Single-Cell DNA Sequencing of AML with Droplet Microfluidics

The Sequence Alignment/Map format and SAMtools

Heng Li, R. Handsaker, Alec Wysoker, et al.. (2009). Bioinformatics. Cited 54,792 times. https://doi.org/10.1093/bioinformatics/btp352

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, M. Lohse, B. Usadel. (2014). Bioinformatics. Cited 54,202 times. https://doi.org/10.1093/bioinformatics/btu170

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

A. McKenna, M. Hanna, E. Banks, et al.. (2010). Genome research. Cited 24,858 times. https://doi.org/10.1101/gr.107524.110

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead, C. Trapnell, Mihai Pop, et al.. (2009). Genome Biology. Cited 21,910 times. https://doi.org/10.1186/gb-2009-10-3-r25

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim, G. Pertea, C. Trapnell, et al.. (2013). Genome Biology. Cited 12,071 times. https://doi.org/10.1186/gb-2013-14-4-r36

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Evan Z. Macosko, Anindita Basu, R. Satija, et al.. (2015). Cell. Cited 6,327 times. https://doi.org/10.1016/j.cell.2015.05.002

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

T. Ley, C. Miller, L. Ding, et al.. (2013). The New England journal of medicine. Cited 4,458 times. https://doi.org/10.1056/NEJMoa1301689

Genomic Classification and Prognosis in Acute Myeloid Leukemia.

E. Papaemmanuil, M. Gerstung, L. Bullinger, et al.. (2016). The New England journal of medicine. Cited 3,359 times. https://doi.org/10.1056/NEJMoa1516192

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

Allon M. Klein, L. Mazutis, Ilke Akartuna, et al.. (2015). Cell. Cited 3,048 times. https://doi.org/10.1016/j.cell.2015.04.044

Analysis of FLT3-activating mutations in 979 patients with acute myelogenous leukemia: association with FAB subtypes and identification of subgroups with poor prognosis.

C. Thiede, C. Steudel, B. Mohr, et al.. (2002). Blood. Cited 1,801 times. https://doi.org/10.1182/BLOOD.V99.12.4326

The Origin and Evolution of Mutations in Acute Myeloid Leukemia

J. Welch, T. Ley, D. Link, et al.. (2012). Cell. Cited 1,557 times. https://doi.org/10.1016/j.cell.2012.06.023

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

A. Rotem, Oren Ram, N. Shoresh, et al.. (2015). Nature biotechnology. Cited 784 times. https://doi.org/10.1038/nbt.3383

Single-cell barcoding and sequencing using droplet microfluidics

R. Zilionis, J. Nainys, A. Veres, et al.. (2016). Nature Protocols. Cited 645 times. https://doi.org/10.1038/nprot.2016.154

Biocompatible surfactants for water-in-fluorocarbon emulsions.

Christian Holtze, A. Rowat, J. Agresti, et al.. (2008). Lab on a chip. Cited 643 times. https://doi.org/10.1039/b806706f

SiC-Seq: Single-cell genome sequencing at ultra high-throughput with microfluidic droplet barcoding

F. Lan, B. Demaree, Noorsher Ahmed, et al.. (2017). Nature biotechnology. Cited 353 times. https://doi.org/10.1038/nbt.3880

Advanced Heat Map and Clustering Analysis Using Heatmap3

Shilin Zhao, Yan Guo, Quanhu Sheng, et al.. (2014). BioMed Research International. Cited 310 times. https://doi.org/10.1155/2014/986048

Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction.

D. P. Jackson, F. Lewis, G. R. Taylor, et al.. (1990). Journal of Clinical Pathology. Cited 293 times. https://doi.org/10.1136/jcp.43.6.499

Optimizing cancer genome sequencing and analysis.

M. Griffith, Christopher A. Miller, O. Griffith, et al.. (2015). Cell systems. Cited 198 times. https://doi.org/10.7490/F1000RESEARCH.1110088.1

Preparation of Genomic DNA from Mammalian Tissue

W. Strauss. (1998). Current Protocols in Molecular Biology. Cited 183 times. https://doi.org/10.1002/0471142727.mb0202s42

Heterogeneous resistance to quizartinib in acute myeloid leukemia revealed by single-cell analysis.

Catherine C. Smith, A. Paguirigan, Grace R. Jeschke, et al.. (2017). Blood. Cited 164 times. https://doi.org/10.1182/blood-2016-04-711820

Single-cell genotyping demonstrates complex clonal diversity in acute myeloid leukemia

A. Paguirigan, Jordan L Smith, S. Meshinchi, et al.. (2015). Science Translational Medicine. Cited 146 times. https://doi.org/10.1126/scitranslmed.aaa0763

Ultrahigh-throughput Mammalian single-cell reverse-transcriptase polymerase chain reaction in microfluidic drops.

Dennis J. Eastburn, A. Sciambi, A. Abate. (2013). Analytical chemistry. Cited 125 times. https://doi.org/10.1021/ac402057q

Monitoring minimal residual disease in acute leukemia: Technical challenges and interpretive complexities.

Xueyan Chen, B. Wood. (2017). Blood reviews. Cited 80 times. https://doi.org/10.1016/j.blre.2016.09.006

Generating electric fields in PDMS microfluidic devices with salt water electrodes.

A. Sciambi, A. Abate. (2014). Lab on a chip. Cited 75 times. https://doi.org/10.1039/c4lc00078a

Identification and genetic analysis of cancer cells with PCR-activated cell sorting

Dennis J. Eastburn, A. Sciambi, A. Abate. (2014). Nucleic Acids Research. Cited 63 times. https://doi.org/10.1093/nar/gku606

RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures

M. Pellegrino, A. Sciambi, Jamie L. Yates, et al.. (2016). BMC Genomics. Cited 24 times. https://doi.org/10.1186/s12864-016-2694-2

Overcoming mutational complexity in acute myeloid leukemia by inhibition of critical pathways

Yoriko Saito, Yoshiki Mochizuki, Ikuko Ogahara, et al.. (2017). Science Translational Medicine. Cited 22 times. https://doi.org/10.1126/scitranslmed.aao1214