E, Clemens V, Crusoe MR, Feser M, Grieb J, Hu X, Miller A, Mühlhaus T, Owen S, Rey M, Schneider G, Schneider J, Schneider K, Weil HL, Wetzels F (2025). BioHackEU24 report: Creating user benefit from ARC-ISA RO-Crate machine-actionability & Increasing FAIRness of digital agrosystem resources by extending Bioschemas, osf.io/x9d6b_v1,[Preprint] 2008
• Lau MYM, Cantiello M, Jermyn AS, MacLeod M, Mandel I, Price DJ (2025). Hot Jupiter engulfment by an early red giant in 3D hydrodynamics, A&A 694:A264 2035
• Prediction of Binding Kinetics of the Interleukin-13-Interleukin-13 Receptor alpha1 Complex (Master's Thesis), Molecular Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 2059
• Ajith P, Seoane PA, Sedda MA, Arcodia R, Badaracco F, Banerjee B, Belgacem E, Benetti G, Benetti S, Bobrick A, Bonforte A, Bortolas E, Braito V, Branchesi M, Burrows A, Cappellaro E, Ceca RD, Chakraborty C, Subrahmanya SC, Coughlin MW, Covino S, Derdzinski A, Doshi A, Falanga M, Foffa S, Franchini A, Frigeri A, Futaana Y, Gerberding O, Gill K, Giovanni MD, Giudice IF, Giustini M, Gläser P, Harms J, Heijningen Jv, Iacovelli F, Kavanagh BJ, Kawamura T, Kenath A, Keppler E, Kobayashi C, Komatsu G, Korol V, Krishnendu N, Kumar P, Longo F, Maggiore M, Mancarella M, Maselli A, Mastrobuono-Battisti A, Mazzarini F, Melandri A, Melini D, Menina S, Miniutti G, Mitra D, Morán-Fraile J, Mukherjee S, Muttoni N, Olivieri M, Onori F, Papa MA, Patat F, Perali A, Piran T, Piranomonte S, Pol AR, Pookkillath MC, Prasad R, Prasad V, Rosa AD, Chowdhury SR, Serafinelli R, Sesana A, Severgnini P, Stallone A, Tissino J, Tkalčić H, Tomasella L, Toscani M, Vartanyan D, Vignali C, Zaccarelli L, Zeoli M, Zuccarello L (2025). The Lunar Gravitational-wave Antenna: mission studies and science case, J. Cosmol. Astropart. Phys. 2025(01):108 2033
• Ulanov E, Qadir GA, Riedmiller K, Friederich P, Gräter F (2025). Predicting hydrogen atom transfer energy barriers using Gaussian process regression, Digital Discovery, 4(2):513–522 1987
• Buchwald M, Memmesheimer P, Moghadam AD, Tuschner I, Suarez LS, Itzel T, Antoni C, Daza J, Gerhards C, Neumaier M, Brochhausen C, Galle PR, Ebert M, Weinmann A, Hesser J, Heuveline V, Teufel A (2025). Comparative evaluation of standard machine learning models for liver fibrosis detection, Z Gastroenterol 63(01):e13-e13 1988
• Qadir GA, Sun Y (2025). Modeling and predicting spatio-temporal dynamics of PM_2.5 concentrations through time-evolving covariance models, Statistica Sinica, published online 1702
• Nag P, Hong Y, Abdulah S, Qadir GA, Genton MG, Sun Y (2025). Efficient large-scale nonstationary spatial covariance function estimation using convolutional neural networks, Journal of Computational and Graphical Statistics, published online 1868
• Brehmer JR, Kraus K, Gneiting T, Herrmann M, Marzocchi W (2025). Enhancing the statistical evaluation of earthquake forecasts—An application to Italy, Seismological Research Letters, published online 1893
• Ahlborn F, Bellinger EP, Hekker S, Basu S, Mokrytska D (2025). The robustness of inferred envelope and core rotation rates of red giant stars from asteroseismology, A&A 693:A274 2013
• Soultanis T, Maltsev K, Bauswein A, Chatziioannou K, Röpke FK, Stergioulas N (2025). Gravitational-wave model for neutron star merger remnants with supervised learning, Phys. Rev. D 111(2),023002 2037
• Schopmans H, Friederich P (2025). Temperature-Annealed Boltzmann Generators, arXiv,cs.LG,2501.19077 2060