NeuroLINCS

Assessing Microscope Image Focus Quality With Deep Learning

Samuel J. Yang, Marc Berndl, D. Michael Ando, Mariya Barch, Arunachalam Narayanaswamy, Eric Christiansen, Stephan Hoyer, Chris Roat, Jane Hung, Curtis T. Rueden, Asim Shankar, Steven Finkbeiner and Philip Nelson

BMC Bioinformatics. 2018 Mar 15;19(1):77. doi: 10.1186/s12859-018-2087-4

PCSF: An R-package for network-based interpretation of high-throughput data.

Akhmedov M, Kedaigle A, Chong RE, Montemanni R, Bertoni F, Fraenkel E, Kwee I.

PLoS Comput Biol. 2017 Jul 31;13(7):e1005694. doi: 10.1371/journal.pcbi.1005694.

Nrf2 mitigates LRRK2- and α-synuclein-induced neurodegeneration by modulating proteostasis.

Skibinski G, Hwang V, Ando DM, Daub A, Lee AK, Ravisankar A, Modan S, Finucane MM, Shaby BA, Finkbeiner S.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1165-1170. doi: 10.1073/pnas.1522872114.

Gene activation of SMN by selective disruption of lncRNA-mediated recruitment of PRC2 for the treatment of spinal muscular atrophy.

Woo CJ, Maier VK, Davey R, Brennan J, Li G, Brothers J 2nd, Schwartz B, Gordo S, Kasper A, Okamoto TR, Johansson HE, Mandefro B, Sareen D, Bialek P, Chau BN, Bhat B, Bullough D, Barsoum J.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1509-E1518. doi: 10.1073/pnas.1616521114. Epub 2017 Feb 13.

Huntington’s Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits

Ryan G. Lim, Chris Quan, Andrea M. Reyes-Ortiz, Sarah E. Lutz, Amanda J. Kedaigle, Theresa A. Gipson, Jie Wu, Gad D. Vatine, Jennifer Stocksdale, Malcolm S. Casale, Clive N. Svendsen, Ernest Fraenkel, David E. Housman, Dritan Agalliu, Leslie M. Thompson

Cell Reports, DOI: https://doi.org/10.1016/j.celrep.2017.04.021

A Comparison of mRNA Sequencing with Random Primed and 3’-Directed Libraries

Yuguang Xiong, Magali Soumillon, Jie Wu, Jens Hansen, Bin Hu, Johan G.C. van Hasselt, Gomathi Jayaraman, Ryan Lim, Mehdi Bouhaddou, Loren Ornelas, James Bochicchio, Lindsay Lenaeus, Jennifer Stocksdale, Jaehee Shim, Emilda Gomez, Dhruv Sareen, Clive Svendsen, Leslie M Thompson, Milind Mahajan, Ravi Iyengar, Eric A Sobie, Evren U Azeloglu, Marc R Birtwistle

BioRXiv, doi: https://doi.org/10.1101/098905

Differentiation of Human Induced Pluripotent Stem Cells to Mammary-like Organoids

Ying Qu, Bingchen Han, Bowen Gao, Shikha Bose, Yiping Gong, Kolja Wawrowsky, Armando E. Giuliano, Dhruv Sareen, Xiaojiang Cui

Stem Cell Reports. 2017 Feb 14;8(2):205-215. doi: 10.1016/j.stemcr.2016.12.023

Developmental alterations in Huntington’s disease neural cells and pharmacological rescue in cells and mice

The HD iPSC Consortium

Nature Neuroscience 20, 648–660 (2017) doi:10.1038/nn.4532

Effect of peptide assay library size and composition in targeted data-independent acquisition-MS analyses

Sarah J. Parker, Vidya Venkatraman, Jennifer E. Van Eyk

Proteomics. 2016 Aug;16(15-16):2221-37. doi: 10.1002/pmic.201600007.

Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease

Pilar Vazquez-Arango, Jane Vowles, Cathy Browne, Elizabeth Hartfield, Hugo J. R. Fernandes, Berhan Mandefro, Dhruv Sareen, William James, Richard Wade-Martins, Sally A. Cowley, Shona Murphy, Dawn O’Reilly

Nucleic Acids Res (2016) 44 (22): 10960-10973. DOI: https://doi.org/10.1093/nar/gkw711

C9ORF72 poly(GA) aggregates sequester and impair HR23 and nucleocytoplasmic transport proteins

Yong-Jie Zhang, Tania F Gendron, Jonathan C Grima, Hiroki Sasaguri, Karen Jansen-West, Ya-Fei Xu, Rebecca B Katzman, Jennifer Gass, Melissa E Murray, Mitsuru Shinohara, Wen-Lang Lin, Aliesha Garrett, Jeannette N Stankowski, Lillian Daughrity, Jimei Tong, Emilie A Perkerson, Mei Yue, Jeannie Chew, Monica Castanedes-Casey, Aishe Kurti, Zizhao S Wang, Amanda M Liesinger, Jeremy D Baker, Jie Jiang, Clotilde Lagier-Tourenne, Dieter Edbauer, Don W Cleveland, Rosa Rademakers, Kevin B Boylan, Guojun Bu, Christopher D Link, Chad A Dickey, Jeffrey D Rothstein, Dennis W Dickson, John D Fryer & Leonard Petrucelli

Nature Neuroscience 19, 668–677 (2016) doi:10.1038/nn.4272

Spinal Muscular Atrophy Patient iPSC-Derived Motor Neurons Have Reduced Expression of Proteins Important in Neuronal Development

Fuller HR, Mandefro B, Shirran SL, Gross AR, Kaus AS, Botting CH, Morris GE, Sareen D.

Front. Cell. Neurosci., 11 January 2016 https://doi.org/10.3389/fncel.2015.00506

ALS Disrupts Spinal Motor Neuron Maturation and Aging Pathways Within Gene Co-Expression Networks.

Ho R, Sances S, Gowing G, Amoroso MW, O’Rourke JG, Sahabian A, Wichterle H, Baloh RH, Sareen D, Svendsen CN

Nat Neurosci. 2016 Sep;19(9):1256-67. doi: 10.1038/nn.4345

Revealing disease-associated pathways by network integration of untargeted metabolomics.

Pirhaji L, Milani P, Leidl M, Curran T, Avila-Pacheco J, Clish CB, White FM, Saghatelian A, Fraenkel E

Nat Methods. 2016 Sep;13(9):770-6. doi: 10.1038/nmeth.3940

A three-groups model for high-throughput survival screens.

Shaby BA, Skibinski G, Ando M, LaDow ES, Finkbeiner S

Biometrics 2016 Sep;72(3):936-44. doi: 10.1111/biom.12479

The expanding biology of the C9orf72 nucleotide repeat expansion in neurodegenerative disease.

Haeusler AR, Donnelly CJ, Rothstein JD

Nat Rev Neurosci. 2016 Jun;17(6):383-95. doi: 10.1038/nrn.2016.38

Clinical Trials in a Dish: The Potential of Pluripotent Stem Cells to Develop Therapies for Neurodegenerative Diseases.

Haston KM, Finkbeiner S

Annu Rev Pharmacol Toxicol. 2016;56:489-510. doi: 10.1146/annurev-pharmtox-010715-103548

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells.

Pamela Milani, Renan Escalante-Chong, Brandon C. Shelley, Natasha L. Patel-Murray, Xiaofeng Xin, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel

Scientific Reports 2016; doi: 10.1038/srep25474

Nucleocytoplasmic transport in C9orf72-mediated ALS/FTD.

Zhang K, Grima JC, Rothstein JD, Lloyd TE

Nucleus 2016 Apr 25;7(2):132-7. doi: 10.1080/19491034.2016.1172152

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.

Tuncbag N, Gosline SJ, Kedaigle A, Soltis AR, Gitter A, Fraenkel E

PLoS Comput Biol. 2016 Apr 20;12(4):e1004879. doi: 10.1371/journal.pcbi.1004879

Methods for SWATH™: Data Independent Acquisition on TripleTOF Mass Spectrometers.

Holewinski RJ, Parker SJ, Matlock AD, Venkatraman V, Van Eyk JE

Methods Mol Biol. 2016;1410:265-79. doi: 10.1007/978-1-4939-3524-6_16

Cell-based screening: extracting meaning from complex data.

Finkbeiner S, Frumkin M, Kassner PD

Neuron 2015 Apr 8;86(1):160-74. doi: 10.1016/j.neuron.2015.02.023

The C9orf72 repeat expansion disrupts nucleocytoplasmic transport

Zhang K, Donnelly CJ, Haeusler AR, Grima JC, Machamer JB, Steinwald P, Daley EL, Miller SJ, Cunningham KM, Vidensky S, Gupta S, Thomas MA, Hong I, Chiu SL, Huganir RL, Ostrow LW, Matunis MJ, Wang J, Sattler R, Lloyd TE, Rothstein J.

Nature 525, 56–61 (03 September 2015) doi:10.1038/nature14973