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--- teaching:2020summer:compan [2020/04/16 10:10]
tischulz [Contents]
+++ teaching:2020summer:compan [2020/07/06 11:52]
tischulz Removed Yannick from schedule
@@ Line 5: / Line 5: @@
 Office: U10-141\\
+\\
+**Important notice:**\\
+The seminar will take place as an online course via Zoom. Details for participation can be found at the [[ https://bis.uni-bielefeld.de/sites/27608/Start.aspx | Lernraum ]].
 ===== Contents =====
-Baed on original research papers, the participants will give oral presentations (20-45 min, optimally about 25 min's) and write short summaries (ca. 5 pages), both in English, about current algorithmic problems in computational pangenomics and their solutions. Each week, we cover another aspect of scientific writing and put it into practice. Deadline for the written summary is one week after the presentation.
+Based on original research papers, the participants will give oral presentations (20-45 min, optimally about 25 min's) and write short summaries (ca. 5 pages), both in English, about current algorithmic problems in computational pangenomics and their solutions. Each week, we cover another aspect of scientific writing and put it into practice. Deadline for the written summary is one week after the presentation.
 ===== Timeline =====
@@ Line 13: / Line 16: @@
 | 22.04.  | Preliminaries, topic selection |   |
-| 29.04.  | -- |      |
+| 29.04.  | Intro to LaTeX, reading | {{ :teaching:2020summer:compan:template.tar | latex sources }}, {{ :teaching:2020summer:compan:reading.pdf | Slides: HowToRead  }} |
-| 06.05.  | Intro to LaTeX, reading |   |
+| 06.05.  | Scientific writing | {{ :teaching:2020summer:compan:scientificwriting.pdf | Slides: ScientificWriting }}, [[ https://de.sharelatex.com/learn/bibtex_bibliography_styles | Bibliography Styles ]] |
-| 13.05.  | Scientific writing |                                        |
+| 13.05.  | Introductions, conclusions | {{ :teaching:2020summer:compan:introsconclusions.pdf | Slides: IntroductionConclusions }} |
-| 20.05.  | Introductions, conclusions |                     |
+| 20.05.  | Math | {{ :teaching:2020summer:compan:math_template.tar | latex sources }},  {{ :teaching:2020summer:compan:math.pdf | Slides: Math }}        |
-| 27.05.  | Math |                                                                                                                                                       |
+| 27.05.  | Tables, figures, algorithms | {{ :teaching:2020summer:compan:algo_template.tar | latex sources }},  {{ :teaching:2020summer:compan:tablesFiguresAlgos.pdf | Slides: TablesFiguresAlgorithms }} |
-| 03.06.  | Tables, figures, algorithms |                                                  |
+| 03.06.  | Checklist, writing | {{ :teaching:2020summer:compan:checklist.pdf | Slides: Checklist }} |
-| 10.06.  | Checklist, writing |                                                                                                                    |
+| 10.06.  | Intro to presentations (in LaTeX Beamer) | {{:teaching:2020summer:compan:beamer_template.tar | latex sources }}, [[ http://texdoc.net/texmf-dist/doc/latex/beamer/beameruserguide.pdf | beamer class doku ]], {{:teaching:2020summer:compan:checklist_presentations.pdf | Slides: Presentation Checklist }} |
-| 17.06.  | Intro to presentations (in LaTeX Beamer) |                                               |
+| 17.06.  | presentations (1) |                                               |
-| 24.06.  | presentations (1) |                                                                                                                    |
+| 24.06.  | presentations (2) |                                                                                                                    |
-| 01.07.  | presentations (2) |   |
+| 01.07.  | presentations (3) |   |
-| 08.07.  | presentations (3) |  |
+| 08.07.  | presentations (4) |  |
-| 15.07.  | presentations (4) |  |
+| 15.07.  | presentations (5) |  |
@@ Line 36: / Line 39: @@
 ^ Slot  ^ Student  ^ Paper                                                                                                                         ^
-|     |   |   |
+|  2   | Tizian  | {{ :teaching:2020summer:compan:bbw089.pdf  | Computational pan-genomics: status, promises and challenges }} |
+|   |  | [[ https://almob.biomedcentral.com/track/pdf/10.1186/s13015-016-0066-8 | Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage ]] |
+|  3  | <del>Yannick</del>  | [[ https://www.biorxiv.org/content/10.1101/695338v2.full.pdf | Bifrost - Highly parallel construction and indexing of colored and compacted de Bruijn graphs ]] |
+|  3  | Marvin  | [[ https://www.biorxiv.org/content/10.1101/234856v1.full.pdf | Sequence variation aware genome references and read mapping with the variation graph toolkit ]] |
+|  4  | Fabian  | [[ https://www.liebertpub.com/doi/pdfplus/10.1089/cmb.2019.0309 | Efficient Construction of a Complete Index for Pan-Genomics Read Alignment ]] |
+|  5  | Leonard  | [[ https://academic.oup.com/bioinformatics/article/35/19/3599/5372677 | Bit-parallel sequence-to-graph alignment ]] |
+|   |   | [[ https://www.biorxiv.org/content/10.1101/2020.01.21.914168v1.full.pdf | BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs ]] |
+|  4  | Aya  | [[ https://link.springer.com/content/pdf/10.1186/s13015-020-00164-3.pdf | Alignment- and reference-free phylogenomics with colored de Bruijn graphs ]] |
+|  5  | Christoph  | [[ https://www.biorxiv.org/content/10.1101/645721v1.full.pdf | Viral quasispecies reconstruction via contig abundance estimation in variation graphs ]] |
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Genome Informatics

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