Hanqing Liu
@Hanq_Liu
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I am a Postdoctoral Fellow in the Ecker lab at the Salk Institute for Biological Studies
La Jolla, CA
Joined February 2017
Thrilled to share our latest work from @JoeEcker lab, using cutting-edge snmC-seq3 and snm3C-seq technologies to generate 301,626 methylomes and 176,003 mC+3C multiome profiles from 117 dissected regions throughout the adult mouse brain. (1/n) https://t.co/APlIJSW7VP
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Happy to see our paper in print -- we show how accounting for gene co-expression can help with robust estimation of enhancer-gene links. Congrats to @FangmingXie @EthanArmand2 and our peerless co-authors, incl @chongyuanluo @JoeEcker @HongkuiZeng Bing Ren and more!
Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes
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Why is social isolation associated with negative valence while social grouping elicits positive reward? How to animals know they are alone or together? Our latest work uncovers two distinct hypothalamic populations underlying social homeostasis.
biorxiv.org
Social grouping increases survival in many species, including humans1,2. By contrast, social isolation generates an aversive state (loneliness) that motivates social seeking and heightens social...
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Future students/postdocs/collaborators—if you are interested in my work, please check out my (temporary) research website. Happy to discuss any potential projects that we could work on together in the future!
tatsuyanobori.com
Nobori Lab @TSL
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So excited to share our latest work with @ecallaway & @JoeEcker using Epi-Retro-Seq, combining retrograde virus tracing & single-cell methylation profiling, to link epigenetic cell types to their long-distance projections. 🧠🔬 (1/8) https://t.co/pS8gTk99RO
biorxiv.org
Single-cell genetic and epigenetic analyses parse the brain’s billions of neurons into thousands of “cell-type” clusters, each residing in different brain structures. Many of these cell types mediate...
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A big thank you to @skypilot_org team for assisting us with all the setups and a special shoutout to @zongheng_yang for the valuable help with edits!
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Last month, we shared a preprint on whole mouse brain atlas🐭🧠 Wondering how we tackled the massive data demands? Our latest blog unveils how @skypilot_org, an open-source cloud computing framework, empowered us to handle atlas-level data in the cloud☁️!
link.medium.com
How we completed a large genomic project using the SkyPilot on the Cloud
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Special thanks to all BICCN consortium collaborators! Your contributions and discussions over the past 5 years have been invaluable. It's been an honor working with you all. (9/9)
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Grateful to all co-authors in the @JoeEcker lab, Ren lab at UCSD, Behrens lab at @salkinstitute , @HongkuiZeng lab at @AllenInstitute , @chongyuanluo lab at UCLA, @Jesse_R_Dixon at Salk.
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This study represents a five-year journey (2017-2022) as part of the NIH BRAIN initiative cell census network (BICCN, https://t.co/KS7y1K0sxW). The manuscript is accompanied by several fantastic brain-wide studies from BICCN, some already on biorxiv, with more to come. (7/n)
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Intragenic epigenetic heterogeneity predicts alternative isoform expression in numerous neuronal and synaptic genes, backed by a whole-brain SMART-seq dataset from @AllenInstitute. (6/n)
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Gene regulatory networks, based on methylome and 3D genome data, link TFs to potential binding elements and downstream genes, predicting key regulators in each cell subclass. (5/n)
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Comparing brain-wide cell-type diversity helped us map gene-specific chromatin conformation landscapes at various scales (compartment, domain, loops, etc.), connecting regulatory elements to target genes. (4/n)
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Our brain-wide spatial methylation patterns let us project epigenomic cells onto complex anatomical structures, aided by a MERFISH dataset generated using spatially diverse genes in this study. (3/n)
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With the in-depth coverage of snmC and snm3C-seq profiles, we identified 4,673 cell clusters and 2.6 million DMRs. Integrating these two companion BICCN datasets (Ren lab at UCSD, @AllenInstitute, @HongkuiZeng), we established a comprehensive multi-omic cell-type taxonomy. (2/n)
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Super excited to share our latest work from @JoeEcker lab, where we generated a single-cell spatiotemporal gene regulatory atlas of plants under pathogen attack by combining time-resolved single-nucleus multiomics and spatial transcriptomics🧬🌱⏳🦠🔬1/n https://t.co/3dcLvMxqGt
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My colleagues and I have been using SkyPilot since August. It saved us a lot of time and 💰 establishing some of the biggest future-looking pipelines on GCP (and potentially on any other cloud). A great tool to invest your time if you are interested in using cloud platforms.
Introducing SkyPilot: Run ML and Data Science jobs on any cloud, with massive cost savings. 🚀 Run jobs on any cloud ⏰ Get GPU/TPU/CPU in 1 click 💵 Reduce > 3x cost https://t.co/Dcu1SgtCCR Read blog: https://t.co/ZF6aPrBKM2 🧵1/
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Our first dataset investigating the chromatin conformation and methylation dynamics during human brain development with > 50,000 sn-m3C profiles from the frontal cortex and hippocampus, led by Matthew Heffel, Jingtian Zhou, @YiZ001UC_, Dong-Sung Lee, and @kangchenghou.
Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus https://t.co/84voXLPqBe
#biorxiv_genomic
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Our single nucleus multi-omic method snmCAT-seq is now published in @CellGenomics. @FangmingXie from @emukamel lab has developed a cross-validation approach using multi-omic info to determine the optimal cluster number. https://t.co/DW9oLzP0kg
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