Computational Challenges in Medical Genomics (Signup)

	A	B	C	D	E	F
1	Name	Topic	Date	#	Paper title	URL

2		Alignment		1	Aligning Optical Maps to De Bruijn Graphs	https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz069/5304362
3	Leopold Franz	Alignment	15.04.2019	2	BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2319-7
4	Hana Pařízková	Alignment	15.04.2019	3	Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences	https://academic.oup.com/bioinformatics/article/32/14/2103/1742895
5		Approximate storage		4	Mash: fast genome and metagenome distance estimation using MinHash	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x
6	Nina Wiedemann	Approximate storage	01.04.2019	5	Ultrafast search of all deposited bacterial and viral genomic data	https://www.nature.com/articles/s41587-018-0010-1
7		Compression		6	GTC: how to maintain huge genotype collections in a compressed form	https://academic.oup.com/bioinformatics/article/34/11/1834/4813738
8		Compression		7	Quark enables semi-reference-based compression of RNA-seq data	https://academic.oup.com/bioinformatics/article/33/21/3380/3920524
9		Data Structures		8	KMC 2: fast and resource-frugal k-mer counting	https://academic.oup.com/bioinformatics/article/31/10/1569/177467
10	Andreas Kreuzmann	Data Structures	01.04.2019	9	Wheeler graphs: A framework for BWT-based data structures	https://www.sciencedirect.com/science/article/pii/S0304397517305285
11		Data Structures		10	Relative Suffix Trees	https://academic.oup.com/comjnl/article/61/5/773/4643569
12		Data Structures		11	Simulating the DNA String Graph in Succinct Space	https://arxiv.org/pdf/1901.10453.pdf
13		Data Structures		12	Faster Repetition-Aware Compressed Suffix Trees based on Block Trees	https://arxiv.org/abs/1902.03274
14		Data Structures		13	Space-efficient merging of succinct de Bruijn graphs	https://arxiv.org/abs/1902.02889
15	Daphna Keidar	Genomic variation		14	Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations	https://www.nature.com/articles/s41598-018-37835-6
16	Peshal Agarwal	Genomic variation	29.04.2019	15	Predicting effects of noncoding variants with deep learning–based sequence model	https://www.nature.com/articles/nmeth.3547
17	Amaris Chen	Genomic variation	29.04.2019	16	A universal SNP and small-indel variant caller using deep neural networks	https://www.nature.com/articles/nbt.4235
18		Genomic variation		17	REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants	https://www.sciencedirect.com/science/article/pii/S0002929716303706
19		Genomic variation		18	A general framework for estimating the relative pathogenicity of human genetic variants	https://www.nature.com/articles/ng.2892
20		Population genetics		19	Mixed-model association for biobank-scale datasets	https://www.nature.com/articles/s41588-018-0144-6
21		Population genetics		20	Fast and accurate long-range phasing in a UK Biobank cohort	https://www.nature.com/articles/ng.3571
22	Kangning Liu	Population genetics	13.05.2019	21	FaST linear mixed models for genome-wide association studies	https://www.nature.com/articles/nmeth.1681
23	Dandan Peng	RNA-Seq Analysis	06.05.2019	22	Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States	https://www.sciencedirect.com/science/article/pii/S2405471217303356?via%3Dihub#mmc4
24		RNA-Seq Analysis		23	ROMA: Representation and Quantification of Module Activity from Target Expression Data	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760130/pdf/fgene-07-00018.pdf
25	Danang	RNA-Seq Analysis	06.05.2019	24	Predicting Splicing from Primary Sequence with Deep Learning	https://www.cell.com/cell/fulltext/S0092-8674(18)31629-5
26	Flurin Hidber	RNA-Seq Analysis		25	Deep generative modeling for single-cell transcriptomics	https://www.nature.com/articles/s41592-018-0229-2
27		Security / Privacy		26	Secure Wavelet Matrix: Alphabet-Friendly Privacy-Preserving String Search for Bioinformatics	https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8310013
28	Bastian Hasslinger	Security / Privacy	13.05.2019	27	Private Computation on Encrypted Genomic Data	https://link.springer.com/chapter/10.1007/978-3-319-16295-9_1
29		Security / Privacy		28	Privacy-Preserving Processing of Raw Genomic Data	https://link.springer.com/chapter/10.1007/978-3-642-54568-9_9
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