| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Hillier, Ladeana W, et al.
(författare)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Tidskriftsartikel (refereegranskat)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 3. |
- Margulies, Elliott H, et al.
(författare)
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- 2007
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 760-774
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Tidskriftsartikel (refereegranskat)abstract
- A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
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| 4. |
- Torre, Ilaria, et al.
(författare)
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Dimensional perception of a ‘smiling McGurkeffect’
- 2021
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Ingår i: 2021 9th International Conference on Affective Computing and Intelligent Interaction (ACII). - : Institute of Electrical and Electronics Engineers (IEEE).
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Konferensbidrag (refereegranskat)abstract
- Multisensory integration influences emotional perception, as the McGurk effect demonstrates for the communication between humans. Human physiology implicitly links the production of visual features with other modes like the audio channel: Face muscles responsible for a smiling face also stretch the vocal cords that results in a characteristic smiling voice. For artificial agents capable of multimodal expression, this linkage is modeled explicitly. In our study, we observe the influence of visual and audio channel on the perception of the agent’s emotional state. We created two virtual characters to control for anthropomorphic appearance. We record videos of these agents either with matching or mismatching emotional expression in the audio and visual channel. In an online study we measured the agent’s perceived valence and arousal. Our results show that a matched smiling voice and smiling face increase both dimensions of the Circumplex model of emotions: ratings of valence and arousal grow. When the channels present conflicting information, any type of smiling results in higher arousal rating, but only the visual channel increases the perceived valence. When engineers are constrained in their design choices, we suggest they should give precedence to convey the artificial agent’s emotional state through the visual channel.
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| 5. |
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| 6. |
- Torre, Ilaria, et al.
(författare)
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The Effect of Audio-Visual Smiles on Social Influence in a Cooperative Human-Agent Interaction Task
- 2021
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Ingår i: ACM Transactions on Computer-Human Interaction. - : ASSOC COMPUTING MACHINERY. - 1073-0516 .- 1557-7325. ; 28:6
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Tidskriftsartikel (refereegranskat)abstract
- Emotional expressivity is essential for human interactions, informing both perception and decision-making. Here, we examine whether creating an audio-visual emotional channel mismatch influences decision-making in a cooperative task with a virtual character. We created a virtual character that was either congruent in its emotional expression (smiling in the face and voice) or incongruent (smiling in only one channel). People (N = 98) evaluated the character in terms of valence and arousal in an online study; then, visitors in a museum played the "lunar survival task" with the character over three experiments (N = 597, 78, 101, respectively). Exploratory results suggest that multi-modal expressions are perceived, and reacted upon, differently than unimodal expressions, supporting previous theories of audio-visual integration.
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| 7. |
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| 8. |
- Torre, Ilaria, et al.
(författare)
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To smile or not to smile : The effect of mismatched emotional expressions in a Human-Robot cooperative task
- 2022
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Ingår i: 2022 31St Ieee International Conference On Robot And Human Interactive Communication (Ieee Ro-Man 2022). - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 8-13
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Konferensbidrag (refereegranskat)abstract
- Emotional expressivity is essential for successful Human-Robot Interaction. However, robots often have different levels of expressivity in their face and voice. Here we ask whether this modality mismatch influences human behaviour and perception of the robot. Participants played a cooperative task with a robot that displayed matched and mismatched smiling expressions in the face and voice. Emotional expressivity did not influence acceptance of robot's recommendations or subjective evaluations of the robot. However, we found that the robot had overall a higher social influence than a virtual character, and was evaluated more positively.
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