Publications

Found 85 results

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2021

Aguiar-Pulido V, Wolujewicz P, Martinez-Fundichely A, Elhaik E, Thareja G, Aleem AAbdel, Chalhoub N, Cuykendall T, Al-Zamer J, Lei Y et al.. 2021. Systems biology analysis of human genomes points to key pathways conferring spina bifida risk.. Proc Natl Acad Sci U S A. 118(51)

2022

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.

Dolgetta A, Johnson M, Fruitman K, Siegel L, Zhou Y, McEwen BS, Kreek MJeanne, Milner TA. 2022. Sex and chronic stress alter the distribution of glutamate receptors within rat hippocampal CA3 pyramidal cells following oxycodone conditioned place preference.. Neurobiol Stress. 17:100431.

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.

Allen M, Huang BS, Notaras MJ, Lodhi A, Barrio-Alonso E, Lituma PJ, Wolujewicz P, Witztum J, Longo F, Chen M et al.. 2022. Spontaneous generation of ASD astrocytes.. Mol Psychiatry. 27(5):2369.

Hochrainer K, Yang W. 2022. Stroke Proteomics: From Discovery to Diagnostic and Therapeutic Applications.. Circ Res. 130(8):1145-1166.

Carnazza KE, Komer LE, Xie YXue, Pineda A, Briano JAntonio, Gao V, Na Y, Ramlall T, Buchman VL, Eliezer D et al.. 2022. Synaptic vesicle binding of α-synuclein is modulated by β- and γ-synucleins.. Cell Rep. 39(2):110675.

2023

Chlebowicz J, Russ W, Chen D, Vega A, Vernino S, White CL, Rizo J, Joachimiak LA, Diamond MI. 2023. Saturation mutagenesis of α-synuclein reveals monomer fold that modulates aggregation.. Sci Adv. 9(43):eadh3457.

Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJune, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K et al.. 2023. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.. bioRxiv.

Lopez-Lee C, Kodama L, Fan L, Wong MYing, Foxe NR, Jiaz L, Yu F, Ye P, Zhu J, Norman K et al.. 2023. Sex Chromosomes and Gonads Shape the Sex-Biased Transcriptomic Landscape in Tlr7-Mediated Demyelination During Aging.. bioRxiv.

Eruysal E, Ravdin L, Zhang C, Kamel H, Iadecola C, Ishii M. 2023. Sexually Dimorphic Association of Circulating Plasminogen Activator Inhibitor-1 Levels and Body Mass Index with Cerebrospinal Fluid Biomarkers of Alzheimer's Pathology in Preclinical Alzheimer's Disease.. J Alzheimers Dis. 91(3):1073-1083.

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.

Sasset L, Chowdhury KH, Manzo OL, Rubinelli L, Konrad C, J Maschek A, Manfredi G, Holland WL, Di Lorenzo A. 2023. Sphingosine-1-phosphate controls endothelial sphingolipid homeostasis via ORMDL.. EMBO Rep. 24(1):e54689.

Fins JJ, Wright MS, Shulman KS, Henderson JM, Schiff ND. 2023. Subject and Family Perspectives from the Central Thalamic Deep Brain Stimulation Trial for Traumatic Brain Injury: Part II.. Camb Q Healthc Ethics. :1-24.

Chiu Y-T, Deutch AY, Wang W, Schmitz GP, Huang KLu, D Kocak D, Llorach P, Bowyer K, Liu B, Sciaky N et al.. 2023. A suite of engineered mice for interrogating psychedelic drug actions.. 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.. 2023. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. bioRxiv.

Bennett NK, Lee M, Orr AL, Nakamura K. 2023. Systems-level analyses dissociate genetic regulators of reactive oxygen species and energy production.. bioRxiv.

2024

Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJune, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K et al.. 2024. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.. Nat Biotechnol.

Stankovic I, Notaras M, Wolujewicz P, Lu T, Lis R, M Ross E, Colak D. 2024. Schizophrenia endothelial cells exhibit higher permeability and altered angiogenesis patterns in patient-derived organoids.. Transl Psychiatry. 14(1):53.

Chambers IG, Ratan RR. 2024. Selenium abandons selenoproteins to inhibit ferroptosis rapidly.. Nat Metab. 6(2):200-202.

Colognesi M, Shkodra A, Gabbia D, Kawamata H, Manfredi PL, Manfredi G, De Martin S. 2024. Sex-dependent effects of the uncompetitive N-methyl-D-aspartate receptor antagonist REL-1017 in G93A-SOD1 amyotrophic lateral sclerosis mice.. Front Neurol. 15:1384829.

Peter CJ, Agarwal A, Watanabe R, Kassim BS, Wang X, Lambert TY, Javidfar B, Evans V, Dawson T, Fridrikh M et al.. 2024. Single chromatin fiber profiling and nucleosome position mapping in the human brain.. Cell Rep Methods. 4(12):100911.

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.

Pellerin D, Méreaux J-L, Boluda S, Danzi MC, Dicaire M-J, Davoine C-S, Genis D, Spurdens G, Ashton C, Hammond JM et al.. 2024. Somatic instability of the FGF14-SCA27B GAA•TTC repeat reveals a marked expansion bias in the cerebellum.. Brain.