@article{JiangOronClarketal.2016,
  author    = {Jiang, Yuxiang and Oron, Tal Ronnen and Clark, Wyatt T. and Bankapur, Asma R. and D'Andrea, Daniel and Lepore, Rosalba and Funk, Christopher S. and Kahanda, Indika and Verspoor, Karin M. and Ben-Hur, Asa and Koo, Da Chen Emily and Penfold-Brown, Duncan and Shasha, Dennis and Youngs, Noah and Bonneau, Richard and Lin, Alexandra and Sahraeian, Sayed M. E. and Martelli, Pier Luigi and Profiti, Giuseppe and Casadio, Rita and Cao, Renzhi and Zhong, Zhaolong and Cheng, Jianlin and Altenhoff, Adrian and Skunca, Nives and Dessimoz, Christophe and Dogan, Tunca and Hakala, Kai and Kaewphan, Suwisa and Mehryary, Farrokh and Salakoski, Tapio and Ginter, Filip and Fang, Hai and Smithers, Ben and Oates, Matt and Gough, Julian and T{\"o}r{\"o}nen, Petri and Koskinen, Patrik and Holm, Liisa and Chen, Ching-Tai and Hsu, Wen-Lian and Bryson, Kevin and Cozzetto, Domenico and Minneci, Federico and Jones, David T. and Chapman, Samuel and BKC, Dukka and Khan, Ishita K. and Kihara, Daisuke and Ofer, Dan and Rappoport, Nadav and Stern, Amos and Cibrian-Uhalte, Elena and Denny, Paul and Foulger, Rebecca E. and Hieta, Reija and Legge, Duncan and Lovering, Ruth C. and Magrane, Michele and Melidoni, Anna N. and Mutowo-Meullenet, Prudence and Pichler, Klemens and Shypitsyna, Aleksandra and Li, Biao and Zakeri, Pooya and ElShal, Sarah and Tranchevent, L{\´e}on-Charles and Das, Sayoni and Dawson, Natalie L. and Lee, David and Lees, Jonathan G. and Sillitoe, Ian and Bhat, Prajwal and Nepusz, Tam{\´a}s and Romero, Alfonso E. and Sasidharan, Rajkumar and Yang, Haixuan and Paccanaro, Alberto and Gillis, Jesse and Sede{\~n}o-Cort{\´e}s, Adriana E. and Pavlidis, Paul and Feng, Shou and Cejuela, Juan M. and Goldberg, Tatyana and Hamp, Tobias and Richter, Lothar and Salamov, Asaf and Gabaldon, Toni and Marcet-Houben, Marina and Supek, Fran and Gong, Qingtian and Ning, Wei and Zhou, Yuanpeng and Tian, Weidong and Falda, Marco and Fontana, Paolo and Lavezzo, Enrico and Toppo, Stefano and Ferrari, Carlo and Giollo, Manuel and Piovesan, Damiano and Tosatto, Silvio C. E. and del Pozo, Angela and Fern{\´a}ndez, Jos{\´e} M. and Maietta, Paolo and Valencia, Alfonso and Tress, Michael L. and Benso, Alfredo and Di Carlo, Stefano and Politano, Gianfranco and Savino, Alessandro and Rehman, Hafeez Ur and Re, Matteo and Mesiti, Marco and Valentini, Giorgio and Bargsten, Joachim W. and van Dijk, Aalt D. J. and Gemovic, Branislava and Glisic, Sanja and Perovic, Vladmir and Veljkovic, Veljko and Almeida-e-Silva, Danillo C. and Vencio, Ricardo Z. N. and Sharan, Malvika and Vogel, J{\"o}rg and Kansakar, Lakesh and Zhang, Shanshan and Vucetic, Slobodan and Wang, Zheng and Sternberg, Michael J. E. and Wass, Mark N. and Huntley, Rachael P. and Martin, Maria J. and O'Donovan, Claire and Robinson, Peter N. and Moreau, Yves and Tramontano, Anna and Babbitt, Patricia C. and Brenner, Steven E. and Linial, Michal and Orengo, Christine A. and Rost, Burkhard and Greene, Casey S. and Mooney, Sean D. and Friedberg, Iddo and Radivojac, Predrag and Veljkovic, Nevena},
  title     = {An expanded evaluation of protein function prediction methods shows an improvement in accuracy},
  series = {Genome Biology},
  volume    = {17},
  journal   = {Genome Biology},
  number    = {184},
  doi       = {10.1186/s13059-016-1037-6},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166293},
  year      = {2016},
  abstract  = {Background A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.},
  language  = {en}
}
@article{IyengarSedorFreedmanetal.2015,
  author    = {Iyengar, Sudha K. and Sedor, John R. and Freedman, Barry I. and Kao, W. H. Linda and Kretzler, Matthias and Keller, Benjamin J. and Abboud, Hanna E. and Adler, Sharon G. and Best, Lyle G. and Bowden, Donald W. and Burlock, Allison and Chen, Yii-Der Ida and Cole, Shelley A. and Comeau, Mary E. and Curtis, Jeffrey M. and Divers, Jasmin and Drechsler, Christiane and Duggirala, Ravi and Elston, Robert C. and Guo, Xiuqing and Huang, Huateng and Hoffmann, Michael Marcus and Howard, Barbara V. and Ipp, Eli and Kimmel, Paul L. and Klag, Michael J. and Knowler, William C. and Kohn, Orly F. and Leak, Tennille S. and Leehey, David J. and Li, Man and Malhotra, Alka and M{\"a}rz, Winfried and Nair, Viji and Nelson, Robert G. and Nicholas, Susanne B. and O'Brien, Stephen J. and Pahl, Madeleine V. and Parekh, Rulan S. and Pezzolesi, Marcus G. and Rasooly, Rebekah S. and Rotimi, Charles N. and Rotter, Jerome I. and Schelling, Jeffrey R. and Seldin, Michael F. and Shah, Vallabh O. and Smiles, Adam M. and Smith, Michael W. and Taylor, Kent D. and Thameem, Farook and Thornley-Brown, Denyse P. and Truitt, Barbara J. and Wanner, Christoph and Weil, E. Jennifer and Winkler, Cheryl A. and Zager, Philip G. and Igo, Jr, Robert P. and Hanson, Robert L. and Langefeld, Carl D.},
  title     = {Genome-wide association and trans-ethnic meta-analysis for advanced diabetic kidney disease: Family Investigation of Nephropathy and Diabetes (FIND)},
  series = {PLoS Genetics},
  volume    = {11},
  journal   = {PLoS Genetics},
  number    = {8},
  doi       = {10.1371/journal.pgen.1005352},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-180545},
  pages     = {e1005352},
  year      = {2015},
  abstract  = {Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45\% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10\(^{-9}\)). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10\(^{-8}\)), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD.},
  language  = {en}
}
@article{FaOliveroRealetal.2015,
  author    = {Fa, John E. and Olivero, Jes{\´u}s and Real, Raimundo and Farf{\´a}n, Miguel A. and M{\´a}rquez, Ana L. and Vargas, J. Mario and Ziegler, Stefan and Wegmann, Martin and Brown, David and Margetts, Barrie and Nasi, Robert},
  title     = {Disentangling the relative effects of bushmeat availability on human nutrition in central Africa},
  series = {Scientific Reports},
  volume    = {5},
  journal   = {Scientific Reports},
  number    = {8168},
  doi       = {10.1038/srep08168},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144110},
  year      = {2015},
  abstract  = {We studied links between human malnutrition and wild meat availability within the Rainforest Biotic Zone in central Africa. We distinguished two distinct hunted mammalian diversity distributions, one in the rainforest areas (Deep Rainforest Diversity, DRD) containing taxa of lower hunting sustainability, the other in the northern rainforest-savanna mosaic, with species of greater hunting potential (Marginal Rainforest Diversity, MRD). Wild meat availability, assessed by standing crop mammalian biomass, was greater in MRD than in DRD areas. Predicted bushmeat extraction was also higher in MRD areas. Despite this, stunting of children, a measure of human malnutrition, was greater in MRD areas. Structural equation modeling identified that, in MRD areas, mammal diversity fell away from urban areas, but proximity to these positively influenced higher stunting incidence. In DRD areas, remoteness and distance from dense human settlements and infrastructures explained lower stunting levels. Moreover, stunting was higher away from protected areas. Our results suggest that in MRD areas, forest wildlife rational use for better human nutrition is possible. By contrast, the relatively low human populations in DRD areas currently offer abundant opportunities for the continued protection of more vulnerable mammals and allow dietary needs of local populations to be met.},
  language  = {en}
}
@article{PerrellaMontagueBrownetal.2022,
  author    = {Perrella, Gina and Montague, Samantha J. and Brown, Helena C. and Garcia Quintanilla, Lourdes and Slater, Alexandre and Stegner, David and Thomas, Mark and Heemskerk, Johan W. M. and Watson, Steve P.},
  title     = {Role of tyrosine kinase Syk in thrombus stabilisation at high shear},
  series = {International Journal of Molecular Sciences},
  volume    = {23},
  journal   = {International Journal of Molecular Sciences},
  number    = {1},
  issn      = {1422-0067},
  doi       = {10.3390/ijms23010493},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-284243},
  year      = {2022},
  abstract  = {Understanding the pathways involved in the formation and stability of the core and shell regions of a platelet-rich arterial thrombus may result in new ways to treat arterial thrombosis. The distinguishing feature between these two regions is the absence of fibrin in the shell which indicates that in vitro flow-based assays over thrombogenic surfaces, in the absence of coagulation, can be used to resemble this region. In this study, we have investigated the contribution of Syk tyrosine kinase in the stability of platelet aggregates (or thrombi) formed on collagen or atherosclerotic plaque homogenate at arterial shear (1000 s\(^{-1}\)). We show that post-perfusion of the Syk inhibitor PRT-060318 over preformed thrombi on both surfaces enhances thrombus breakdown and platelet detachment. The resulting loss of thrombus stability led to a reduction in thrombus contractile score which could be detected as early as 3 min after perfusion of the Syk inhibitor. A similar loss of thrombus stability was observed with ticagrelor and indomethacin, inhibitors of platelet adenosine diphosphate (ADP) receptor and thromboxane A\(_2\) (TxA\(_2\)), respectively, and in the presence of the Src inhibitor, dasatinib. In contrast, the Btk inhibitor, ibrutinib, causes only a minor decrease in thrombus contractile score. Weak thrombus breakdown is also seen with the blocking GPVI nanobody, Nb21, which indicates, at best, a minor contribution of collagen to the stability of the platelet aggregate. These results show that Syk regulates thrombus stability in the absence of fibrin in human platelets under flow and provide evidence that this involves pathways additional to activation of GPVI by collagen.},
  language  = {en}
}