HITS Publications

2023

• Rahman MT, Koski MK, Panecka-Hofman J, Schmitz W, Kastaniotis AJ, Wade RC, Wierenga RK, Hiltunen JK, Autio KJ (2023). An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration, Nat Commun 14(1),619 1583
• Roussaki M, Magoulas GE, Fotopoulou T, Santarem N, Barrias E, Pöhner I, Luelmo S, Afroudakis P, Georgikopoulou K, Nevado PT, Eick J, Bifeld E, Corral MJ, Jiménez-Antón MD, Ellinger B, Kuzikov M, Fragiadaki I, Scoulica E, Gul S, Clos J, Prousis KC, Torrado JJ, Alunda JM, Wade RC, Souza Wd, Silva ACd, Calogeropoulou T (2023). Design, synthesis and biological evaluation of antiparasitic dinitroaniline-ether phospholipid hybrids, Bioorganic Chemistry 138:106615 1677
• Franz F, Tapia-Rojo R, Winograd-Katz S, Boujemaa-Paterski R, Li W, Unger T, Albeck S, Aponte-Santamaría C, Garcia-Manyes S, Medalia O, Geiger B, Gräter F (2023). Allosteric activation of vinculin by talin, Nat Commun 14, 4311 (2023) 1505
• Fedorov R, Gryn’ova G (2023). Unlocking the Potential: Predicting Redox Behavior of Organic Molecules, from Linear Fits to Neural Networks, J. Chem. Theory Comput.,acs.jctc.3c00355 1685
• Fatima M, Strube M (2023). Cross-lingual Science Journalism: Select, Simplify and Rewrite Summaries for Non-expert Readers, Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics, Toronto, Ontario, Canada, July 2023 1678
• Liu W, Fu X, Strube M (2023). Modeling Structural Similarities between Documents for Coherence Assessment with Graph Convolutional Networks, Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics, Toronto, Ontario, Canada, July 2023 1679
• Liu W, Strube M (2023). Annotation-Inspired Implicit Discourse Relation Classification with Auxiliary Discourse Connective Generation, Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics, Toronto, Ontario, Canada, July 2023 1680
• Kirschner M, Golebiewski M, Moser H, consortium E, 5 I2 (2023). ISO/TS 9491-1:2023 Biotechnology — Predictive computational models in personalized medicine research — Part 1: Constructing, verifying and validating models, ISO/TS 9491-1:2023 Biotechnology — Predictive computational models in personalized medicine research — Part 1: Constructing, verifying and validating models. International Organization for Standardization (ISO), Geneva, Switzerland. https://www.iso.org/standard/83516.html 1668
• Llenga S, Gryn’ova G (2023). Matrix of orthogonalized atomic orbital coefficients representation for radicals and ions, The Journal of Chemical Physics 158(21),214116 1682
• Gomez GM, D’Arrigo G, Sanchez CP, Berger F, Wade RC, Lanzer M (2023). PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport, PLoS Pathog 19(6):e1011436 1683
• Lahén N, Naab T, Kauffmann G, Szécsi D, Hislop JM, Rantala A, Kozyreva A, Walch S, Hu C (2023). Formation of star clusters and enrichment by massive stars in simulations of low-metallicity galaxies with a fully sampled initial stellar mass function, Monthly Notices of the Royal Astronomical Society 522(2):3092-3116 1664
• Resin J (2023). From classification accuracy to proper scoring rules: Elicitability of probabilistic top list predictions, Journal of Machine Learning Research, 24(173):1–21 1681
• Ernst M, Gryn'ova G (2023). Engineering Host–Guest Interactions in Organic Framework Materials for Drug Delivery, Helvetica Chimica Acta,e202300013 1675
• Zhao W, Strube M, Eger S (2023). DiscoScore: Evaluating text generation with BERT and discourse coherence, Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics, Dubrovnik, Croatia, May 2023, pp.3865-3883 1588
• Resin J (2023). A simple algorithm for exact multinomial tests, Journal of Computational and Graphical Statistics, 32(2):539–550 1504
• Muñiz‐Chicharro A, Votapka LW, Amaro RE, Wade RC (2023). Brownian dynamics simulations of biomolecular diffusional association processes, WIREs Comput Mol Sci 13(3),e1649 1555
• Schulze S, Fransson C, Kozyreva A, Chen T, Yaron O, Jerkstrand A, Gal-Yam A, Sollerman J, Yan L, Kangas T, Leloudas G, Omand CM, Smartt SJ, Yang Y, Nicholl M, Sarin N, Yao Y, Brink TG, Sharon A, Rossi A, Chen P, Chen Z, Cikota A, De K, Drake AJ, Filippenko AV, Fremling C, Freour L, Fynbo JPU, Ho AY, Inserra C, Irani I, Kuncarayakti H, Lunnan R, Mazzali P, Ofek EO, Palazzi E, Perley DA, Pursiainen M, Rothberg B, Shingles LJ, Smith K, Taggart K, Tartaglia L, Zheng W, Anderson JP, Cassara L, Christensen E, Djorgovski SG, Galbany L, Gkini A, Graham MJ, Gromadzki M, Groom SL, Hiramatsu D, Howell DA, Kasliwal MM, McCully C, Müller-Bravo TE, Paiano S, Paraskeva E, Pessi PJ, Polishook D, Rau A, Rigault M, Rusholme B (2023). 1100 Days in the Life of the Supernova 2018ibb – the Best Pair-Instability Supernova Candidate, to date, arXiv e-prints:arXiv:2305.05796 1661
• Ono M, Nozawa T, Nagataki S, Kozyreva A, Orlando S, Miceli M, Chen K (2023). The impact of effective matter mixing based on three-dimensional hydrodynamical models on the molecule formation in the ejecta of SN 1987A, arXiv e-prints:arXiv:2305.02550 1662
• Schulze S, Fransson C, Kozyreva A, Chen T, Yaron O, Jerkstrand A, Gal-Yam A, Sollerman J, Yan L, Kangas T, Leloudas G, Omand CM, Smartt SJ, Yang Y, Nicholl M, Sarin N, Yao Y, Brink TG, Sharon A, Rossi A, Chen P, Chen Z, Cikota A, De K, Drake AJ, Filippenko AV, Fremling C, Freour L, Fynbo JP, Ho AY, Inserra C, Irani I, Kuncarayakti H, Lunnan R, Mazzali P, Ofek EO, Palazzi E, Perley DA, Pursiainen M, Rothberg B, Shingles LJ, Smith K, Taggart K, Tartaglia L, Zheng W, Anderson JP, Cassara L, Christensen E, Djorgovski SG, Galbany L, Gkini A, Graham MJ, Gromadzki M, Groom SL, Hiramatsu D, Howell DA, Kasliwal MM, McCully C, Müller-Bravo TE, Paiano S, Paraskeva E, Pessi PJ, Polishook D, Rau A, Rigault M, Rusholme B (2023). 1100 Days in the Life of the Supernova 2018ibb – the Best Pair-Instability Supernova Candidate, to date, arXiv e-prints:arXiv:2305.05796 1663
• Dimitriadis G, Maguire K, Karambelkar VR, Lebron RJ, Liu C, Kozyreva A, Miller AA, Ridden-Harper R, Anderson JP, Chen T, Coughlin M, Valle MD, Drake A, Galbany L, Gromadzki M, Groom SL, Gutiérrez CP, Ihanec N, Inserra C, Johansson J, Müller-Bravo TE, Nicholl M, Polin A, Rusholme B, Schulze S, Sollerman J, Srivastav S, Taggart K, Wang Q, Yang Y, Young DR (2023). SN 2021zny: an early flux excess combined with late-time oxygen emission suggests a double white dwarf merger event, Monthly Notices of the Royal Astronomical Society 521(1):1162-1183 1665
• Haupt S (2023). Mathematical modeling of Lynch syndrome carcinogenesis (Doctoral Thesis) 1658
• Bracher J, Koster N, Krüger F, Lerch S (2023). Learning to forecast: The Probabilistic Time Series Forecasting Challenge, The American Statistician, published online 1660
• Wittner R, Holub P, Mascia C, Frexia F, Müller H, Plass M, Allocca C, Betsou F, Burdett T, Cancio I, Chapman A, Chapman M, Courtot M, Curcin V, Eder J, Elliot M, Exter K, Goble C, Golebiewski M, Kisler B, Kremer A, Leo S, Lin‐Gibson S, Marsano A, Mattavelli M, Moore J, Nakae H, Perseil I, Salman A, Sluka J, Soiland‐Reyes S, Strambio‐De‐Castillia C, Sussman M, Swedlow JR, Zatloukal K, Geiger J (2023). Toward a common standard for data and specimen provenance in life sciences, Learning Health Systems,e10365 1655
• Nunez FP, Gianniotis N, Polsterer K (2023). A Gaussian process cross-correlation approach to time-delay estimation in active galactic nuclei, A&A 1657
• Rennekamp B, Karfusehr C, Kurth M, Ünal A, Riedmiller K, Gryn’ova G, Hudson DM, Gräter F (2023). Collagen breaks at weak sacrificial bonds taming its mechanoradicals, Nat Commun 14, 2075 (2023). 1540
• Kutzki F, Butera D, Lay AJ, Maag D, Chiu J, Woon H, Kubař T, Elstner M, Aponte-Santamaría C, Hogg PJ, Gräter F (2023). Disulfide Bond Reduction and Exchange in von-Willebrand-Factor’s C4-Domain Undermines Platelet Binding, Journal of Thrombosis and Haemostasis (2023). 1651
• Dupuy A, Santamaría CA, Yeheskel A, Hortle E, Oehlers SH, Gräter F, Hogg PJ, Passam FH, Chiu J (2023). Mechano-Redox Control of Macrophage-1 Antigen De-Adhesion From ICAM-1 (Intercellular Adhesion Molecule 1) by Protein Disulfide Isomerase Promotes Directional Movement Under Flow, Circulation Research (2023). 1652
• Kurth M, Barayeu U, Gharibi H, Kuzhelev A, Riedmiller K, Zilke J, Noack K, Denysenkov V, Kappl R, Prisner TF, Zubarev RA, Dick TP, Gräter F (2023). DOPA Residues Endow Collagen with Radical Scavenging Capacity, Angew. Chem. Int. Ed. 2023, e202216610 1566
• Dimitriadis T, Liu X, Schnaitmann J (2023). Encompassing tests for value at risk and expected shortfall multistep forecasts based on inference on the boundary, Journal of Financial Econometrics, 21(2):412–444 1381
• Hoga Y, Dimitriadis T (2023). On testing equal conditional predictive ability under measurement error, Journal of Business & Economic Statistics, 41(2):364–376 1439
• Djorgovski S, Mahabal A, Graham M, Polsterer K, Krone-Martins A (2023). Applications of AI in Astronomy 1622
• Dudas D, Wittig U, Rey M, Weidemann A, Muller W (2023). Improved insights into the SABIO-RK database via visualization., Database (Oxford). 2023 Mar 31;2023:baad011. doi: 10.1093/database/baad011. 1656
• Diedrich L, Brosz M, Abele T, Steinke S, Gräter F, Göpfrich K, Aponte-Santamaría C (2023). Energetics and kinetics of membrane permeation of photoresists for bioprinting, bioRxiv 1676
• Tempest KI, Craig GC, Brehmer JR (2023). Convergence of forecast distributions in a 100,000‐member idealised convective‐scale ensemble, Quarterly Journal of the Royal Meteorological Society, 149(752):677–702 1569
• Ahadova A, Stenzinger A, Seppälä T, Hüneburg R, Kloor M, Bläker H, Wittemann J, Endris V, Gerling L, Bertram V, Neumuth MT, Witt J, Graf S, Kristiansen G, Hommerding O, Haupt S, Zeilmann A, Heuveline V, Kazdal D, Gebert J, Doeberitz MvK, Mecklin J, Nattermann J (2023). A “two-in-one hit” model of shortcut carcinogenesis in MLH1 Lynch syndrome carriers, Gastroenterology 1639
• Gneiting T, Wolffram D, Resin J, Kraus K, Bracher J, Dimitriadis T, Hagenmeyer V, Jordan AI, Lerch S, Phipps K, Schienle M (2023). Model diagnostics and forecast evaluation for quantiles, Annual Review of Statistics and Its Application, 10:597–621 1549
• Perez S, Makshakova O, Angulo J, Bedini E, Bisio A, Paz JLd, Fadda E, Guerrini M, Hricovini M, Hricovini M, Lisacek F, Nieto PM, Pagel K, Pairardi G, Richter R, Samsonov SA, Vivès RA, Nikitovic D, Blum SR (2023). Glycosaminoglycans: What Remains To Be Deciphered?, JACS Au,jacsau.2c00569 1636
• Gneiting T, Lerch S, Schulz B (2023). Probabilistic solar forecasting: Benchmarks, post-processing, verification, Solar Energy, 252:72–80 1571
• Dominguez-Valentin M, Haupt S, Seppälä TT, Sampson JR, Sunde L, Bernstein I, Jenkins MA, Engel C, Aretz S, Nielsen M, Capella G, Balaguer F, Evans DG, Burn J, Holinski-Feder E, Bertario L, Bonanni B, Lindblom A, Levi Z, Macrae F, Winship I, Plazzer J, Sijmons R, Laghi L, Valle AD, Heinimann K, Dębniak T, Fruscio R, Lopez-Koestner F, Alvarez-Valenzuela K, Katz LH, Laish I, Vainer E, Vaccaro C, Carraro DM, Monahan K, Half E, Stakelum A, Winter D, Kennelly R, Gluck N, Sheth H, Abu-Freha N, Greenblatt M, Rossi BM, Bohorquez M, Cavestro GM, Lino-Silva LS, Horisberger K, Tibiletti MG, Nascimento Id, Thomas H, Rossi NT, Silva LAd, Zaránd A, Ruiz-Bañobre J, Heuveline V, Mecklin J, Pylvänäinen K, Renkonen-Sinisalo L, Lepistö A, Peltomäki P, Therkildsen C, Madsen MG, Burgdorf SK, Hopper JL, Win AK, Haile RW, Lindor N, Gallinger S, Marchand LL, Newcomb PA, Figueiredo J, Buchanan DD, Thibodeau SN, Doeberitz MvK, Loeffler M, Rahner N, Schröck E, Steinke-Lange V, Schmiegel W, Vangala D, Perne C, Hüneburg R, Redler S, Büttner R, Weitz J, Pineda M, Duenas N, Vidal JB, Moreira L, Sánchez A, Hovig E, Nakken S, Green K, Lalloo F, Hill J, Crosbie E, Mints M, Goldberg Y, Tjandra D, Broeke SWt, Kariv R, Rosner G, Advani SH, Thomas L, Shah P, Shah M, Neffa F, Esperon P, Pavicic W, Torrezan GT, Bassaneze T, Martin CA, Moslein G, Moller P (2023). Mortality by age, gene and gender in carriers of pathogenic mismatch repair gene variants receiving surveillance for early cancer diagnosis and treatment: a report from the prospective Lynch syndrome database, eClinicalMedicine:101909 1644
• Konig M, Gleeson P, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Schreiber F (2023). Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022., J Integr Bioinform. 2023 Mar 29;20(1):20230004. doi: 10.1515/jib-2023-0004. eCollection 2023 Mar 1. 1654
• Moran-Fraile J, Schneider F, Roepke F, Ohlmann S, Pakmor R, Soultanis T, Bauswein A (2023). Gravitational wave emission from dynamical stellar interactions, A&A 1643
• Cabezudo AC, Athanasiou C, Tsengenes A, Wade RC (2023). Scaling Protein–Water Interactions in the Martini 3 Coarse-Grained Force Field to Simulate Transmembrane Helix Dimers in Different Lipid Environments, J. Chem. Theory Comput.,acs.jctc.2c00950 1635
• Müller W, Mertova L (2023). ReStoRunT: Simple Recording, Storing, Running and Tracing changes in Spreadsheets, In: König-Ries, B., Scherzinger, S., Lehner, W. & Vossen, G. (Hrsg.), BTW 2023. Gesellschaft für Informatik e.V.. DOI: 10.18420/BTW2023-57 1666
• Ehret T, Heißenberg T, Buhr Sd, Aponte-Santamaría C, Steinem C, Gräter F (2023). FERM domains recruit ample PI(4,5)P2s to form extensive protein-membrane attachments, Biophysical Journal 1649
• Buhr J, Franz F, Gräter F (2023). Intrinsically disordered region of talin’s FERM domain functions as an initial PIP2 recognition site, Biophysical Journal 1650
• Riedmiller K, Reiser P, Bobkova E, Maltsev K, Gryn'ova G, Friederich P, Gräter F (2023). Predicting reaction barriers of hydrogen atom transfer in proteins, ChemRxiv 1621
• Lauterbach S, Dienhart H, Range J, Malzacher S, Sporing JD, Rother D, Pinto MF, Martins P, Lagerman CE, Bommarius AS, Host AV, Woodley JM, Ngubane S, Kudanga T, Bergmann FT, Rohwer JM, Iglezakis D, Weidemann A, Wittig U, Kettner C, Swainston N, Schnell S, Pleiss J (2023). EnzymeML: seamless data flow and modeling of enzymatic data., Nat Methods. 2023 Feb 9. doi: 10.1038/s41592-022-01763-1. 1612
• Nuñez FP, Bruckmann C, Desamutara S, Czerny B, Panda S, Lobban AP, Pietrzyński G, Polsterer KL (2023). Modeling photometric reverberation mapping data for the next generation of big data surveys. Quasar accretion disks sizes with the LSST, Monthly Notices of the Royal Astronomical Society,stad286 1630
• Maltsev K (2023). Stellar gravitational collapse, singularity formation and theory breakdown, The Sixteenth Marcel Grossmann Meeting,pp.3596-3625,WORLD SCIENTIFIC 1608
• Röpke FK, Lach F, Gronow S, Sim SA, Callan FP, Collins CE (2023). Modeling Type Ia supernovae with explosions in white dwarfs near and below the Chandrasekhar mass, The Sixteenth Marcel Grossmann Meeting,pp.4420-4426,WORLD SCIENTIFIC 1610
• Csörnyei G, Vogl C, Taubenberger S, Flörs A, Blondin S, Cudmani MG, Holas A, Kressierer S, Leibundgut B, Hillebrandt W (2023). Family dispute: do Type IIP supernova siblings agree on their distance?, Astronomy and Astrophysics - A&A 1611
• Schweder F (2023). Probabilistic Modelling of Time Series for explorative Big Data Analysis in Astronomy (Master's Thesis) 1626
• Czerny B, Cao S, Jaiswal VK, Karas V, Khadka N, Martínez-Aldama ML, Naddaf MH, Panda S, Nuñez FP, Prince R, Ratra B, Sniegowska M, Yu Z, Zajaček M (2023). Accretion disks, quasars and cosmology: meandering towards understanding, Astrophys Space Sci 368(2),8 1628
• Zaunseder E, Mütze U, Garbade SF, Haupt S, Feyh P, Hoffmann GF, Heuveline V, Kölker S (2023). Machine Learning Methods Improve Specificity in Newborn Screening for Isovaleric Aciduria, Metabolites 13(2):304 1631
• Criswell AW, Miller J, Woldemariam N, Soultanis T, Bauswein A, Chatziioannou K, Coughlin MW, Jones G, Mandic V (2023). Hierarchical Bayesian method for constraining the neutron star equation of state with an ensemble of binary neutron star postmerger remnants, Phys. Rev. D 107(4),043021 1641
• Ehlert C, Piras A, Schleicher J, Gryn’ova G (2023). Metal-Free Molecular Catalysts for the Oxygen Reduction Reaction: Electron Affinity as an Activity Descriptor, J. Phys. Chem. Lett. 14(2):476-480 1568
• Ernst M, Poręba T, Gnägi L, Gryn’ova G (2023). Locating Guest Molecules inside Metal–Organic Framework Pores with a Multilevel Computational Approach, J. Phys. Chem. C 127(1):523-531 1567
• Keulen SCv, Martin J, Colizzi F, Frezza E, Trpevski D, Diaz NC, Vidossich P, Rothlisberger U, Kotaleski JH, Wade RC, Carloni P (2023). Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain, WIREs Comput Mol Sci 13(1) 1493
• Kaeser M (2023). Computational Investigation of the Structure Kinetics Relationship of Small-Molecule Compounds Binding the Histamine-1-Receptor (Master's Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg, 2022, Giulia D’Arrigo and Rebecca C. Wade (HITS Tutor) 1582
• Cornelio C, Stuehmer J, Hu SX, Hospedales T (2023). Learning where and when to reason in neuro-symbolic inference, In International Conference on Learning Representations 1596
• Schröter J, Dattner T, Hüllein J, Jayme A, Heuveline V, Hoffmann GF, Kölker S, Lenz D, Opladen T, Popp B, Schaaf CP, Staufner C, Syrbe S, Uhrig S, Hübschmann D, Brennenstuhl H (2023). aRgus: Multilevel visualization of non-synonymous single nucleotide variants & advanced pathogenicity score modeling for genetic vulnerability assessment, Computational and Structural Biotechnology Journal 21:1077-1083 1613
• Leaman R, Islamaj R, Adams V, Alliheedi MA, Almeida JR, Antunes R, Bevan R, Chang Y, Erdengasileng A, Hodgskiss M, Ida R, Kim H, Li K, Mercer RE, Mertová L, Mobasher G, Shin H, Sung M, Tsujimura T, Yeh W, Lu Z (2023). Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII, Database 2023,baad005 1642
• Chavhan R, Gouk H, Stuehmer J, Heggan C, Yaghoobi M, Hospedales T (2023). Amortised Invariance Learning for Contrastive Self-Supervision, In The Eleventh International Conference on Learning Representations 1653
• Mobasher G, Müller W, Krebs O, Gertz M (2023). WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with Cost-sensitive Learning, Ghadeer Mobasher, Wolfgang Müller, Olga Krebs, and Michael Gertz. 2023. WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with Cost-sensitive Learning. In The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, pages 427–438, Toronto, Canada. Association for Computational Linguistics. 1684
• Remme R, Kaczun T, Scheurer M, Dreuw A, Hamprecht FA (2023). KineticNet: Deep learning a transferable kinetic energy functional for orbital-free density functional theory, arXiv,physics.chem-ph,2305.13316 1688