Publications¶

2022¶

Maslan A, Altemose N, Mishra R, Marcus J, Brennan LD, Sundararajan K, Karpen G, Straight AF, Streets A. “Mapping protein-DNA interactions with DiMeLo-seq” bioRxiv (2022) https://doi.org/10.1101/2022.07.03.498618

Chen, T., Cao, C., Zhang, J., Streets Id, A., Li, T., & Huangid, Y. “Histologically resolved multiomics enables precise molecular profiling of human intratumor heterogeneity.” PLOS Biology, 20(7), e3001699. https://doi.org/10.1371/JOURNAL.PBIO.3001699

Gupta, A., Shamsi, F., Patti, M. E., Tseng, Y.-H., & Streets, A. “Mapping the temporal transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq.” BioRxiv, (2022) 2022.05.30.494007. https://doi.org/10.1101/2022.05.30.494007

Dorlhiac, G. F., Landry, M. P., & Streets, A. “Leveraging isotopologues as a general strategy to image neurotransmitters with vibrational microscopy.” arXiv (2022) https://doi.org/10.48550/arxiv.2205.05798

Muñoz, A., Theusch, E., Kuang, Y.-L., Nalula, G., Peaslee, C., Dorlhiac, G., Landry, M. P., Streets, A., Krauss, R. M., Iribarren, C., Mattis, A. N., & Medina, M. W. (2022). Undifferentiated Induced Pluripotent Stem Cells as a Genetic Model for Nonalcoholic Fatty Liver Disease. Cellular and Molecular Gastroenterology and Hepatology. https://doi.org/10.1016/J.JCMGH.2022.07.009

Altemose N*, Maslan A*, Smith OK*, Sundararajan K*, Brown RR, Detweiler A, Neff N, Miga KH, Straight AF†, Streets A†, “DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome-wide,” Nature Methods, 19, 711-723 (2022) https://doi.org/10.1038/s41592-022-01475-6 [bioRxiv, DOI: 10.1101/2021.07.06.451383]

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†, “Complete genomic and epigenetic maps of human centromeres,” Science, (2022) DOI: 10.1126/science.abl4178

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†, “A Python library for probabilistic analysis of single-cell omics data” Nature Biotechnology, 40, 163-166 (2022)

Li B, Maslan A, Kitayama SE, Pierce C, Streets A, Sohn L, “Mechanical phenotyping reveals unique biomechanical responses in retinoic acid-resistant acute promyelocytic leukemia” iScience, 25(2) (2022)

Gupta A, Shamsi F, Altemose N, Dorlhiac G, Cypess AM, White AP, Yosef N, Patti ME, Tseng Y, Streets A †, “Characterization of transcript enrichment and detection bias in single-nuclei RNA-seq for mapping of distinct human adipocyte lineages” Genome Research, 32, 242-257 (2022) [bioRxiv, 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, McIntyre L, Lutes LK, Huang TS, Robey EA†, Yosef N†, Streets A†, “Single-cell multi-omic analysis of thymocyte development reveals NFAT as a driver of CD4/CD8 lineage commitment,” bioRxiv. (2021) DOI: 10.1101/2021.07.12.452119

Zhang X, Dorlhiac G, Landry MP, Streets A, “Multimodal measurements of phototoxicity in laser-based imaging,” bioRxiv (2021) (submitted)

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).

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. “The complete sequence of a human genome.” bioRxiv, (2021) DOI: 10.1101/2021.05.26.445798

A Gayoso*, R Lopez*, G Xing*, P Boyeau, K Wu, M Jayasuriya, E Melhman, M Langevin, Y Liu, J Samaran, G Misrachi, A Nazaret, O Clivio, C Xu, T Ashuach, M Lotfollahi, V Svensson, E da Veiga Beltrame, C Talavera-López, L Pachter, FJ Theis, A Streets, MI Jordan, J Regier, and N Yosef†, “scvi-tools: a library for deep probabilistic analysis of single-cell omics data.” bioRxiv (2021) DOI: 10.1101/2021.04.28.441833

Li B, Maslan A, Streets A, Sohn L, “Mechanical phenotyping of acute promyelocytic leukemia reveals unique biomechanical responses in retinoic acid-resistant populations.” bioRxiv, (2021), DOI: 10.1101/2021.04.25.441378

Shamsi F., Piper M., Ho LL., Huang TL, Gupta A, Streets A, Lynes MD, Tseng YH, “Vascular smooth muscle-derived Trpv1+ progenitors are a source of cold-induced thermogenic adipocytes.” Nature Metabolism 3, 485–495 (2021). https://doi.org/10.1038/s42255-021-00373-z

Kim S, Dorlhiac G, Cortim Chaves R, Zalavadia M, Streets A †, “Paper-thin multilayer microfluidic devices with integrated valves” Lab on a Chip, (2021) advance article https://doi.org/10.1039/D0LC01217C

Gayoso A _, Steier Z _, Lopez R, Regier J, Nazor KL, Streets A †, Yosef N†. “Joint probabilistic modeling of single-cell multi-omic data with totalVI” Nature Methods, 18, p272–282(2021)

Lutes LK, Steier Z, McIntyre LL, Pandey S, Kaminski J, Hoover AR, Ariotti S, Streets A, Yosef N, Robey EA†, “T cell self-reactivity during thymic development dictates the timing of positive selection.” eLife 2021;10:e65435 doi: 10.7554/eLife.65435 (bioRxiv)

2020¶

N Altemose, A Maslan, A Lai, JA White, A Streets†. “μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells” Cell Systems 11(4) Oct 2020 DOI (bioRxiv 2019 DOI: https://doi.org/10.1101/706903 pdf)

T Chen*, A Gupta*, M Zalavadia, A Streets†. “µCB-seq: Microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells” Lab Chip adv. online 2020 DOI (bioRxiv, DOI: 10.1101/2020.02.18.954974 pdf)

A Gayoso*, Z Steier*, R Lopez, J Regier, KL NAzor, A Streets†, N Yosef†. “Joint probabilistic modeling of paired transcriptome and proteome measurements in single cells” bioRxiv, DOI: 10.1101/2020.05.08.083337 pdf

2019¶

A Gayoso, R Lopez, Z Steier, J Regier, A Streets†, N Yosef†. “A Joint Model of RNA Expression and Surface Protein Abundance in Single Cells” bioRxiv, DOI: https://doi.org/10.1101/791947 pdf

SE Bezci, B Werbner, M Zhou, KG Malollari, G Dorlhiac, C Carraro, A Streets, GD O’Connell†. “Radial variation in biochemical composition of the bovine caudal intervertebral disc” JOR Spine 2(3) DOI

M Segal, A Ingargiola, E Lerner, S Yoon Chung, JA White, A Streets , S Weiss, X Michalet†. “High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins” Methods, 169:21-45 DOI

Lai A, Altemose N, White JA, Streets A†. “On-ratio PDMS bonding for multilayer microfluidic device fabrication” Journal of Micromechanics and Microengineering, 29(10), 107001 DOI pdf

2018¶

Gupta A, Dorlhiac G, Streets A†. “Quantitative imaging of lipid droplets in single cells” Analyst 144, 753-765 (2019) DOI pdf

2017¶

White JA, Streets A†. “Controller for microfluidic large-scale integration” HardwareX (online 2017), Vol 3 Apr 2018, p135-145, DOI: 10.1016/j.ohx.2017.10.002 pdf

Chen T, Cao, C, Zhang J, Streets A, Huang Y†, Li T†. “Stimulated Raman Scattering Micro-dissection Sequencing (SMD-Seq) for Morphology-specific Genomic Analysis of Oral Squamous Cell Carcinoma” bioRxiv (2017) DOI: 10.1101/121616 pdf

Wu AR†, Wang L†, Streets A†, Huang Y†. “Single-Cell Transcriptional Analysis” Annual Review of Analytical Chemistry, Vol 10 (2017) pdf

2016¶

Cao C, Zhou D, Chen T, Streets A†, Huang Y†. “Label-free digital quantification of lipid droplets in single cells by stimulated Raman microscopy on a microfluidic platform.” Analytical Chemistry, 88(9), 4931-4939 (2016) pdf

2014¶

Streets A, Huang Y. “How deep is enough in single-cell RNA-seq?” Nature Biotech, 32, 1005-1006 (2014) pdf

Shen J, Jiang D, Fu Y, Wu X, Guo H, Feng B, Pang Y, Streets A, Tang F, Huang Y. “H3K4me3 epigenomic landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells.” Cell Research 25:143–147.

Streets A, Li A, Chen T, Huang Y. “Imaging without fluorescence: Non-linear optical microscopy for quantitative cellular imaging.” Analytical Chemistry, 96(17), p8506-8513, (2014) pdf

Streets A*, Zhang X*, Cao C, Pang Y, Wu X, Xiong L, Yang L, Fu Y, Zhao L, Tang F, and Huang Y. “Microfluidic single-cell whole-transcriptome sequencing.” Proceedings of the National Academy of Sciences, 111(19) 7048-7053 (2014) pdf

Streets A, Huang Y. “Microfluidics for biological measurements with single-molecule resolution.” Current Opinion in Biotechnology, 25(1), 69-77 (2014) pdf

2013¶

Chen T, Lu F, Streets A, Fei P, Quan J, Huang Y. “Optical imaging of non-fluorescent nanodiamonds in live cells using transient absorption microscopy.” Nanoscale, 5, 4701 (2013)

Streets A, Huang Y. “Chip in a Lab: Microfluidics for next generation life science research.” Biomicrofluidics, 7 011302, (2013) pdf

Streets A, Sourigues Y, Kopito RR, Melki R, Quake SR. “Simultaneous measurement of amyloid fibril formation by dynamic light scattering and fluorescence reveal complex aggregation kinetics.” PLOS ONE, 8(1), e54541 (2013) pdf

2011¶

Kim SH*, Streets A*, Lin RR, Quake SR, Weiss S, Majumdar DS. “High-throughput single-molecule optofluidic analysis.” Nature Methods, 8:3, 242-245 (2011) 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¶

Streets A, Quake SR. “Ostwald ripening of clusters during protein crystallization.” Physical Review Letters, 104, 178102 (2010) pdf

*contributed equally

†corresponding author