Publication

2023

TC Lu*, M Brbić*, YJ Park, T Jackson, J Chen, SS Kolluru, Y Qi, NS Katheder, XT Cai, S Lee, YC Chen, N Auld, D Welsch, S D’Souza, AO Pisco, RC Jones, J Leskovec, EC Lai, HJ Bellen, L Luo, H Jasper#, SR Quake#, H Li#
Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution. bioRxiv [link][PDF]
*This study provides the most comprehensive aging features across the entire organism. Check our user-friendly web portal for your favorite cell type or gene [AFCA].

B Wang, H Martini-Stoica, C Qi, TC Lu, S Wang, W Xiong, Y Qi, Y Xu, MSardiello, H Li, H Zheng#
TFEB-vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy. bioRxiv [link]

S Gao, Y Qi, Q Zhang, A Mohammed, Y Lee, Y Guan, H Li#, Y Fu#, M Wang#
Aging Atlas Reveals Cell-Type-Specific Regulation of Pro-longevity Strategies. bioRxiv [link]
*Aging Atlas of C. elegans web portal [link]

A Raz*, G Vida*, S Stern*, S Mahadevaraju*, J Fingerhut*, J Viveiros*, S Pal*, J Grey*, M Grace*, C Berry, H Li, J Janssens, W Saelens, Z Shao, C Hun, Y Yamashita, T Przytycka, B Oliver, J Brill, H Krause, E Matunis, H White-Cooper, S DiNardo#, M Fuller#
Emergent dynamics of adult stem cell lineages from single-nucleus and single-cell RNA-Seq of Drosophila testes. eLife 12:e82201 [link]

2022

H Li*, J Janssens*, M Waegeneer, S Kolluru, K Davie, V Gardeux, W Saelens, F David, M Brbić, K Spanier, J Leskovec, C McLaughlin, Q Xie, R Jones, K Brueckner,J Shim, S Tattikota,F Schnorrer, K Rust, T Nystul, Z Carvalho-Santos, C Ribeiro, S Pal, S Mahadevaraju, T Przytycka, A Allen, S Goodwin, C Berry, M Fuller,H White-Cooper, E Matunis, S  DiNardo, A Galenza, L O’Brien, J Dow, FCA Consortium, H Jasper, B Oliver, N Perrimon#, B Deplancke#, S Quake#, L Luo#, S Aerts#
Fly Cell Atlas: a single-nucleus transcriptomic atlas of the adult fruit fly. (2022) Science Vol 375, Issue 6584
[link] [PDF][Supplement PDF][FlyCellAtlas website]

C McLaughlin*, Y Qi*, S Quake#, L Luo#, H Li#
Isolation and RNA sequencing of single nuclei from Drosophila tissues. (2022) STAR Protocols 3 (2), 101417 [link][PDF]

D Task, C Lin, A Vulpe,  A Afify,  S Ballou,  M Brbić, P Schlegel, J Raji, G. Jefferis, H Li,  K Menuz, C Potter#
Chemoreceptor Co-Expression in Drosophila Olfactory Neurons. (2022) eLife 2022; 11:e72599 [link][PDF]

Q Xie*, J Li*, H Li, ND Udeshi, T Svinkina, S Kohani, R Guajardo, DR Mani, C Xu, T Li, S Han, W Wei, SA Shuster, DJ Luginbuhl, AY Ting, SA Carr, L Luo#
Transcription factor control of dendrite targeting via combinatorial cell-surface codes. (2022) Neuron [link][PDF]

J Xu*, Y Liu*, H Li, A Tarashansky, C Kalicki, R Hung, Y Hu, A Comjean, S Kolluru, B Wang, S Quake, L Luo, A McMahon, J A.T. Dow, N Perrimon#
Transcriptional and functional motifs defining renal function revealed by single nuclear sequencing. (2022) PNAS [link][PDF]

M Herre*, O Goldman*, TC Lu,  G Caballero-Vidal, Y Qi, Z Gilbert, Z Gong, T Morita, S Rahiel, M Ghaninia, R Ignell, B  Matthews, H Li, L Vosshall, M Younger*#
Non-Canonical Odor Coding in the Mosquito. (2022) Cell 185, 3104–3123 [link][PDF]

S Lee, Y Chen, FCA Consortium, A Gillen, J Taliaferro, B Deplancke, H Li, EC Lai#
Diverse cell-specific patterns of alternative polyadenylation in Drosophila. (2022) Nature Communications 13, 5372 (2022) [link][PDF]

2021

Li, T.#, Fu, TM., Li, H., Xie, Q., Luginbuhl, D., Betzig, E., Luo, L#
Cellular Bases of Olfactory Circuit Assembly Revealed by Systematic Time-Lapse Imaging. (2021) Cell 5107-5121.e14 [link] [PDF]

Cai, X., Li, H., Borch Jensen, M., Maksoud, E., Borneo, J., Liang, Y., Quake S., Luo, L., Pejmun, P., and Jasper, H#
Gut cytokines modulate olfaction through metabolic reprogramming of glia. (2021) Nature 596 (7870), 97-102 [link] [PDF]

McLaughlin*, C., Brbic*, M., Xie, Q., Li, T., Horns, F., Kolluru, S.S., Kebschull, J., Vacek, D., Xie, A., Li, J., Jones R., Leskovec, J., Quake S.#, Luo, L.#, Li, H.
Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila. (2021) eLife 2021;10:e63856. [link] [PDF]

Xie, Q., Brbic, M., Horns, F., Kolluru, S.S., Jones R., Li, J., Reddy, A., Xie, A., Kohani S., Li, Z., McLaughlin, C., Li, T., Xu, C., Vacek, D., Luginbuhl, D., Leskovec, J., Quake S.#, Luo, L.#, Li, H.
Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons. (2021) eLife 2021;10:e63450. [link][PDF]

2017-2020

Li, H.#
Single-cell RNA sequencing in Drosophila: Technologies and applications.
(2020) Wiley Dev Biol e396. (invited Review) [link] [PDF]

Li, H.,*^# Li, T*., Horns, F., Li, J., Xie, Q., Xu, C., Wu, B., Kebschull, J.M., McLaughlin, C.N., Kolluru, S.S., Jones R.J., Vacek, D., Xie, A., Luginbuhl, D.J., Quake S.R.^#, Luo, L.#
Single-cell transcriptomes reveal diverse regulatory strategies for olfactory receptor expression and axon targeting (2020) Curr. Biol. 30, 1189–1198.e5. [link] [PDF]

Li, J.*#, Han, S.*, Li, H., Udeshi, N.D., Svinkina, T., Mani, D.R., Xu, C., Guajardo, R., Xie, Q., Li, T., Luginbuhl, D.J., Wu, B., McLaughlin, C.N., Xie, A., Kaewsapsak, P., Quake S.R., Carr, S.A., Ting, A.Y.#, Luo, L.#
Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators. (2020). Cell 180, 373–386.e15. [link] [PDF]

Wenderski, W., Wang, L., Krokhotin, A., Walsh, J.J., Li, H., Shoji, H., Ghosh, S., George, R.D., Miller, E.L., Elias, L., Gillespie, M.A., Son, E.Y., Staahl, B.T., Baek, S.T., Stanley, V., Moncada, C., Shipony, Z., Linker, S.B., Marchetto, M.C, Gage, F.G., Chen, D., Sultan, T., Zaki, M.S., Ranish, J.A., Miyakawa, T., Luo, L., Malenka R.C., Crabtree, G.R.#, Gleeson, J.G.#
Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism. (2020) Proc. Natl. Acad. Sci. USA 117, 10055–10066. [link] [PDF]

Tracy Cai, X., Li, H., Safyan, A., Gawlik, J., Pyrowolakis, G., and Jasper, H.#
AWD regulates timed activation of BMP signaling in intestinal stem cells to maintain tissue homeostasis. (2019). Nat. Commun. 10, 2988. [link] [PDF]

Xie, Q.*, Wu, B.*, Li, J., Xu, C., Li, H., Luginbuhl, D.J., Wang, X., Ward, A., and Luo, L.#
Transsynaptic Fish-lips signaling prevents misconnections between nonsynaptic partner olfactory neurons. (2019). Proc. Natl. Acad. Sci. USA 116, 16068–16073. [link] [PDF]

Li, H.*, Shuster, S.A.*, Li, J.*, and Luo, L.#
Linking neuronal lineage and wiring specificity. (2018). Neural Dev. 13, 5. (invited Review) [link] [PDF]

Li, J., Guajardo, R., Xu, C., Wu, B., Li, H., Li, T., Luginbuhl, D.J., Xie, X., and Luo, L.#
Stepwise wiring of the Drosophila olfactory map requires specific Plexin B levels. (2018). Elife 7:e39088. [link] [PDF]

Li, H.*, Horns, F.*, Wu, B., Xie, Q., Li, J., Li, T., Luginbuhl, D.J., Quake, S.R.#, and Luo, L.#
Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing. (2017). Cell 171, 1206–1220.e22. [link] [PDF]

2013-2016

Li, H., Qi, Y., and Jasper, H.#
Preventing Age-Related Decline of Gut Compartmentalization Limits Microbiota Dysbiosis and Extends Lifespan. (2016). Cell Host Microbe 19, 240–253. [link] [PDF]

Li, H., Qi, Y., and Jasper, H.#
Ubx dynamically regulates Dpp signaling by repressing Dad expression during copper cell regeneration in the adult Drosophila midgut. (2016). Dev. Biol. 419, 373–381. [link] [PDF]

Li, H., and Jasper, H.#
Gastrointestinal stem cells in health and disease: from flies to humans. (2016). Dis. Model. Mech. 9, 487–499. (invited Review) [link] [PDF]

Ayyaz, A., Li, H., and Jasper, H.#
Haemocytes control stem cell activity in the Drosophila intestine. (2015). Nat. Cell Biol.17, 736–748. [link] [PDF]

Li, H.,^# and Wei, C.^#
Diet, gut microbiota and obesity. (2015). J Nutrition Health Food Sci 3 (4), 1-6 (invited Review) [link] [PDF]

Hine, C.M., Li, H., Xie, L., Mao, Z., Seluanov, A.#, and Gorbunova, V.#
Regulation of Rad51 promoter. (2014). Cell Cycle 13, 2038–2045. [link] [PDF]

Li, H., Qi, Y., and Jasper, H.#
Dpp signaling determines regional stem cell identity in the regenerating adult Drosophila gastrointestinal tract. (2013). Cell Rep.4, 10–18. [link] [PDF]

(*co-first, #co-corresponding)

Fly cell atlas