Preprints
DiMeLo-cito: a one-tube protocol for mapping protein-DNA interactions reveals CTCF bookmarking in mitosis
Gamarra N, Chittenden C, Sundararajan K, Schwartz JP, Lundqvist S, Robles D, Dixon-Luinenburg O, Marcus J, Maslan A, Franklin JM, Streets A, Straight AF, Altemose N., bioRxiv, doi: https://doi.org/10.1101/2025.03.11.642717
SRS microscopy identifies inhibition of vitellogenesis as a mediator of lifespan extension by caloric restriction in C. elegans
Yang B, Manifold B, Han W, DeSousa C, Zhu W, Streets A†, Titov DV†
bioRxiv, doi: https://doi.org/10.1101/2025.01.31.636008
Scvi-hub: an actionable repository for model-driven single cell analysis
Ergen, C., Valiollah Pour Amiri, V., Kim, M., Streets, A., Gayoso, A., Yosef, N., bioRxiv, doi: 10.1101/2024.03.01.582887
Imaging neurotransmitter transport in live cells with stimulated Raman scattering microscopy
Manifold B, Dorlhiac G, Landry M†, Streets A†
arXiv, doi: https://doi.org/10.48550/arXiv.2205.05798
Published Manuscripts
2024
Consensus prediction of cell type labels in single-cell data with popV
Ergen C, Xing G, Xu C, Kim M, Jayasuriya M, McGeever E, Oliveira Pisco A, Streets A, Yosef N., Nature Genetics, 56(12):2731-2738. doi: 10.1038/s41588-024-01993-3.
Mapping protein–DNA interactions with DiMeLo-seq
Maslan A, Altemose N, Marcus J, Mishra R, Brennan LD, Sundararajan K, Karpen G, Straight AF, Streets A, Nature Protocols, 19, 3697–3720 doi: https://doi.org/10.1038/s41596-024-01032-9
(preprint: https://doi.org/10.1101/2022.07.03.498618)
2023
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells
Gayoso A, Weiler P, Lotfollahi M, Klein D, Hong J, Streets A, Theis FJ† and Yosef N†, Nature Methods, 21 (1), 50-59, https://doi.org/10.1038/s41592-023-01994-w,
(preprint doi: https://doi.org/10.1101/2022.08.12.503709)
Single-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitment
Steier Z,Aylard DA , McIntyre LL, Baldwin I, Kim EJY, Lutes LK, Ergen C, Huang TS, Robey EA†, Yosef N† and Streets A†, Nature immunology 24 (9), 1579-1590
(preprint doi: 10.1101/2021.07.12.452119)
Towards an active droplet-based microfluidic platform for programmable fluid handling
Cao, X., Buryska, T., Yang, T., Wang, J., Fischer, P., Streets, A., Stavrakis, S. and deMello, A. (2023), Lab on a Chip, The Royal Society of Chemistry, Vol. 23 No. 8, pp. 2029–2038, doi: 10.1039/D3LC00015J.
Mapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Gupta A, Efthymiou V, Kodani SD, Shamsi F, Patti ME, Tseng YH and Streets A, Molecular Metabolism, Vol. 74, p. 101746, doi: https://doi.org/10.1016/j.molmet.2023.101746.
Loss of TJP1 disrupts gastrulation patterning and increases differentiation toward the germ cell lineage in human pluripotent stem cells
Vasic I, Libby ARG, Maslan A, Bulger EA, Zalazar D, Compagno MZK, Streets A, Tomoda, K, Yamanaka S. and McDevitt TC, Developmental cell 58 (16), 1477-1488. e5
2022
Histologically resolved multiomics enables precise molecular profiling of human intratumor heterogeneity
Chen T, Cao, C, Zhang J, Streets A†, Li T†, & Huang Y†, PLOS Biology, 20(7), e3001699. https://doi.org/10.1371/JOURNAL.PBIO.3001699
(preprint doi: https://doi.org/10.1101/121616)
Undifferentiated Induced Pluripotent Stem Cells as a Genetic Model for Nonalcoholic Fatty Liver Disease
Muñoz A, Theusch E, Kuang Y-L, Nalula G, Peaslee C, Dorlhiac G, Landry MP, Streets A, Krauss RM, Iribarren C, Mattis AN, Medina MW, Cellular and Molecular Gastroenterology and Hepatology doi: https://doi.org/10.1016/J.JCMGH.2022.07.009
DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome-wide
Altemose N*, Maslan A*, Smith OK*, Sundararajan K*, Brown RR, Detweiler A, Neff N, Miga KH, Straight AF†, Streets A†, Nature Methods, 19, 711-723, doi: https://doi.org/10.1038/s41592-022-01475-6
(preprint: https://doi.org/10.1101/2021.07.06.451383)
Complete genomic and epigenetic maps of human centromeres
N Altemose, GA Logsdon, AV Bzikadze, P Sidhwani, SA Langley, GV Caldas, SJ Hoyt, L Uralsky, FD Ryabov, CJ Shew, MEG Sauria, M Borchers, A Gershman, A Mikheenko, VA Shepelev, T Dvorkina, O Kunyavskaya, MR Vollger, A Rhie, AM McCartney, M Asri, R Lorig-Roach, K Shafin, S Aganezov, D Olson, L Gomes de Lima, T Potapova, GA Hartley, M Haukness, P Kerpedjiev, F Gusev, K Tigyi, S Brooks, A Young, S Nurk, S Koren , SR Salama, B Paten, EI Rogaev, A Streets, GH Karpen, A Dernburg, BA Sullivan, AF Straight, TJ Wheeler, JL Gerton, EE Eichler, AM Phillippy, W Timp, MY Dennis, RJ O’Neill, JM Zook, MC Schatz, PA Pevzner, M Diekhans, CH Langley, IA Alexandrov†, KH Miga†, Science, 376 (6588), 44–53 DOI: 10.1126/science.abl4178
The complete sequence of a human genome.
S Nurk, S Koren, A Rhie, M Rautiainen, A V Bzikadze, A Mikheenko, M R. Vollger, N Altemose, L Uralsky, A Gershman, S Aganezov, S J. Hoyt, M Diekhans, G A. Logsdon, M Alonge, S E. Antonarakis, M Borchers, G G. Bouffard, S Y. Brooks, G V. Caldas, H Cheng, CS Chin, W Chow, L G. de Lima, P C. Dishuck, R Durbin, T Dvorkina, I T. Fiddes, G Formenti, R S. Fulton, A Fungtammasan, E Garrison, P G.S. Grady, T A. Graves-Lindsay, I M. Hall, N F. Hansen, G A. Hartley, M Haukness, K Howe, M W. Hunkapiller, C Jain, M Jain, E D. Jarvis, P Kerpedjiev, M Kirsche, M Kolmogorov, J Korlach, M Kremitzki, H Li, V V. Maduro, T Marschall, A M. McCartney, J McDaniel, D E. Miller, J C. Mullikin, E W. Myers, N D. Olson, B Paten, P Peluso, P A. Pevzner, D Porubsky, T Potapova, E I. Rogaev, J A. Rosenfeld, S L. Salzberg, V A. Schneider, F J. Sedlazeck, K Shafin, C J. Shew, A Shumate, Y Sims, A F. A. Smit, D C. Soto, I Sović, J M. Storer, A Streets, B A. Sullivan, F Thibaud-Nissen, J Torrance, J Wagner, B P. Walenz, A Wenger, J M. D. Wood, C Xiao, S M. Yan, A C. Young, S Zarate, U Surti, R C. McCoy, S Y. Dennis, I A. Alexandrov, J L. Gerton, R J. O’Neill, W Timp, J M. Zook, M C. Schatz, E E. Eichler, K H. Miga, A M. Phillippy. Science, (2022) DOI: 10.1126/science.abj6987
(Preprint DOI: 10.1101/2021.05.26.445798)
A Python library for probabilistic analysis of single-cell omics data
A Gayoso*, R Lopez*, G Xing*, P Boyeau, J Hong, V Amiri, K Wu, M Jayasuriya, E Melhman, M Langevin, Y Liu, J Samaran, G Misrachi, A Nazaret, O Clivio, C Xu, T Ashuach, M Gabitto, M Lotfollahi, V Svensson, E da Veiga Beltrame, V Kleshchevnikov, C Talavera-López, L Pachter, FJ Theis, A Streets, MI Jordan, J Regier, and N Yosef†, Nature Biotechnology, 40, 163-166
Mechanical phenotyping reveals unique biomechanical responses in retinoic acid-resistant acute promyelocytic leukemia
Li B, Maslan A, Kitayama SE, Pierce C, Streets A, Sohn L, iScience, 25(2) (2022)
(Preprint DOI: 10.1101/2021.04.25.441378)
Characterization of transcript enrichment and detection bias in single-nuclei RNA-seq for mapping of distinct human adipocyte lineages
Gupta A, Shamsi F, Altemose N, Dorlhiac G, Cypess AM, White AP, Yosef N, Patti ME, Tseng Y, Streets A †, Genome Research, 32, 242-257 (2022)
(Preprint doi: https://doi.org/10.1101/2021.03.24.435852)
Bangs D, Tsitsiklis A, Steier Z, Shiao WC, Kaminski J, Streets A, Yosef N, Robey E. “CXCR3 regulates stem and proliferative CD8+ T cells during chronic infection by promoting interactions with DCs in splenic bridging channels,” CellReports, 38(3) (2022)
2021
Steier Z, Maslan A,Streets A †, “Joint Analysis of Transcriptome and Proteome Measurements in Single cells with TotalVI,” Book chapter in: Single Cell ‘Omics of Neuronal Cells, edited by J.V. Sweedler, J.H. Eberwine, S.E. Fraser, Neuromethods Series, Springer Nature, 2021, (accepted for publication).
Vascular smooth muscle-derived Trpv1+ progenitors are a source of cold-induced thermogenic adipocytes
Shamsi F., Piper M., Ho LL., Huang TL, Gupta A, Streets A, Lynes MD, Tseng YH, Nature Metabolism 3, 485–495 (2021). https://doi.org/10.1038/s42255-021-00373-z
Paper-thin multilayer microfluidic devices with integrated valves
Kim S, Dorlhiac G, Cortim Chaves R, Zalavadia M, Streets A †, Lab on a Chip, (2021) advance article https://doi.org/10.1039/D0LC01217C
Joint probabilistic modeling of single-cell multi-omic data with totalVI
Gayoso A *, Steier Z *, Lopez R, Regier J, Nazor KL, Streets A †, Yosef N†. Nature Methods, 18, p272–282
(Preprint doi: https://doi.org/10.1101/2020.05.08.083337)
T cell self-reactivity during thymic development dictates the timing of positive selection
Lutes LK, Steier Z, McIntyre LL, Pandey S, Kaminski J, Hoover AR, Ariotti S, Streets A, Yosef N, Robey EA†, eLife 2021;10:e65435 doi: 10.7554/eLife.65435 (bioRxiv)
2020
μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells
N Altemose, A Maslan, A Lai, JA White, A Streets†. Cell Systems 11(4) Oct 2020 DOI (bioRxiv 2019 DOI: https://doi.org/10.1101/706903 pdf)
µCB-seq: Microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells
T Chen*, A Gupta*, M Zalavadia, A Streets†. Lab Chip adv. online 2020 DOI (bioRxiv, DOI: 10.1101/2020.02.18.954974 pdf)
2019
A Joint Model of RNA Expression and Surface Protein Abundance in Single Cells
A Gayoso, R Lopez, Z Steier, J Regier, A Streets†, N Yosef†. bioRxiv, DOI: https://doi.org/10.1101/791947 pdf
Radial variation in biochemical composition of the bovine caudal intervertebral disc
SE Bezci, B Werbner, M Zhou, KG Malollari, G Dorlhiac, C Carraro, A Streets, GD O’Connell†. JOR Spine 2(3) DOI
High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins
M Segal, A Ingargiola, E Lerner, S Yoon Chung, JA White, A Streets , S Weiss, X Michalet†. Methods, 169:21-45 DOI
On-ratio PDMS bonding for multilayer microfluidic device fabrication
Lai A, Altemose N, White JA, Streets A†. Journal of Micromechanics and Microengineering, 29(10), 107001 DOI pdf
2018
Quantitative imaging of lipid droplets in single cells
Gupta A, Dorlhiac G, Streets A†. Analyst 144, 753-765 (2019) DOI pdf
2017
Controller for microfluidic large-scale integration
White JA, Streets A†. HardwareX (online 2017)
Single-Cell Transcriptional Analysis
Wu AR†, Wang L†, Streets A†, Huang Y†. Annual Review of Analytical Chemistry, Vol 10 (2017) pdf
2016
Label-free digital quantification of lipid droplets in single cells by stimulated Raman microscopy on a microfluidic platform
Cao C, Zhou D, Chen T, Streets A†, Huang Y†. Analytical Chemistry, 88(9), 4931-4939 (2016) pdf
2014
How deep is enough in single-cell RNA-seq?
Streets A, Huang Y. Nature Biotech, 32, 1005-1006 (2014) pdf
H3K4me3 epigenomic landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells
Shen J, Jiang D, Fu Y, Wu X, Guo H, Feng B, Pang Y, Streets A, Tang F, Huang Y. Cell Research 25:143–147.
Imaging without fluorescence: Non-linear optical microscopy for quantitative cellular imaging
Streets A, Li A, Chen T, Huang Y. Analytical Chemistry, 96(17), p8506-8513, (2014) pdf
Microfluidic single-cell whole-transcriptome sequencing
Streets A*, Zhang X*, Cao C, Pang Y, Wu X, Xiong L, Yang L, Fu Y, Zhao L, Tang F, and Huang Y, Proceedings of the National Academy of Sciences, 111(19) 7048-7053 (2014) pdf
Microfluidics for biological measurements with single-molecule resolution
Streets A, Huang Y, Current Opinion in Biotechnology, 25(1), 69-77 (2014) pdf
2013
Optical imaging of non-fluorescent nanodiamonds in live cells using transient absorption microscopy
Chen T, Lu F, Streets A, Fei P, Quan J, Huang Y, Nanoscale, 5, 4701-4705 (2013) doi: https://doi.org/10.1039/c3nr33794j
Chip in a Lab: Microfluidics for next generation life science research
Streets A, Huang Y, Biomicrofluidics, 7, 011302 (2013) doi: https://doi.org/10.1063/1.4789751 pdf
Simultaneous measurement of amyloid fibril formation by dynamic light scattering and fluorescence reveal complex aggregation kinetics
Streets A, Sourigues Y, Kopito RR, Melki R, Quake SR, PLOS ONE, 8, e54541 (2013) doi: https://doi.org/10.1371/journal.pone.0054541 pdf
2011
High-throughput single-molecule optofluidic analysis
Kim SH*, Streets A*, Lin RR, Quake SR, Weiss S, Majumdar DS, Nature Methods, 8, 242-245 (2011) doi: https://doi.org/10.1038/nmeth.1569 pdf
-Highlighted in Physics Today ”Microfluidic devices streamline fluorescence experiments.” April (2011), p16-19 DOI: 10.1063/1.3580484
-Highlighted in Nature methods “News and Views: A triple threat to single molecules.” 8 213-215 DOI: 10.1038/nmeth0311-213
2010
Ostwald ripening of clusters during protein crystallization
Streets A, Quake SR, Physical Review Letters, 104, 178102 (2010) doi: https://doi.org/10.1103/PhysRevLett.104.178102 pdf
*contributed equally
†corresponding author
this link will direct you to Aaron’s publication list in google scholar