Lee S - Search Results

1

Sustainable data analysis with Snakemake.

Mölder F, Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, Forster J, Lee S, Twardziok SO, Kanitz A, Wilm A, Holtgrewe M, Rahmann S, Nahnsen S, Köster J. Mölder F, et al. Among authors: lee s. F1000Res. 2021 Jan 18;10:33. doi: 10.12688/f1000research.29032.2. eCollection 2021. F1000Res. 2021. PMID: 34035898 Free PMC article.

2

Tibanna: software for scalable execution of portable pipelines on the cloud.

Lee S, Johnson J, Vitzthum C, Kırlı K, Alver BH, Park PJ. Lee S, et al. Bioinformatics. 2019 Nov 1;35(21):4424-4426. doi: 10.1093/bioinformatics/btz379. Bioinformatics. 2019. PMID: 31077294 Free PMC article.

3

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.

Fan J, Lee HO, Lee S, Ryu DE, Lee S, Xue C, Kim SJ, Kim K, Barkas N, Park PJ, Park WY, Kharchenko PV. Fan J, et al. Among authors: lee ho, lee s. Genome Res. 2018 Aug;28(8):1217-1227. doi: 10.1101/gr.228080.117. Epub 2018 Jun 13. Genome Res. 2018. PMID: 29898899 Free PMC article.

4

NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.

Lee S, Lee S, Ouellette S, Park WY, Lee EA, Park PJ. Lee S, et al. Among authors: lee ea. Nucleic Acids Res. 2017 Jun 20;45(11):e103. doi: 10.1093/nar/gkx193. Nucleic Acids Res. 2017. PMID: 28369524 Free PMC article.

5

The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data.

Reiff SB, Schroeder AJ, Kırlı K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoğlu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ. Reiff SB, et al. Among authors: lee s. Nat Commun. 2022 May 2;13(1):2365. doi: 10.1038/s41467-022-29697-4. Nat Commun. 2022. PMID: 35501320 Free PMC article.

6

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data.

Jain D, Chu C, Alver BH, Lee S, Lee EA, Park PJ. Jain D, et al. Among authors: lee ea, lee s. Bioinformatics. 2021 May 23;37(8):1045-1051. doi: 10.1093/bioinformatics/btaa923. Bioinformatics. 2021. PMID: 33136153 Free PMC article.

7

BamSnap: a lightweight viewer for sequencing reads in BAM files.

Kwon M, Lee S, Berselli M, Chu C, Park PJ. Kwon M, et al. Among authors: lee s. Bioinformatics. 2021 Apr 19;37(2):263-264. doi: 10.1093/bioinformatics/btaa1101. Bioinformatics. 2021. PMID: 33416869 Free PMC article.

8

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data.

Wang S, Lee S, Chu C, Jain D, Kerpedjiev P, Nelson GM, Walsh JM, Alver BH, Park PJ. Wang S, et al. Among authors: lee s. Genome Biol. 2020 Mar 23;21(1):73. doi: 10.1186/s13059-020-01986-5. Genome Biol. 2020. PMID: 32293513 Free PMC article.

9

Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs.

Lee S, Bakker CR, Vitzthum C, Alver BH, Park PJ. Lee S, et al. Bioinformatics. 2022 Mar 4;38(6):1729-1731. doi: 10.1093/bioinformatics/btab870. Bioinformatics. 2022. PMID: 34978573 Free PMC article.

10

HiGlass: web-based visual exploration and analysis of genome interaction maps.

Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg N. Kerpedjiev P, et al. Among authors: lee s. Genome Biol. 2018 Aug 24;19(1):125. doi: 10.1186/s13059-018-1486-1. Genome Biol. 2018. PMID: 30143029 Free PMC article.

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