Feil Family Brain & Mind Research Institute

Publications

Found 20 results

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Prjibelski AD, Mikheenko A, Joglekar A, Smetanin A, Jarroux J, Lapidus AL, Tilgner HU. 2023. Accurate isoform discovery with IsoQuant using long reads.. Nat Biotechnol.

Li D, Li J, Johann DJ, Butler D, Chen G, Foox J, Gong B, Jones W, Kreil DP, Kusko R et al.. 2025. Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations.. NPJ Precis Oncol. 9(1):182.

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Hu W, Foord C, Hsu J, Fan L, Corley MJ, Lanjewar SN, Xu S, Belchikov N, He Y, Pang APS et al.. 2025. Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.. Nat Biotechnol.

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Michielsen L, Hsu J, Joglekar A, Belchikov N, Reinders MJT, Tilgner HU, Mahfouz A. 2026. Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.. Genome Biol. 27(1)

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Joglekar A, Foord C, Jarroux J, Pollard S, Tilgner HU. 2023. From words to complete phrases: insight into single-cell isoforms using short and long reads.. Transcription. :1-13.

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Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. 2019. Getting the Entire Message: Progress in Isoform Sequencing.. Front Genet. 10:709.

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Biegler MT, Fedrigo O, Collier P, Mountcastle J, Haase B, Tilgner HU, Jarvis ED. 2022. Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9.. Sci Rep. 12(1):4369.

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Biegler MT, Belay K, Wang W, Szialta C, Collier P, Luo J-D, Haase B, Gedman GL, Sidhu AV, Harter E et al.. 2024. Pronounced early differentiation underlies zebra finch gonadal germ cell development.. Dev Biol. 517:73-90.

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Stein AN, Joglekar A, Poon C-L, Tilgner HU. 2022. ScisorWiz: Visualizing Differential Isoform Expression in Single-Cell Long-Read Data.. Bioinformatics.

Mikheenko A, Prjibelski AD, Joglekar A, Tilgner HU. 2022. Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.. Genome Res. 32(4):726-737.

Gupta I, Collier PG, Haase B, Mahfouz A, Joglekar A, Floyd T, Koopmans F, Barres B, Smit AB, Sloan SA et al.. 2018. Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells.. Nat Biotechnol.

Belchikov N, Hu W, Fan L, Joglekar A, He Y, Foord C, Jarroux J, Hsu J, Pollard S, Amin S et al.. 2025. A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain.. Cell Rep. 44(9):116198.

Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED et al.. 2023. Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development.. bioRxiv.

Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Marrocco J, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O et al.. 2024. Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain.. Nat Neurosci.

Hardwick SA, Hu W, Joglekar A, Fan L, Collier PG, Foord C, Balacco J, Lanjewar S, Sampson MMcGuirk, Koopmans F et al.. 2022. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.. Nat Biotechnol.

Foord C, Prjibelski AD, Hu W, Michielsen L, Vandelli A, Narykov O, Evans B, Hsu J, Belchikov N, Jarroux J et al.. 2025. A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types.. Nat Commun. 16(1):8093.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G et al.. 2023. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. bioRxiv.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G et al.. 2024. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. Nat Methods. 21(7):1349-1363.

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Gong B, Li D, Łabaj PP, Pan B, Novoradovskaya N, Thierry-Mieg D, Thierry-Mieg J, Chen G, Lucas ABergstrom, LoCoco JS et al.. 2024. Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing.. Sci Data. 11(1):892.

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Foord C, Hsu J, Jarroux J, Hu W, Belchikov N, Pollard S, He Y, Joglekar A, Tilgner HU. 2023. The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing. Nat Methods. 20(1):20-24.