HITS Publications

2016

• Jones S, Andrassy R, Sandalski S, Davis A, Woodward P, Herwig F (2016). Idealized hydrodynamic simulations of turbulent oxygen-burning shell convection in 4pi geometry, Mon. Not. R. Astron. Soc. 465(3):2991-3010 288
• Zakhartsev M, Medvedeva I, Orlov Y, Akberdin I, Krebs O, Schulze WX (2016). Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation, BMC Plant Biol 16(1) 29
• Tong R, Wade RC, Bruce NJ (2016). Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties, Proteins 84(12):1844-1858 171
• Touré V, Mazein A, Waltemath D, Balaur I, Saqi M, Henkel R, Pellet J, Auffray C (2016). STON: exploring biological pathways using the SBGN standard and graph databases., BMC Bioinformatics 17(1) 202
• Kugler SD, Gianniotis N, Polsterer KL (2016). A spectral model for multimodal redshift estimation, 2016 IEEE Symposium Series on Computational Intelligence (SSCI),pp.1-8,IEEE 473
• Gryn’ova G, Corminboeuf C (2016). Implications of Charge Penetration for Heteroatom-Containing Organic Semiconductors, J. Phys. Chem. Lett. 7(24):5198-5204 504
• Sadiq SK (2016). Reaction–diffusion basis of retroviral infectivity, Phil. Trans. R. Soc. A 374:20160148 169
• Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D (2016). Notions of similarity for systems biology models., Brief Bioinform:bbw090 198
• Polsterer K (2016). Dealing with Uncertain Multimodal Photometric Redshift Estimations, Proc. IAU 12(S325):156-165. 2016 106
• Disanto A (2016). Uncertain Photometric Redshifts with Deep Learning Methods, IAU Symposium, Astroinformatics, vol. 325, Eds: Brescia, M. and Djorgovski, G. and Feigelson, E. and Longo, G. and S. Cavuoti, eds., Oct 2016 107
• Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016). VSEARCH: a versatile open source tool for metagenomics, PeerJ, 4:e2584, Oct 2016 123
• Polsterer KL (2016). Dealing with Uncertain Multimodal Photometric Redshift Estimations., Proc. IAU 12(S325):156-165 208
• Crawford E, Norris R, Polsterer K (2016). WTF? Discovering the Unexpected in next-generation radio continuum surveys, In Astronomical Data Analysis Software an Systems XXV (ADASS XXV), vol. 496 of Astronomical Society of the Pacific Conference Series, Eds: Taylor, A. R. and Rosolowsky, E., Sep 2016 105
• Polsterer K, Gieseke F (2016). Probability Density Functions for Astronomy, In Astronomical Data Analysis Software an Systems XXV (ADASS XXV), vol. 496 of Astronomical Society of the Pacific Conference Series, Eds: Taylor, A. R. and Rosolowsky, E., Sep 2016 108
• Lensink MF, Velankar S, Kryshtafovych A, Huang S, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Lee GR, Seok C, Qin S, Zhou H, Ritchie DW, Maigret B, Devignes M, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, Zundert Gv, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim H, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Carpio CAD, Ichiishi E, Marze N, Kuroda D, Burman SSR, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ (2016). Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment, Proteins 84:323-348 180
• Jones S, Röpke FK, Pakmor R, Seitenzahl IR, Ohlmann ST, Edelmann PVF (2016). Do electron-capture supernovae make neutron stars?. First multidimensional hydrodynamic simulations of the oxygen deflagration, A&A 593:A72 433
• Ozboyaci M, Martinez M, Wade RC (2016). An efficient low storage and memory treatment of gridded interaction fields for simulations of macromolecular association, J. Chem. Theory Comput. 12(9):4563-4577 173
• Öztürk MA, Pachov GV, Wade RC, Cojocaru V (2016). Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome, Nucleic Acids Res 44(14):6599-6613 176
• Ohlmann ST, Röpke FK, Pakmor R, Springel V, Müller E (2016). Magnetic Field Amplification During the Common Envelope Phase, Mon. Not. R. Astron. Soc: Lett. 462(1):L121-L125 431
• Borsari C, Luciani R, Pozzi C, Poehner I, Henrich S, Trande M, Cordeiro-da-Silva A, Santarem N, Baptista C, Tait A, Pisa FD, Iacono LD, Landi G, Gul S, Wolf M, Kuzikov M, Ellinger B, Reinshagen J, Witt G, Gribbon P, Kohler M, Keminer O, Behrens B, Costantino L, Nevado PT, Bifeld E, Eick J, Clos J, Torrado J, Jiménez-Antón MD, Corral MJ, Alunda JM, Pellati F, Wade RC, Ferrari S, Mangani S, Costi MP (2016). Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs, J. Med. Chem. 59(16):7598-7616 174
• Bulla M, Sim SA, Kromer M, Seitenzahl IR, Fink M, Ciaraldi-Schoolmann F, Röpke FK, Hillebrandt W, Pakmor R, Ruiter AJ, Taubenberger S (2016). Predicting polarization signatures for double-detonation and delayed-detonation models of Type Ia supernovae, Mon. Not. R. Astron. Soc. 462(1):1039-1056 432
• Schibich D, Gloge F, Pöhner I, Björkholm P, Wade RC, Heijne Gv, Bukau B, Kramer G (2016). Global profiling of SRP interaction with nascent polypeptides, Nature 536(7615):219-223 172
• Seitenzahl IR, Kromer M, Ohlmann ST, Ciaraldi-Schoolmann F, Marquardt K, Fink M, Hillebrandt W, Pakmor R, Röpke FK, Ruiter AJ, Sim SA, Taubenberger S (2016). Three-dimensional simulations of gravitationally confined detonations compared to observations of SN 1991T, A&A 592:A57 426
• Mendoza-Temis JJ, Wu MR, Martínez-Pinedo G, Langanke K, Bauswein A, Janka H, Frank A (2016). On the robustness of the r-process in neutron-star mergers against variations of nuclear masses, J. Phys.: Conf. Ser. 730:012018 436
• Pignatari M, Herwig F, Hirschi R, Bennett M, Rockefeller G, Fryer C, Timmes FX, Ritter C, Heger A, Jones S, Battino U, Dotter A, Trappitsch R, Diehl S, Frischknecht U, Hungerford A, Magkotsios G, Travaglio C, Young P (2016). NuGrid Stellar Data Set. I.Stellar Yields from H to Bi for Stars with Metallicities Z = 0.02 and Z = 0.01, ApJS 225(2):24 438
• Stank A, Richter S, Wade RC (2016). ProSAT+: visualizing sequence annotations on 3D structure, Protein Engineering, Design and Selection 29(8):281-284 178
• Posch S, Aponte-Santamaría C, Schwarzl R, Karner A, Radtke M, Gräter F, Obser T, König G, Brehm MA, Gruber HJ, Netz RR, Baldauf C, Schneppenheim R, Tampé R, Hinterdorfer P (2016). Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor., Data Brief 8:1080-7 1121
• Ehm W (2016). Reproducibility from the perspective of meta-analysis, In Reproducibility: Principles, Problems, Practices, and Prospects, Eds: Atmanspacher H, Maasen S, Wiley, Hoboken, pp. 141–167 129
• Dugard CK, Mertz RA, Rayon C, Mercadante D, Hart C, Benatti MR, Olek AT, SanMiguel PJ, Cooper BR, Reiter W, McCann MC, Carpita NC (2016). The Cell Wall Arabinose-Deficient Arabidopsis thaliana Mutant murus5 Encodes a Defective Allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2, Plant Physiol. 171(3):1905-1920 165
• Wild K, Bange G, Motiejunas D, Kribelbauer J, Hendricks A, Segnitz B, Wade RC, Sinning I (2016). Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex, Journal of Molecular Biology 428(14):2880-2897 177
• Ohlmann ST (2016). Hydrodynamics of the Common Envelope Phase in Binary Stellar Evolution (Doctoral Thesis), Ruprecht-Karls-Universität Heidelberg, 2016, available at http://www.ub.uni-heidelberg.de/archiv/21513 441
• Rosales AB (2016). Low Mach Number Simulations of Convective Boundary Mixing in Classical Novae (Doctoral Thesis), Julius-Maximilians-Universität Würzburg, 2016, available at https://opus.uni-wuerzburg.de/opus4-wuerzburg/frontdoor/index/index/docId/13286 442
• Simon GB, Burger M, Hartnick T, Iozzi A, Wienhard A (2016). On order-preserving representations, Journal of the London Mathematical Society 94(2):525-544 897
• Côté B, Ritter C, O’Shea BW, Herwig F, Pignatari M, Jones S, Fryer CL (2016). Uncertainties in Galactic Chemical Evolution Models, ApJ 824(2):82 439
• Resch B, Summa A, Zeile P, Strube M (2016). Citizen-centric urban planning through extracting emotion information from Twitter in an interdisciplinary space-time-linguistics algorithm, UP 1(2):114 196
• Schoch N, Kißler F, Stoll M, Engelhardt S, Simone Rd, Wolf I, Bendl R, Heuveline V (2016). Comprehensive patient-specific information preprocessing for cardiac surgery simulations, Int J CARS 11(6):1051-1059 147
• Gianniotis N, Kügler SD, Tiňo P, Polsterer KL (2016). Model-coupled autoencoder for time series visualisation, Neurocomputing 192:139-146 472
• Terada Y, Maeda K, Fukazawa Y, Bamba A, Ueda Y, Katsuda S, Enoto T, Takahashi T, Tamagawa T, Röpke FK, Summa A, Diehl R (2016). Measurements of the Soft Gamma-Ray Emission from SN2014J with Suzaku, ApJ 823(1):43 429
• Kromer M, Fremling C, Pakmor R, Taubenberger S, Amanullah R, Cenko SB, Fransson C, Goobar A, Leloudas  , Taddia F, Röpke FK, Seitenzahl IR, Sim SA, Sollerman J (2016). The peculiar Type Ia supernova iPTF14atg: Chandrasekhar-mass explosion or violent merger?, Mon. Not. R. Astron. Soc. 459(4):4428-4439 430
• Subramanian SR, Singam ERA, Berinski M, Subramanian V, Wade RC (2016). Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen, J. Phys. Chem. B 120(33):8580-8589 179
• Magee MR, Kotak R, Sim SA, Kromer M, Rabinowitz D, Smartt SJ, Baltay C, Campbell HC, Chen T, Fink M, Gal-Yam A, Galbany L, Hillebrandt W, Inserra C, Kankare E, Guillou LL, Lyman JD, Maguire K, Pakmor R, Röpke FK, Ruiter AJ, Seitenzahl IR, Sullivan M, Valenti S, Young DR (2016). The type Iax supernova, SN 2015H. A white dwarf deflagration candidate, A&A 589:A89 428
• Gianniotis N, Schnörr C, Molkenthin C, Bora SS (2016). Approximate variational inference based on a finite sample of Gaussian latent variables, Pattern Anal Applic 19(2):475-485 471
• Pöhner IA, Panecka J, Wade RC (2016). What determines docking performance in drug discovery? A case study of PTR1, an anti-parasitic target, Journal of Cheminformatics 2016, 8(Suppl 1):P46 553
• Clark JA, Bauswein A, Stergioulas N, Shoemaker D (2016). Observing gravitational waves from the post-merger phase of binary neutron star coalescence, Class. Quantum Grav. 33(8):085003 437
• Stank A, Kokh DB, Fuller JC, Wade RC (2016). Protein Binding Pocket Dynamics, Acc. Chem. Res. 49(5):809-815 181
• Nickerson D, Atalag K, Bono Bd, Geiger J, Goble C, Hollmann S, Lonien J, Müller W, Regierer B, Stanford NJ, Golebiewski M, Hunter P (2016). The Human Physiome: how standards, software, and innovative service infrastructures are providing the building blocks to make it achievable., Interface Focus 6(2):20150103 200
• Bromberger M, Bastian P, Bergeest J, Conrad C, Heuveline V, Rohr K, Karl W (2016). FPGA-accelerated Richardson-Lucy Deconvolution for 3D Image Data, In Proceedings International Symposium on Biomedical Imaging (ISBI), pp. Prague, Czech Republic, Apr 2016 68
• Bromberger M, Karl W, Heuveline V (2016). Reducing Energy Consumption of Data Transfers using Runtime Data Type Conversion, In Proceedings Conference on Architecture of Computing Systems - ARCS, Nuremberg, Germany, Apr 2016 69
• Ruiz-Lapuente P, The L, Hartmann DH, Ajello M, Canal R, Röpke FK, Ohlmann ST, Hillebrandt W (2016). The Origin of the Cosmic Gamma-ray Background in the MeV Range, ApJ 820(2):142 425
• Panov IV, Korneev IY, Blinnikov SI, Röpke F (2016). Neutron excess number and nucleosynthesis of heavy elements in a type Ia supernova explosion, Jetp Lett. 103(7):431-434 427
• Gdynia G, Sauer SW, Kopitz J, Fuchs D, Duglova K, Ruppert T, Miller M, Pahl J, Cerwenka A, Enders M, Mairbäurl H, Kamiński MM, Penzel R, Zhang C, Fuller JC, Wade RC, Benner A, Chang-Claude J, Brenner H, Hoffmeister M, Zentgraf H, Schirmacher P, Roth W (2016). The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration, Nat Commun 7(1),10764 735
• Fetzer A, Metzger J, Katic D, März K, Wagner M, Philipp P, Engelhardt S, Weller T, Zelzer S, Franz AM, Schoch N, Heuveline V, Maleshkova M, Rettinger A, Speidel S, Wolf I, Kenngott H, Mehrabi A, Müller-Stich BP, Maier-Hein L, Meinzer H, Nolden M (2016). Towards an open-source semantic data infrastructure for integrating clinical and scientific data in cognition-guided surgery, Medical Imaging 2016: PACS and Imaging Informatics: Next Generation and Innovations,p.97890O,SPIE 144
• Kratzke J, Rengier F, Weis C, Beller CJ, Heuveline V (2016). In vitro flow assessment: from PC-MRI to computational fluid dynamics including fluid-structure interaction, Medical Imaging 2016: Physics of Medical Imaging,p.97835C,SPIE 145
• Lösel P, Heuveline V (2016). Enhancing a diffusion algorithm for 4D image segmentation using local information, Medical Imaging 2016: Image Processing,p.97842L,SPIE 146
• Schoch N, Philipp P, Weller T, Engelhardt S, Volovyk M, Fetzer A, Nolden M, Simone RD, Wolf I, Maleshkova M, Rettinger A, Studer R, Heuveline V (2016). Cognitive tools pipeline for assistance of mitral valve surgery, Medical Imaging 2016: Image-Guided Procedures, Robotic Interventions, and Modeling,p.978603,SPIE 148
• Lippok S, Kolšek K, Löf A, Eggert D, Vanderlinden W, Müller JP, König G, Obser T, Röhrs K, Schneppenheim S, Budde U, Baldauf C, Aponte-Santamaría C, Gräter F, Schneppenheim R, Rädler JO, Brehm MA (2016). von Willebrand factor is dimerized by protein disulfide isomerase, Blood 127(9):1183-1191 160
• Bauswein A, Stergioulas N, Janka H (2016). Exploring properties of high-density matter through remnants of neutron-star mergers, Eur. Phys. J. A 52(3) 435
• Regierer B, Hollmann S, Golebiewski M (2016). NORM-SYS – harmonizing standardization processes for model and data exchange in systems biology, EMBnet j. 21(A):813 1348
• Khan KM, Mesaik MA, Abdalla OM, Rahim F, Soomro S, Halim SA, Mustafa G, Ambreen N, Khalid AS, Taha M, Perveen S, Alam MT, Hameed A, Ul-Haq Z, Ullah H, Rehman ZU, Siddiqui RA, Voelter W (2016). The immunomodulation potential of the synthetic derivatives of benzothiazoles: Implications in immune system disorders through in vitro and in silico studies, Bioorganic Chemistry 64:21-28 187
• Pahnke K, Brandt J, Gryn'ova G, Lin CY, Altintas O, Schmidt FG, Lederer A, Coote ML, Barner-Kowollik C (2016). Entropy-Driven Selectivity for Chain Scission: Where Macromolecules Cleave, Angew. Chem. Int. Ed. 55(4):1514-1518 506
• Rafiullah R, Aslamkhan M, Paramasivam N, Thiel C, Mustafa G, Wiemann S, Schlesner M, Wade RC, Rappold GA, Berkel S (2016). Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family, J Med Genet 53(2):138-144 185
• Just O, Obergaulinger M, Janka H, Bauswein A, Schwarz N (2016). Neutron-star Merger Ejecta as Obstacles to Neutrino-powered Jets of Gamma-Ray Bursts, ApJ 816(2):L30 424
• Goriely S, Bauswein A, Janka H, Panebianco S, Sida J, Lemaître J, Hilaire S, Dubray N (2016). The r-process nucleosynthesis during the decompression of neutron star crust material, J. Phys.: Conf. Ser. 665:012052 434
• Elliott G, Ghanem D, Krüger F (2016). Forecasting conditional probabilities of binary outcomes under misspecification, Review of Economics and Statistics 98(4):742–755 132
• Ehm W, Gneiting T, Jordan A, Krueger F (2016). Of quantiles and expectiles: Consistent scoring functions, Choquet representations and forecast rankings (with discussion and reply), Journal of the Royal Statistical Society: Series B (Statistical Methodology), 78(3):505–562 49
• Disanto A, Cavuoti S, Brescia M, Donalek C, Longo G, Riccio G, Djorgovski S (2016). An analysis of feature relevance in the classification of astronomical transients with machine learning methods, Monthly Notices of the Royal Astronomical Society, 457:3119–3132 99
• Kügler S, Gianniotis N, Polsterer K (2016). An explorative approach for inspecting Kepler data, Monthly Notices of the Royal Astronomical Society, 455(4):4399–4405 102
• Polsterer K, Gieseke F, Igel C, Doser B, Gianniotis N (2016). Parallelized rotation and flipping INvariant Kohonen maps (PINK) on GPUs, In European Symposium on Artificial Neural Networks (ESANN), pp. 405–410 103
• Barbera P (2016). Efficient and Massively Parallel Implementation of the Evolutionary Placement Algorithm (Master's Thesis), Computer Science, Karlsruhe Institute of Technology, 2016, Alexandros Stamatakis(Tutor) 109
• Darriba D (2016). Selection of models of genomic evolution in HPC environments (Doctoral Thesis), Computer Science, University of A Coruna, 2016, Guillermo López Taboada(Tutor), Alexandros Stamatakis(HITS Tutor) 110
• Kobert K (2016). Mathematical Problems in Molecular Evolution and Next Generation Sequencing (Doctoral Thesis), Computer Science, Karlsruhe Institute of Technology, 2016, Alexandros Stamatakis(Tutor) 111
• Psonis N (2016). Molecular Phylogeny and Phylogeography of the Podarcis tauricus (Sauria: Lacertidae) Species Subgroup (Doctoral Thesis), Department of Biology, University of Crete, 2016, Nikolaos Poulakakis(Tutor), Alexandros Stamatakis(HITS Tutor) 112
• Mahé F, Vargas Cd, Bass D, Czech L, Stamatakis A, Lara E, Singer D, Mayor J, Bunge J, Sernaker S, Siemensmeyer T, Trautmann I, Romac S, Berney C, Kozlov A, Mitchell EA, Seppey CVW, Egge E, Lentendu G, Wirth R, Trueba G, Dunthorn M (2016). Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites, biorxiv;050997v3,[Preprint] 114
• Scholl C, Kobert K, Flouri T, Stamatakis A (2016). The divisible load balance problem with shared cost and its application to phylogenetic inference, In Parallel and Distributed Processing Symposium Workshops, 2016 IEEE International, pp. 408–417 115
• Darriba D, Weiß M, Stamatakis A (2016). Prediction of missing sequences and branch lengths in phylogenomic data, Bioinformatics, 32(9):1331–1337 116
• Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A (2016). Does the choice of nucleotide substitution models matter topologically?, BMC Bioinformatics, 17(1):143 117
• Skourtanioti E, Kapli P, Ilgaz Ç, Kumlutaş Y, Avcı A, Ahmadzadeh F, Crnobrnja–Isailović J, Gherghel I, Lymberakis P, Poulakakis N (2016). A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes, Molecular Phylogenetics and Evolution, 103:199–214 118
• Ahmadzadeh F, Flecks M, Carretero MA, Böhme W, Ihlow F, Kapli P, Miraldo A, Rödder D (2016). Separate histories in both sides of the Mediterranean: phylogeny and niche evolution of ocellated lizards, Journal of Biogeography, 43(6):1242–1253 119
• Kornilios P, Thanou E, Kapli P, Parmakelis A, Chatzaki M (2016). Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae, Molecular Phylogenetics and Evolution, 98:300–313 120
• Renner SS, Grimm GW, Kapli P, Denk T (2016). Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth–death clock model, Phil. Trans. R. Soc. B, 371(1699):20150135 121
• Kobert K, Stamatakis A, Flouri T (2016). Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations, Systematic Biology 122
• Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A (2016). Phylogeny-aware identification and correction of taxonomically mislabeled sequences, Nucleic Acids Research, 44(11):5022–5033 124
• Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T (2016). Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo, biorxiv;063875v1,[Preprint] 125
• Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Bonada N, Cartwright D, Chuluunbat S, Cocks GV, others (2016). The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life, Phil. Trans. R. Soc. B, vol. 371(1702), p. 20160025 126
• Hoang DT, Vinh LS, Flouri T, Stamatakis A, Häseler Av, Minh BQ (2016). A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation, In Knowledge and Systems Engineering (KSE), 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE), Hanoi, 2016, pp. 1–6 127
• Baran S, Lerch S (2016). Mixture EMOS model for calibrating ensemble forecasts of wind speed, Environmetrics, 27(2):116–130 128
• Ehm W, Wackermann J (2016). Geometric–optical illusions and Riemannian geometry, Journal of Mathematical Psychology, 71:28–38 130
• Fiedler J (2016). Distances, Gegenbauer expansions, curls, and dimples: On dependence measures for random fields (Doctoral Thesis), PhD Thesis, Faculty of Mathematics and Computer Science, Heidelberg University 133
• Hemri S (2016). Probabilistic forecasting based on hydrometeorological ensembles (Doctoral Thesis), PhD Thesis, Faculty of Mathematics, Karlsruhe Institute of Technology 135
• Hemri S, Haiden T, Pappenberger F (2016). Discrete postprocessing of total cloud cover ensemble forecasts, Monthly Weather Review, 144(7):2565–2577 136
• Jordan A (2016). Facets of forecast evaluation (Doctoral Thesis), PhD Thesis, Faculty of Mathematics, Karlsruhe Institute of Technology 137
• Krüger F, Nolte I (2016). Disagreement versus uncertainty: Evidence from distribution forecasts, Journal of Banking & Finance, 72:S172–S186 138
• Lerch S (2016). Probabilistic forecasting and comparative model assessment, with focus on extreme events (Doctoral Thesis), PhD Thesis, Faculty of Mathematics, Karlsruhe Institute of Technology 139
• Schefzik R (2016). A similarity-based implementation of the Schaake shuffle, Monthly Weather Review, 144(5):1909–1921 141
• Schefzik R (2016). Combining parametric low‐dimensional ensemble postprocessing with reordering methods, Quarterly Journal of the Royal Meteorological Society, 142(699):2463–2477 142
• Fissler T, Ziegel JF, Gneiting T (2016). Expected shortfall is jointly elicitable with value-at-risk: Implications for backtesting, Risk Magazine, January:58–61 143
• Schoch N, Speidel S, Sure-Vetter Y, Heuveline V (2016). Towards Semantic Simulation for Patient-Specific Surgery Assistance, Proc. First International Workshop on Surgical Data Science, 1:58-63 149
• Wlotzka M, Heuveline V, Klatt S, Kraus D, Haas E, Kiese K, Butterbach-Bahl K, Kraft P, Breuer L (2016). Parallel multiphysics simulations using OpenPALM with application to hydro-biogeochemistry coupling, Proc. 6th International Conference on High-Performance Scientific Computing 2015 (LNCS Springer), pp. [in press] 150
• Mercadante D, Milles S, Fuertes G, Svergun D, Lemke EA, Gräter F (2016). Rescuing the Over-Collapse of Intrinsically Disordered Proteins using a Force Field Derived by a New Paradigm, Biophysical Journal, 110(3):556a 163
• Aramburu IV, Mercadante D, Milles S, Ringkjøbing M, Banterle N, Koehler C, Tyagi S, Clarke J, Shammas SL, Blackledge M, others (2016). Plasticity of Nucleoporin Nuclear Transport Receptor Interactions-Molecular Description of a Highly Dynamic, Ultrafast Interaction Mechanism, Biophysical Journal, 110(3):357a 166
• Tursch A, Mercadante D, Tennigkeit J, Gräter F, Özbek S (2016). Minicollagen cysteine-rich domains encode distinct modes of polymerization to form stable nematocyst capsules, Scientific Reports, vol. 6 167
• Kent LM, Loo TS, Melton LD, Mercadante D, Williams MA, Jameson GB (2016). Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control, Journal of Biological Chemistry, 291(3):1289–1306 168
• Gundić M, Tomić A, Wade RC, Matovina M, Karačić Z, Kazazić S, Tomić S (2016). Human DPP III – Keap1 Interactions: A Combined Experimental And Computational study, Croat. Chem. Acta 2016, 89(2), 217–228 170
• Kokh DB, Czodrowski P, Rippmann F, Wade RC (2016). Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets, J. Chem. Theory Comput. 12(8):4100-4113 175
• Ozboyaci M, Kokh DB, Wade RC (2016). Three steps to Gold: Mechanism of protein adsorption to a gold surface revealed by Brownian and molecular dynamics simulations, Phys. Chem. Chem. Phys. 18(15):10191-10200 182
• Yu X, Kokh DB, Nandekar P, Mustafa G, Richter S, Wade RC (2016). Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer, High Performance Computing in Science and Engineering ´15,pp.255-264,Springer International Publishing 184
• Ozboyaci M, Kokh DB, Corni S, Wade RC (2016). Modeling and simulation of protein–surface interactions: achievements and challenges, Quart. Rev. Biophys. 49,e4 186
• Yu X, Nandekar P, Mustafa G, Cojocaru V, Lepesheva GI, Wade RC (2016). Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design, Biochimica et Biophysica Acta (BBA) - General Subjects 1860(1):67-78 188
• Heinzerling B, Judea A, Strube M (2016). HITS at TAC KBP 2015: Entity discovery and linking, and event nugget detection, In Proceedings of the Text Analysis Conference, National Institute of Standards and Technology, Gaithersburg, Maryland, USA, 16–17 November 2015 189
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