HITS Publications

2022

• 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 (2022). How talin allosterically activates vinculin 1505
• Gneiting T, Walz E (2022). Receiver operating characteristic (ROC) movies, universal ROC (UROC) curves, and coefficient of predictive ability (CPA), Machine Learning, 111:2769–2797 1375
• Resin J (2022). A simple algorithm for exact multinomial tests, Journal of Computational and Graphical Statistics, published online 1504
• Liang S, Kades K, Fink M, Full P, Weber T, Kleesiek J, Strube M, Maier-Hein K (2022). Fine-tuning BERT models for summarizing German radiology findings, Proceedings of the 4th Clinical Natural Language Processing Workshop, Seattle, Washington, July 2022 1498
• Chai H, Strube M (2022). Incorporating Centering Theory into Neural Coreference Resolution, Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. Seattle, Washington, July 2022 1496
• Eriksson O, Bhalla US, Blackwell KT, Crook SM, Keller D, Kramer A, Linne M, Saudargienė A, Wade RC, Kotaleski JH (2022). Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows, eLife 11,e69013 1495
• Keulen SCv, Martin J, Colizzi F, Frezza E, Trpevski D, Diaz NC, Vidossich P, Rothlisberger U, Kotaleski JH, Wade RC, Carloni P (2022). Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain, WIREs Comput Mol Sci 1493
• Pöhner I, Quotadamo A, Panecka-Hofman J, Luciani R, Santucci M, Linciano P, Landi G, Pisa FD, Iacono LD, Pozzi C, Mangani S, Gul S, Witt G, Ellinger B, Kuzikov M, Santarem N, Cordeiro-da-Silva A, Costi MP, Venturelli A, Wade RC (2022). Multitarget, Selective Compound Design Yields Potent Inhibitors of a Kinetoplastid Pteridine Reductase 1, J. Med. Chem.,acs.jmedchem.2c00232 1494
• Bayer S, Dimitriadis T (2022). Regression-based expected shortfall backtesting, Journal of Financial Econometrics, 20(3):437–471 1405
• Gneiting T, Vogel P (2022). Receiver operating characteristic (ROC) curves: Equivalences, beta model, and minimum distance estimation, Machine Learning, 111:2147–2159 1421
• Shingles LJ, Flörs A, Sim SA, Collins CE, Röpke FK, Seitenzahl IR, Shen KJ (2022). Modelling the ionization state of Type Ia supernovae in the nebular phase, Monthly Notices of the Royal Astronomical Society 512(4):6150-6163 1488
• Jeon S, Strube M (2022). Entity-based Neural Local Coherence Modeling, In Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (ACL). Dublin, Ireland, May 2022 1471
• Brosz M, Michelarakis N, Bunz UHF, Aponte-Santamaría C, Gräter F (2022). Martini 3 coarse-grained force field for poly(para-phenylene ethynylene)s., Physical Chemistry Chemical Physics,24(17):9998-10010 1478
• Lerch S, Polsterer K (2022). Convolutional autoencoders for spatially-informed ensemble post-processing 1483
• Ernst M, Gryn'ova G (2022). Strength and Nature of Host‐Guest Interactions in Metal‐Organic Frameworks from a Quantum‐Chemical Perspective, ChemPhysChem 23(8) 1476
• Cramer EY, Ray EL, Lopez VK, Bracher J, Brennen A, Castro Rivadeneira AJ, Gerding A, Gneiting T, (282 further coauthors) , Walker JW, Slayton RB, Johansson MA, Biggerstaff M, Reich NG (2022). Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States, Proceedings of the National Academy of Sciences, 119(15):e2113561119 1475
• Liu Z, Röpke FK, Zeng Y (2022). Signatures of a Surviving Helium-star Companion in Type Ia Supernovae and Constraints on the Progenitor Companion of SN 2011fe, ApJ 928(2):146 1489
• Ondratschek PA, Röpke FK, Schneider FRN, Fendt C, Sand C, Ohlmann ST, Pakmor R, Springel V (2022). Bipolar planetary nebulae from common-envelope evolution of binary stars, A&A 660:L8 1490
• Martin I, Nava M, Wickström S, Gräter F (2022). ATP allosterically stabilizes integrin-linked kinase for efficient force generation, Proceedings of the National Academy of Sciences,119(11) 1257
• Rogdakis T, Charou D, Latorrata A, Papadimitriou E, Tsengenes A, Athanasiou C, Papadopoulou M, Chalikiopoulou C, Katsila T, Ramos I, Prousis KC, Wade RC, Sidiropoulou K, Calogeropoulou T, Gravanis A, Charalampopoulos I (2022). Development and Biological Characterization of a Novel Selective TrkA Agonist with Neuroprotective Properties against Amyloid Toxicity, Biomedicines 10(3):614 1470
• Andrassy R, Higl J, Mao H, Mocák M, Vlaykov DG, Arnett WD, Baraffe I, Campbell SW, Constantino T, Edelmann PVF, Goffrey T, Guillet T, Herwig F, Hirschi R, Horst L, Leidi G, Meakin C, Pratt J, Rizzuti F, Röpke FK, Woodward P (2022). Dynamics in a stellar convective layer and at its boundary: Comparison of five 3D hydrodynamics codes, A&A 659:A193 1472
• Lach F, Callan FP, Sim SA, Röpke FK (2022). Models of pulsationally assisted gravitationally confined detonations with different ignition conditions, A&A 659:A27 1491
• Eisenberg P, Albert L, Teuffel J, Zitzow E, Michaelis C, Jarick J, Sehlke C, Große L, Bader N, Nunes-Alves A, Kreikemeyer B, Schindelin H, Wade RC, Fiedler T (2022). The Non-phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase GapN Is a Potential New Drug Target in Streptococcus pyogenes, Front. Microbiol. 13,802427 1448
• Gómez-Flores CL, Maag D, Kansari M, Vuong V, Irle S, Gräter F, Kubař T, Elstner M (2022). Accurate Free Energies for Complex Condensed-Phase Reactions Using an Artificial Neural Network Corrected DFTB/MM Methodology., Journal of chemical theory and computation,18(2):1213-1226 1454
• Hoga Y, Dimitriadis T (2022). On testing equal conditional predictive ability under measurement error, Journal of Business & Economic Statistics, published online 1439
• Daday C, Buhr Sd, Mercadante D, Gräter F (2022). Mechanical force can enhance c-Src kinase activity by impairing autoinhibition., Biophysical Journal 1453
• Paiardi G, Richter S, Oreste P, Urbinati C, Rusnati M, Wade RC (2022). The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms, Journal of Biological Chemistry 298(2):101507 1437
• Soultanis T, Bauswein A, Stergioulas N (2022). Analytic models of the spectral properties of gravitational waves from neutron star merger remnants, Phys. Rev. D 105(4),043020 1479
• Lach F, Callan FP, Bubeck D, Röpke FK, Sim SA, Schrauth M, Ohlmann ST, Kromer M (2022). Type Iax supernovae from deflagrations in Chandrasekhar mass white dwarfs, A&A 658:A179 1492
• Martin IM, Aponte-Santamaría C, Schmidt L, Hedtfeld M, Iusupov A, Musacchio A, Gräter F (2022). Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region., Journal of Molecular Biology,434(1):167387 1438
• Jordan AI, Mühlemann A, Ziegel JF (2022). Characterizing the optimal solutions to the isotonic regression problem for identifiable functionals, Annals of the Institute of Statistical Mathematics, 74:489–514 1368
• Schulz B, Lerch S (2022). Machine learning methods for postprocessing ensemble forecasts of wind gusts: A systematic comparison, Monthly Weather Review, 150(1):235–257 1379
• Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N (2022). SPART: A versatile and standardized data exchange format for species partition information, Molecular Ecology Resources 22(1):430-438 1430
• Teuffel J (2022). Molecular Dynamics Simulation of a Mammalian Cytochrome P450 Protein and its Interaction with Substrates and Redox-Partners (Master's Thesis), Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg, 2022, Goutam Mukherjee (HITS Tutor) and Rebecca C. Wade 1445
• Battino U, Lederer-Woods C, Travaglio C, Röpke FK, Gibson B (2022). Slow White Dwarf Mergers as a New Galactic Source of Trans-Iron Elements, EPJ Web Conf. 260:06002 1469
• Keer LD, Steenberge PV, Reyniers M, Gryn'ova G, Aitken HM, Coote ML (2022). New mechanism for autoxidation of polyolefins: kinetic Monte Carlo modelling of the role of short-chain branches, molecular oxygen and unsaturated moieties, Polym. Chem.,10.1039.D1PY01659H 1477
• Plier J, Zisler M, Furkel J, Knoll M, Marx A, Fischer A, Polsterer K, Konstandin MH, Petra S (2022). Learning Features via Transformer Networks for Cardiomyocyte Profiling, Bildverarbeitung für die Medizin 2022,pp.167-172,Springer Fachmedien Wiesbaden 1481
• Srivastava A, Rastogi A, Rao A, Shoeb AAM, Abid A, Fisch A, Brown AR, Santoro A, Gupta A, Garriga-Alonso A, Kluska A, Lewkowycz A, Agarwal A, Power A, Ray A, Warstadt A, Kocurek AW, Safaya A, Tazarv A, Xiang A, Parrish A, Nie A, Hussain A, Askell A, Dsouza A, Slone A, Rahane A, Iyer AS, Andreassen A, Madotto A, Santilli A, Stuhlmüller A, Dai A, La A, Lampinen A, Zou A, Jiang A, Chen A, Vuong A, Gupta A, Gottardi A, Norelli A, Venkatesh A, Gholamidavoodi A, Tabassum A, Menezes A, Kirubarajan A, Mullokandov A, Sabharwal A, Herrick A, Efrat A, Erdem A, Karakaş A, Roberts BR, Loe BS, Zoph B, Bojanowski B, Özyurt B, Hedayatnia B, Neyshabur B, Inden B, Stein B, Ekmekci B, Lin BY, Howald B, Diao C, Dour C, Stinson C, Argueta C, Ramírez CF, Singh C, Rathkopf C, Meng C, Baral C, Wu C, Callison-Burch C, Waites C, Voigt C, Manning CD, Potts C, Ramirez C, Rivera CE, Siro C, Raffel C, Ashcraft C, Garbacea C, Sileo D, Garrette D, Hendrycks D, Kilman D, Roth D, Freeman D, Khashabi D, Levy D, González DM, Perszyk D, Hernandez D, Chen D, Ippolito D, Gilboa D, Dohan D, Drakard D, Jurgens D, Datta D, Ganguli D, Emelin D, Kleyko D, Yuret D, Chen D, Tam D, Hupkes D, Misra D, Buzan D, Mollo DC, Yang D, Lee D, Shutova E, Cubuk ED, Segal E, Hagerman E, Barnes E, Donoway E, Pavlick E, Rodola E, Lam E, Chu E, Tang E, Erdem E, Chang E, Chi EA, Dyer E, Jerzak E, Kim E, Manyasi EE, Zheltonozhskii E, Xia F, Siar F, Martínez-Plumed F, Happé F, Chollet F, Rong F, Mishra G, Winata GI, Melo Gd, Kruszewski G, Parascandolo G, Mariani G, Wang G, Jaimovitch-López G, Betz G, Gur-Ari G, Galijasevic H, Kim H, Rashkin H, Hajishirzi H, Mehta H, Bogar H, Shevlin H, Schütze H, Yakura H, Zhang H, Wong HM, Ng I, Noble I, Jumelet J, Geissinger J, Kernion J, Hilton J, Lee J, Fisac JF, Simon JB, Koppel J, Zheng J, Zou J, Kocoń J, Thompson J, Kaplan J, Radom J, Sohl-Dickstein J, Phang J, Wei J, Yosinski J, Novikova J, Bosscher J, Marsh J, Kim J, Taal J, Engel J, Alabi J, Xu J, Song J, Tang J, Waweru J, Burden J, Miller J, Balis JU, Berant J, Frohberg J, Rozen J, Hernandez-Orallo J, Boudeman J, Jones J, Tenenbaum JB, Rule JS, Chua J, Kanclerz K, Livescu K, Krauth K, Gopalakrishnan K, Ignatyeva K, Markert K, Dhole KD, Gimpel K, Omondi K, Mathewson K, Chiafullo K, Shkaruta K, Shridhar K, McDonell K, Richardson K, Reynolds L, Gao L, Zhang L, Dugan L, Qin L, Contreras-Ochando L, Morency L, Moschella L, Lam L, Noble L, Schmidt L, He L, Colón LO, Metz L, Şenel LK, Bosma M, Sap M, Hoeve Mt, Farooqi M, Faruqui M, Mazeika M, Baturan M, Marelli M, Maru M, Quintana MJR, Tolkiehn M, Giulianelli M, Lewis M, Potthast M, Leavitt ML, Hagen M, Schubert M, Baitemirova MO, Arnaud M, McElrath M, Yee MA, Cohen M, Gu M, Ivanitskiy M, Starritt M, Strube M, Swędrowski M, Bevilacqua M, Yasunaga M, Kale M, Cain M, Xu M, Suzgun M, Tiwari M, Bansal M, Aminnaseri M, Geva M, Gheini M, T MV, Peng N, Chi N, Lee N, Krakover NG, Cameron N, Roberts N, Doiron N, Nangia N, Deckers N, Muennighoff N, Keskar NS, Iyer NS, Constant N, Fiedel N, Wen N, Zhang O, Agha O, Elbaghdadi O, Levy O, Evans O, Casares PAM, Doshi P, Fung P, Liang PP, Vicol P, Alipoormolabashi P, Liao P, Liang P, Chang P, Eckersley P, Htut PM, Hwang P, Miłkowski P, Patil P, Pezeshkpour P, Oli P, Mei Q, Lyu Q, Chen Q, Banjade R, Rudolph RE, Gabriel R, Habacker R, Delgado RR, Millière R, Garg R, Barnes R, Saurous RA, Arakawa R, Raymaekers R, Frank R, Sikand R, Novak R, Sitelew R, LeBras R, Liu R, Jacobs R, Zhang R, Salakhutdinov R, Chi R, Lee R, Stovall R, Teehan R, Yang R, Singh S, Mohammad SM, Anand S, Dillavou S, Shleifer S, Wiseman S, Gruetter S, Bowman SR, Schoenholz SS, Han S, Kwatra S, Rous SA, Ghazarian S, Ghosh S, Casey S, Bischoff S, Gehrmann S, Schuster S, Sadeghi S, Hamdan S, Zhou S, Srivastava S, Shi S, Singh S, Asaadi S, Gu SS, Pachchigar S, Toshniwal S, Upadhyay S, Shyamolima , Debnath , Shakeri S, Thormeyer S, Melzi S, Reddy S, Makini SP, Lee S, Torene S, Hatwar S, Dehaene S, Divic S, Ermon S, Biderman S, Lin S, Prasad S, Piantadosi ST, Shieber SM, Misherghi S, Kiritchenko S, Mishra S, Linzen T, Schuster T, Li T, Yu T, Ali T, Hashimoto T, Wu T, Desbordes T, Rothschild T, Phan T, Wang T, Nkinyili T, Schick T, Kornev T, Telleen-Lawton T, Tunduny T, Gerstenberg T, Chang T, Neeraj T, Khot T, Shultz T, Shaham U, Misra V, Demberg V, Nyamai V, Raunak V, Ramasesh V, Prabhu VU, Padmakumar V, Srikumar V, Fedus W, Saunders W, Zhang W, Vossen W, Ren X, Tong X, Zhao X, Wu X, Shen X, Yaghoobzadeh Y, Lakretz Y, Song Y, Bahri Y, Choi Y, Yang Y, Hao Y, Chen Y, Belinkov Y, Hou Y, Hou Y, Bai Y, Seid Z, Zhao Z, Wang Z, Wang ZJ, Wang Z, Wu Z (2022). Beyond the Imitation Game: Quantifying and extrapolating the capabilities of language models, https://arxiv.org/abs/2206.04615 1499