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Items: 16

1.

Massively multiplex chemical transcriptomics at single cell resolution.

Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers F, Shendure J, Trapnell C.

Science. 2019 Dec 5. pii: eaax6234. doi: 10.1126/science.aax6234. [Epub ahead of print]

PMID:
31806696
2.

Supervised classification enables rapid annotation of cell atlases.

Pliner HA, Shendure J, Trapnell C.

Nat Methods. 2019 Oct;16(10):983-986. doi: 10.1038/s41592-019-0535-3. Epub 2019 Sep 9.

PMID:
31501545
3.

The accessible chromatin landscape of the murine hippocampus at single-cell resolution.

Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC.

Genome Res. 2019 May;29(5):857-869. doi: 10.1101/gr.243725.118. Epub 2019 Apr 1.

4.

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J.

Science. 2018 Sep 28;361(6409):1380-1385. doi: 10.1126/science.aau0730. Epub 2018 Aug 30.

5.

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C.

Mol Cell. 2018 Sep 6;71(5):858-871.e8. doi: 10.1016/j.molcel.2018.06.044. Epub 2018 Aug 2.

6.

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J.

Cell. 2018 Aug 23;174(5):1309-1324.e18. doi: 10.1016/j.cell.2018.06.052. Epub 2018 Aug 2.

7.

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.

Nicolas A, Kenna KP, Renton AE, Ticozzi N, Faghri F, Chia R, Dominov JA, Kenna BJ, Nalls MA, Keagle P, Rivera AM, van Rheenen W, Murphy NA, van Vugt JJFA, Geiger JT, Van der Spek RA, Pliner HA, Shankaracharya, Smith BN, Marangi G, Topp SD, Abramzon Y, Gkazi AS, Eicher JD, Kenna A; ITALSGEN Consortium, Mora G, Calvo A, Mazzini L, Riva N, Mandrioli J, Caponnetto C, Battistini S, Volanti P, La Bella V, Conforti FL, Borghero G, Messina S, Simone IL, Trojsi F, Salvi F, Logullo FO, D'Alfonso S, Corrado L, Capasso M, Ferrucci L; Genomic Translation for ALS Care (GTAC) Consortium, Moreno CAM, Kamalakaran S, Goldstein DB; ALS Sequencing Consortium, Gitler AD, Harris T, Myers RM; NYGC ALS Consortium, Phatnani H, Musunuri RL, Evani US, Abhyankar A, Zody MC; Answer ALS Foundation, Kaye J, Finkbeiner S, Wyman SK, LeNail A, Lima L, Fraenkel E, Svendsen CN, Thompson LM, Van Eyk JE, Berry JD, Miller TM, Kolb SJ, Cudkowicz M, Baxi E; Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, Benatar M, Taylor JP, Rampersaud E, Wu G, Wuu J; SLAGEN Consortium, Lauria G, Verde F, Fogh I, Tiloca C, Comi GP, Sorarù G, Cereda C; French ALS Consortium, Corcia P, Laaksovirta H, Myllykangas L, Jansson L, Valori M, Ealing J, Hamdalla H, Rollinson S, Pickering-Brown S, Orrell RW, Sidle KC, Malaspina A, Hardy J, Singleton AB, Johnson JO, Arepalli S, Sapp PC, McKenna-Yasek D, Polak M, Asress S, Al-Sarraj S, King A, Troakes C, Vance C, de Belleroche J, Baas F, Ten Asbroek ALMA, Muñoz-Blanco JL, Hernandez DG, Ding J, Gibbs JR, Scholz SW, Floeter MK, Campbell RH, Landi F, Bowser R, Pulst SM, Ravits JM, MacGowan DJL, Kirby J, Pioro EP, Pamphlett R, Broach J, Gerhard G, Dunckley TL, Brady CB, Kowall NW, Troncoso JC, Le Ber I, Mouzat K, Lumbroso S, Heiman-Patterson TD, Kamel F, Van Den Bosch L, Baloh RH, Strom TM, Meitinger T, Shatunov A, Van Eijk KR, de Carvalho M, Kooyman M, Middelkoop B, Moisse M, McLaughlin RL, Van Es MA, Weber M, Boylan KB, Van Blitterswijk M, Rademakers R, Morrison KE, Basak AN, Mora JS, Drory VE, Shaw PJ, Turner MR, Talbot K, Hardiman O, Williams KL, Fifita JA, Nicholson GA, Blair IP, Rouleau GA, Esteban-Pérez J, García-Redondo A, Al-Chalabi A; Project MinE ALS Sequencing Consortium, Rogaeva E, Zinman L, Ostrow LW, Maragakis NJ, Rothstein JD, Simmons Z, Cooper-Knock J, Brice A, Goutman SA, Feldman EL, Gibson SB, Taroni F, Ratti A, Gellera C, Van Damme P, Robberecht W, Fratta P, Sabatelli M, Lunetta C, Ludolph AC, Andersen PM, Weishaupt JH, Camu W, Trojanowski JQ, Van Deerlin VM, Brown RH Jr, van den Berg LH, Veldink JH, Harms MB, Glass JD, Stone DJ, Tienari P, Silani V, Chiò A, Shaw CE, Traynor BJ, Landers JE.

Neuron. 2018 Mar 21;97(6):1268-1283.e6. doi: 10.1016/j.neuron.2018.02.027.

8.

The cis-regulatory dynamics of embryonic development at single-cell resolution.

Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM.

Nature. 2018 Mar 22;555(7697):538-542. doi: 10.1038/nature25981. Epub 2018 Mar 14.

9.

Reversed graph embedding resolves complex single-cell trajectories.

Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, Trapnell C.

Nat Methods. 2017 Oct;14(10):979-982. doi: 10.1038/nmeth.4402. Epub 2017 Aug 21.

10.

TBK1 is associated with ALS and ALS-FTD in Sardinian patients.

Borghero G, Pugliatti M, Marrosu F, Marrosu MG, Murru MR, Floris G, Cannas A, Occhineri P, Cau TB, Loi D, Ticca A, Traccis S, Manera U, Canosa A, Moglia C, Calvo A, Barberis M, Brunetti M, Gibbs JR, Renton AE, Errichiello E, Zoledziewska M, Mulas A, Qian Y, Din J, Pliner HA, Traynor BJ, Chiò A; ITALSGEN and SARDINALS Consortia.

Neurobiol Aging. 2016 Jul;43:180.e1-5. doi: 10.1016/j.neurobiolaging.2016.03.028. Epub 2016 Apr 9.

PMID:
27156075
11.

Genome-Wide Identification and Expression of Xenopus F-Box Family of Proteins.

Saritas-Yildirim B, Pliner HA, Ochoa A, Silva EM.

PLoS One. 2015 Sep 1;10(9):e0136929. doi: 10.1371/journal.pone.0136929. eCollection 2015.

12.

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.

Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J.

Science. 2015 May 22;348(6237):910-4. doi: 10.1126/science.aab1601. Epub 2015 May 7.

13.

A genome-wide association study of myasthenia gravis.

Renton AE, Pliner HA, Provenzano C, Evoli A, Ricciardi R, Nalls MA, Marangi G, Abramzon Y, Arepalli S, Chong S, Hernandez DG, Johnson JO, Bartoccioni E, Scuderi F, Maestri M, Gibbs JR, Errichiello E, Chiò A, Restagno G, Sabatelli M, Macek M, Scholz SW, Corse A, Chaudhry V, Benatar M, Barohn RJ, McVey A, Pasnoor M, Dimachkie MM, Rowin J, Kissel J, Freimer M, Kaminski HJ, Sanders DB, Lipscomb B, Massey JM, Chopra M, Howard JF Jr, Koopman WJ, Nicolle MW, Pascuzzi RM, Pestronk A, Wulf C, Florence J, Blackmore D, Soloway A, Siddiqi Z, Muppidi S, Wolfe G, Richman D, Mezei MM, Jiwa T, Oger J, Drachman DB, Traynor BJ.

JAMA Neurol. 2015 Apr;72(4):396-404. doi: 10.1001/jamaneurol.2014.4103.

14.

Genetic architecture of ALS in Sardinia.

Borghero G, Pugliatti M, Marrosu F, Marrosu MG, Murru MR, Floris G, Cannas A, Parish LD, Occhineri P, Cau TB, Loi D, Ticca A, Traccis S, Manera U, Canosa A, Moglia C, Calvo A, Barberis M, Brunetti M, Pliner HA, Renton AE, Nalls MA, Traynor BJ, Restagno G, Chiò A; ITALSGEN and SARDINALS Consortia.

Neurobiol Aging. 2014 Dec;35(12):2882.e7-2882.e12. doi: 10.1016/j.neurobiolaging.2014.07.012. Epub 2014 Jul 18.

15.

Mutations in the Matrin 3 gene cause familial amyotrophic lateral sclerosis.

Johnson JO, Pioro EP, Boehringer A, Chia R, Feit H, Renton AE, Pliner HA, Abramzon Y, Marangi G, Winborn BJ, Gibbs JR, Nalls MA, Morgan S, Shoai M, Hardy J, Pittman A, Orrell RW, Malaspina A, Sidle KC, Fratta P, Harms MB, Baloh RH, Pestronk A, Weihl CC, Rogaeva E, Zinman L, Drory VE, Borghero G, Mora G, Calvo A, Rothstein JD; ITALSGEN, Drepper C, Sendtner M, Singleton AB, Taylor JP, Cookson MR, Restagno G, Sabatelli M, Bowser R, Chiò A, Traynor BJ.

Nat Neurosci. 2014 May;17(5):664-666. doi: 10.1038/nn.3688. Epub 2014 Mar 30.

16.

Searching for Grendel: origin and global spread of the C9ORF72 repeat expansion.

Pliner HA, Mann DM, Traynor BJ.

Acta Neuropathol. 2014 Mar;127(3):391-6. doi: 10.1007/s00401-014-1250-x. Epub 2014 Feb 5.

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