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Items: 21

1.

Transcriptional profiling of single fiber cells in a transgenic paradigm of an inherited childhood cataract reveals absence of molecular heterogeneity.

Bhat SP, Gangalum RK, Kim D, Mangul S, Kashyap RK, Zhou X, Elashoff D.

J Biol Chem. 2019 Jun 26. pii: jbc.RA119.008853. doi: 10.1074/jbc.RA119.008853. [Epub ahead of print]

2.

Challenges and recommendations to improve the installability and archival stability of omics computational tools.

Mangul S, Mosqueiro T, Abdill RJ, Duong D, Mitchell K, Sarwal V, Hill B, Brito J, Littman RJ, Statz B, Lam AK, Dayama G, Grieneisen L, Martin LS, Flint J, Eskin E, Blekhman R.

PLoS Biol. 2019 Jun 20;17(6):e3000333. doi: 10.1371/journal.pbio.3000333. eCollection 2019 Jun.

3.

MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.

LaPierre N, Mangul S, Alser M, Mandric I, Wu NC, Koslicki D, Eskin E.

BMC Genomics. 2019 Jun 6;20(Suppl 5):423. doi: 10.1186/s12864-019-5699-9.

4.

Systematic benchmarking of omics computational tools.

Mangul S, Martin LS, Hill BL, Lam AK, Distler MG, Zelikovsky A, Eskin E, Flint J.

Nat Commun. 2019 Mar 27;10(1):1393. doi: 10.1038/s41467-019-09406-4. Review.

5.

How bioinformatics and open data can boost basic science in countries and universities with limited resources.

Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E.

Nat Biotechnol. 2019 Mar;37(3):324-326. doi: 10.1038/s41587-019-0053-y. No abstract available.

PMID:
30833765
6.

Improving the usability and archival stability of bioinformatics software.

Mangul S, Martin LS, Eskin E, Blekhman R.

Genome Biol. 2019 Feb 27;20(1):47. doi: 10.1186/s13059-019-1649-8.

7.

Spatial Analysis of Single Fiber Cells of the Developing Ocular Lens Reveals Regulated Heterogeneity of Gene Expression.

Gangalum RK, Kim D, Kashyap RK, Mangul S, Zhou X, Elashoff D, Bhat SP.

iScience. 2018 Dec 21;10:66-79. doi: 10.1016/j.isci.2018.11.024. Epub 2018 Nov 17.

8.

A Comprehensive Map of Genetic Variation in the World's Largest Ethnic Group-Han Chinese.

Chiang CWK, Mangul S, Robles C, Sankararaman S.

Mol Biol Evol. 2018 Nov 1;35(11):2736-2750. doi: 10.1093/molbev/msy170.

PMID:
30169787
9.

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia.

Olde Loohuis LM, Mangul S, Ori APS, Jospin G, Koslicki D, Yang HT, Wu T, Boks MP, Lomen-Hoerth C, Wiedau-Pazos M, Cantor RM, de Vos WM, Kahn RS, Eskin E, Ophoff RA.

Transl Psychiatry. 2018 May 10;8(1):96. doi: 10.1038/s41398-018-0107-9.

10.

Involving undergraduates in genomics research to narrow the education-research gap.

Mangul S, Martin LS, Eskin E.

Nat Biotechnol. 2018 Apr 5;36(4):369-371. doi: 10.1038/nbt.4113. No abstract available.

PMID:
29621227
11.

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.

Mangul S, Yang HT, Strauli N, Gruhl F, Porath HT, Hsieh K, Chen L, Daley T, Christenson S, Wesolowska-Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Levanon EY, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N.

Genome Biol. 2018 Feb 15;19(1):36. doi: 10.1186/s13059-018-1403-7.

12.

Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX.

Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E.

Trends Biotechnol. 2017 Oct;35(10):901-903. doi: 10.1016/j.tibtech.2017.06.007. Epub 2017 Jul 15.

PMID:
28720283
13.

HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads.

Mangul S, Yang TH, Hormozdiari F, Dainis AM, Tseng E, Ashley EA, Zelikovsky A, Eskin E.

IEEE Trans Nanobioscience. 2017 Mar;16(2):108-115. doi: 10.1109/TNB.2017.2675981. Epub 2017 Mar 17.

PMID:
28328508
14.

Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.

Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, Zelikovsky A.

J Comput Biol. 2017 Jun;24(6):558-570. doi: 10.1089/cmb.2016.0146. Epub 2016 Nov 30.

15.

Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data.

Kang EY, Martin LJ, Mangul S, Isvilanonda W, Zou J, Ben-David E, Han B, Lusis AJ, Shifman S, Eskin E.

Genetics. 2016 Nov;204(3):1057-1064. doi: 10.1534/genetics.115.177246. Epub 2016 Oct 7.

16.

CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma.

Schokrpur S, Hu J, Moughon DL, Liu P, Lin LC, Hermann K, Mangul S, Guan W, Pellegrini M, Xu H, Wu L.

Sci Rep. 2016 Jun 30;6:29032. doi: 10.1038/srep29032.

17.

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.

Mangul S, Caciula A, Al Seesi S, Brinza D, Mӑndoiu I, Zelikovsky A.

BMC Genomics. 2014;15 Suppl 5:S7. doi: 10.1186/1471-2164-15-S5-S7. Epub 2014 Jul 14.

18.

Accurate viral population assembly from ultra-deep sequencing data.

Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E.

Bioinformatics. 2014 Jun 15;30(12):i329-37. doi: 10.1093/bioinformatics/btu295.

19.

Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.

Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A.

In Silico Biol. 2011-2012;11(5-6):251-61. doi: 10.3233/ISB-2012-0459.

PMID:
23202426
20.

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A.

BMC Bioinformatics. 2011;12 Suppl 6:S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.

21.

Estimation of alternative splicing isoform frequencies from RNA-Seq data.

Nicolae M, Mangul S, Măndoiu II, Zelikovsky A.

Algorithms Mol Biol. 2011 Apr 19;6(1):9. doi: 10.1186/1748-7188-6-9.

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