eSSENCE Publications
Below you will find a list of all peer-reviewed publications in scientific journals and conference proceedings from the eSSENCE research groups in 2010-2014.

Acknowledgements and logos
We ask all eSSENCE researchers to acknowledge the research program in their publications/presentations:

For work directly funded by eSSENCE:
This work was supported by the Swedish strategic research programme eSSENCE.

For work originating from the eSSENCE environment, irrespective funding:
This work forms part of the Swedish strategic research programme eSSENCE.

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AuthorsTitleJournal / ConferenceYear
Jörg Tiedemann, Fabienne Cap, Jenna Kanerva, Filip Ginter, Sara Stymne, Robert Östling and Marion Weller-Di MarcoPhrase-Based SMT for Finnish with More Data, Better Models and Alternative Alignment and Translation ToolsFirst Conference on Machine Translation (WMT 2016), vol. , p. 2016
Oscar Sagemo and Sara StymneThe UU Submission to the Machine Translation Quality Estimation TaskFirst Conference on Machine Translation (WMT 2016), vol. , p. 2016
Sara StymneFeature Exploration for Cross-Lingual Pronoun PredictionFirst Conference on Machine Translation (WMT 2016), vol. , p. 2016
Joakim Nivre, Marie-Catherine de Marneffe, Filip Ginter, Yoav Goldberg, Jan Hajic, Christopher D. Manning, Ryan McDonald, Slav Petrov, Sampo Pyysalo, Natalia Silveira, Reut Tsarfaty, and Daniel ZemanUniversal dependencies v1: A multilingual treebank collectionProceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016), vol. , p. 2016
Kaja Dobrovoljc and Joakim NivreThe universal dependencies treebank of spoken SlovenianProceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016), vol. , p. 2016
Mojgan Seraji, Filip Ginter, and Joakim NivreUniversal dependencies for PersianProceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016), vol. , p. 2016
Marie Dubremetz and Joakim NivreSyntax matters for rhetorical structure: The case of chiasmusFifth Workshop on Computational Linguistics for Literature, vol. , p. 2016
Miryam de Lhoneux and Joakim NivreShould have, would have, could have. investigating verb group representations for parsing with universal dependenciesProceedings of the Workshop on Multilingual and Cross­-lingual Methods in NLP, vol. , p. 2016
Matthieu Constant and Joakim NivreA transition-based system for joint lexical and syntactic analysisthe 54th Annual Meeting of the Association for Computational Linguistics, vol. , p. 2016
Yan Shao and Joakim NivreApplying neural networks to English-Chinese named entity transliterationThe Sixth Named Entity Workshop, vol. , p. 2016
O. Ishaq, S.K. Sadanandan, and C. Wählby Deep Fish: Deep Learning-Based Classification of Zebrafish Deformation for High-Throughput ScreeningJournal of Biomolecular Screening / SLAS Discovery, vol. 22, p. 102-1072016
C. WählbyThe quest for multiplexed spatially resolved transcriptional profilingNature Methods, vol. 13, p. 623-6242016
M. Mignardi, O. Ishaq, X. Qian, and C. WählbyBridging Histology and Bioinformatics - Computational Analysis of Spatially Resolved TranscriptomicsProceedings of the IEEE, vol. 105, p. 530-5412016
D. J. Matuszewski, C. Wählby, J. C. Puigvert, and I-M. Sintorn.PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening DataPLoS ONE, vol. 11, p. e01515542016
P. Ranefall and C. WählbyGlobal gray-level thresholding based on object sizeCytometry A, vol. 89, p. 385-3902016
S.K. Sadanandan, P. Ranefall, and C. WählbyFeature Augmented Deep Neural Networks for Segmentation of CellsLecture Notes in Computer Science Computer Vision - ECCV 2016 Workshops, vol. 9913, p. 231-2432016
Norbert Jeszenöi, Mónika Bálint, István Horváth, David van der Spoel and Csaba HetényiExploration of Interfacial Hydration Networks of Target-Ligand ComplexesJ. Chem. Inf. Model. , vol. 56, p. 148-1582016
Haiyang Zhang, Yongqin Lv, Tianwei Tan and David van der Spoel:Protein Encapsulation in Metal-Organic FrameworksJ. Phys. Chem. B, vol. 120, p. 477-4842016
Jin Zhang, Badamkhatan Tuguldur and David van der SpoelCorrection to Force Field Benchmark of Organic Liquids II: Gibbs Energy of SolvationJ. Chem. Inf. Model., vol. 56, p. 819-8202016
Marie-Claire Bellissent-Funel, Ali Hassanali, Martina Havenith, Richard Henchman, Peter Pohl, Fabio Sterpone, David van der Spoel, Yao Xu, and Angel E GarciaWater Determines the Structure and Dynamics of ProteinsChem. Rev., vol. 116, p. 7673-76972016
Mohammad Ghahremanpour and Paul van Maaren and Jonas Ditz and Roland Lindh and David van der SpoelLarge-Scale Calculations of Gas Phase Thermochemistry: Enthalpy of Formation, Standard Entropy and Heat CapacityJ. Chem. Phys., vol. 145, p. 1143052016
Ahmet Yildirim, Jin Zhang, Sergio Manzetti and David van der SpoelBinding of Pollutants to Biomolecules - A Simulation StudyChem. Res. Toxicol. , vol. 29, p. 1679-16882016
Haiyang Zhang, Chunhua Yin, Hai Yan and David van der SpoelEvaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest ComplexesJ. Chem. Inf. Model., vol. 56, p. 2080-20922016
Sergio Manzetti and Marcel PatekThe accurate wavefunction of the active space of the rhenium dimer resolved using the ab initio Brueckner coupled-cluster method. Structural Chemistry, vol. 27, p. 1071–10802016
S. Manzetti, O. Andersen, C. Garcia and E. CamposMolecular simulation of carbon nanotubes as sorptive materials: sorption effects towards retene, perylene and cholesterol to 100 degrees Celsius and above.Mol. Simul., vol. 42, p. 1183-11922016
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