Pavlichin DS - Search Results

1

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.

Lee H, Greer SU, Pavlichin DS, Zhou B, Urban AE, Weissman T; Human Pangenome Reference Consortium; Ji HP. Lee H, et al. Among authors: pavlichin ds. Cell Rep Methods. 2023 Aug 2;3(8):100543. doi: 10.1016/j.crmeth.2023.100543. eCollection 2023 Aug 28. Cell Rep Methods. 2023. PMID: 37671027 Free PMC article.

2

The human genome contracts again.

Pavlichin DS, Weissman T, Yona G. Pavlichin DS, et al. Bioinformatics. 2013 Sep 1;29(17):2199-202. doi: 10.1093/bioinformatics/btt362. Epub 2013 Jun 22. Bioinformatics. 2013. PMID: 23793748

3

Compressing Tabular Data via Pairwise Dependencies.

Pavlichin DS, Ingber A, Weissman T. Pavlichin DS, et al. Proc Data Compress Conf. 2017 Apr;2017:455. doi: 10.1109/DCC.2017.82. Epub 2017 May 11. Proc Data Compress Conf. 2017. PMID: 29046897 Free PMC article. No abstract available.

4

Chained Kullback-Leibler Divergences.

Pavlichin DS, Weissman T. Pavlichin DS, et al. Proc IEEE Int Symp Info Theory. 2016 Jul;2016:580-584. doi: 10.1109/ISIT.2016.7541365. Epub 2016 Aug 11. Proc IEEE Int Symp Info Theory. 2016. PMID: 29130024 Free PMC article.

5

Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies.

Lau BT, Pavlichin D, Hooker AC, Almeda A, Shin G, Chen J, Sahoo MK, Huang C, Pinsky BA, Lee H, Ji HP. Lau BT, et al. medRxiv [Preprint]. 2020 Nov 4:2020.11.02.20224816. doi: 10.1101/2020.11.02.20224816. medRxiv. 2020. Update in: Genome Med. 2021 Apr 19;13(1):62. doi: 10.1186/s13073-021-00882-2. PMID: 33173909 Free PMC article. Updated. Preprint.

6

Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations.

Lee H, Shuaibi A, Bell JM, Pavlichin DS, Ji HP. Lee H, et al. Among authors: pavlichin ds. NAR Cancer. 2020 Dec;2(4):zcaa034. doi: 10.1093/narcan/zcaa034. Epub 2020 Dec 10. NAR Cancer. 2020. PMID: 33345188 Free PMC article.

7

Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies.

Lau BT, Pavlichin D, Hooker AC, Almeda A, Shin G, Chen J, Sahoo MK, Huang CH, Pinsky BA, Lee HJ, Ji HP. Lau BT, et al. Genome Med. 2021 Apr 19;13(1):62. doi: 10.1186/s13073-021-00882-2. Genome Med. 2021. PMID: 33875001 Free PMC article.

8

KmerKeys: a web resource for searching indexed genome assemblies and variants.

Pavlichin DS, Lee H, Greer SU, Grimes SM, Weissman T, Ji HP. Pavlichin DS, et al. Nucleic Acids Res. 2022 Jul 5;50(W1):W448-W453. doi: 10.1093/nar/gkac266. Nucleic Acids Res. 2022. PMID: 35474383 Free PMC article.

9

Tumor-associated microbiome features of metastatic colorectal cancer and clinical implications.

An HJ, Partha MA, Lee H, Lau BT, Pavlichin DS, Almeda A, Hooker AC, Shin G, Ji HP. An HJ, et al. Among authors: pavlichin ds. Front Oncol. 2024 Jan 18;13:1310054. doi: 10.3389/fonc.2023.1310054. eCollection 2023. Front Oncol. 2024. PMID: 38304032 Free PMC article.

10

Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.

Bisaria N, Greenfeld M, Limouse C, Pavlichin DS, Mabuchi H, Herschlag D. Bisaria N, et al. Among authors: pavlichin ds. Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):E4956-65. doi: 10.1073/pnas.1525082113. Epub 2016 Aug 4. Proc Natl Acad Sci U S A. 2016. PMID: 27493222 Free PMC article.

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