Cydney Nielsen
Cydney Nielsen
Visualization Designer / Data Scientist
Verified email at - Homepage
Cited by
Cited by
The genome sequence of the filamentous fungus Neurospora crassa
JE Galagan, SE Calvo, KA Borkovich, EU Selker, ND Read, D Jaffe, ...
Nature 422 (6934), 859-868, 2003
Conserved role of intragenic DNA methylation in regulating alternative promoters
AK Maunakea, RP Nagarajan, M Bilenky, TJ Ballinger, C D’Souza, ...
Nature 466 (7303), 253-257, 2010
Hereditary diffuse gastric cancer syndrome: CDH1 mutations and beyond
S Hansford, P Kaurah, H Li-Chang, M Woo, J Senz, H Pinheiro, ...
JAMA oncology 1 (1), 23-32, 2015
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution
P Eirew, A Steif, J Khattra, G Ha, D Yap, H Farahani, K Gelmon, S Chia, ...
Nature 518 (7539), 422-426, 2015
Determinants of targeting by endogenous and exogenous microRNAs and siRNAs
CB Nielsen, N Shomron, R Sandberg, E Hornstein, J Kitzman, CB Burge
Rna 13 (11), 1894-1910, 2007
De novo transcriptome assembly with ABySS
I Birol, SD Jackman, CB Nielsen, JQ Qian, R Varhol, G Stazyk, RD Morin, ...
Bioinformatics 25 (21), 2872-2877, 2009
Biased chromatin signatures around polyadenylation sites and exons
N Spies, CB Nielsen, RA Padgett, CB Burge
Molecular cell 36 (2), 245-254, 2009
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
A McPherson, A Roth, E Laks, T Masud, A Bashashati, AW Zhang, G Ha, ...
Nature genetics 48 (7), 758-767, 2016
The Human Epigenome Browser at Washington University
X Zhou, B Maricque, M Xie, D Li, V Sundaram, EA Martin, BC Koebbe, ...
Nature Methods 8 (12), 989-990, 2011
Interfaces of malignant and immunologic clonal dynamics in ovarian cancer
AW Zhang, A McPherson, K Milne, DR Kroeger, PT Hamilton, A Miranda, ...
Cell 173 (7), 1755-1769. e22, 2018
Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs
AKL Leung, AG Young, A Bhutkar, GX Zheng, AD Bosson, CB Nielsen, ...
Nature structural & molecular biology 18 (2), 237-244, 2011
Histological transformation and progression in follicular lymphoma: a clonal evolution study
R Kridel, FC Chan, A Mottok, M Boyle, P Farinha, K Tan, B Meissner, ...
PLoS medicine 13 (12), e1002197, 2016
Visualizing genomes: techniques and challenges
CB Nielsen, M Cantor, I Dubchak, D Gordon, T Wang
Nature methods 7 (Suppl 3), S5-S15, 2010
Clonal decomposition and DNA replication states defined by scaled single-cell genome sequencing
E Laks, A McPherson, H Zahn, D Lai, A Steif, J Brimhall, J Biele, B Wang, ...
Cell 179 (5), 1207-1221. e22, 2019
Visualizing biological data—now and in the future
SI O'Donoghue, AC Gavin, N Gehlenborg, DS Goodsell, JK Hériché, ...
Nature methods 7 (Suppl 3), S2-S4, 2010
Patterns of intron gain and loss in fungi
CB Nielsen, B Friedman, B Birren, CB Burge, JE Galagan
PLoS biology 2 (12), e422, 2004
Clonal genotype and population structure inference from single-cell tumor sequencing
A Roth, A McPherson, E Laks, J Biele, D Yap, A Wan, MA Smith, ...
Nature methods 13 (7), 573-576, 2016
ABySS-Explorer: visualizing genome sequence assemblies
CB Nielsen, SD Jackman, I Birol, SJM Jones
IEEE transactions on visualization and computer graphics 15 (6), 881-888, 2009
E-scape: interactive visualization of single-cell phylogenetics and cancer evolution
MA Smith, CB Nielsen, FC Chan, A McPherson, A Roth, H Farahani, ...
Nature methods 14 (6), 549-550, 2017
Variant view: visualizing sequence variants in their gene context
JA Ferstay, CB Nielsen, T Munzner
IEEE transactions on visualization and computer graphics 19 (12), 2546-2555, 2013
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