Publications

Our work appears in the journals Science, Cell, Nature, Neuron, Nature Medicine, and Genes & Development, among others. Our most recent relevant publications are listed on this page. 

View our full list of publications here.

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A single-cell multiomic analysis identifies molecular and gene-regulatory mechanisms dysregulated in developing Down syndrome neocortex

Vuong CK, Weber A, Seong P, Matoba N, Chen YJ, Peyer J, Younesi S, Salinda A, Gomez D, Rivas G, Morales A, Shafie B, Zhang P, Nichterwitz S, Qi L, Fernandez NT, Friedman E, Love MI, Gandal MJ, Geschwind DH, Lowry WE, Stein JL and de la Torre-Ubieta L

Science. 2026; Apr 23;392(6796):eaea1259.doi: 10.1126/science.aea1259.

PMID: 42024758

Perspectives: Early dynamics of the genome in Down syndrome (Science), Mapping the molecular effects of Down syndrome in the developing brain (Nat. Rev. Neurosci) 

Research Highlight: Scientists map how Down syndrome reshapes brain development before birth

Development of Molecular Neuropathology in Down Syndrome across the Lifespan

Bhattacharyya A, de La Torre-Ubieta L, Zhu Y, Head E, Swarup V and Sousa A. 

Journal of Neuroscience. 2025 Nov 12 Nov 12;45(46):e1365252025. doi: 10.1523/JNEUROSCI.1365-25.2025

PMID: 41224669

Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis

Aygün N, Vuong, C, Krupa O, Mory J, Le B, Valone J, Liang D, Shafie, B, Zhang P, Salinda A, Wen C, Gandal MJ, Love MI, de la Torre-Ubieta L* and Stein JL*.

AJHG. 2024; Aug 10:S0002-9297(24)00259-3; doi.org/10.1016/j.ajhg.2024.07.015

PMID: 39168119

Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms.

Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ*, de la Torre-Ubieta L*.

Science. 2024; May 24;384(6698):eadh7688.doi: 10.1126/science.adh7688

PMID: 38781356

Research Highlight: Sequencing of the developing human brain uncovers hundreds of thousands of new gene transcripts

Defining the evolutionary and gene regulatory logic of vertebrate neuronal diversity

de la Torre-Ubieta L.

Neuron. 2022; Jan 5;110(1):3-5. doi: 10.1016/j.neuron.2021.12.013.

PMID: 34990577

A Single-Cell Transcriptomic Atlas of Human Neocortical Development During Mid-gestation

Polioudakis D*, de la Torre-Ubieta L*, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, Hinz FI, Sabri S, Lowry WE, Gerstein MB, Plath K, Geschwind DH. 

Neuron. 2019; Sep 4;103(5):785-801. doi: 10.1016/j.neuron.2019.06.011.

PMID: 31303374 

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis.

de la Torre-Ubieta L, Stein JL, Won H, Opland CK, Liang D, Lu D, Geschwind DH.

Cell. 2018; 172(1-2):289-304.e18.

PMID: 29307494

Preview in Cell:  Weaving New Insights for the Genetic Regulation of Human Cognitive Phenotypes 

Research Highlight in Nature Reviews Neuroscience: Neural development: 'Enhancing' human cognition

Self-Organized Cerebral Organoids with Human-Specific Features Predict Effective Drugs to Combat Zika Virus Infection.

Watanabe M, Buth JE, Vishlaghi N, de la Torre-Ubieta L, Taxidis J, Khakh BS, Coppola G, Pearson CA, Yamauchi K, Gong D, Dai X, Damoiseaux R, Aliyari R, Liebscher S, Schenke-Layland K, Caneda C, Huang EJ, Zhang Y, Cheng G, Geschwind DH, Golshani P, Sun R, Novitch BG.

Cell reports. 2017; 21(2):517-532. 

PMID: 29020636 PMCID: PMC5637483

Chromosome conformation elucidates regulatory relationships in developing human brain.

Won H, de la Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, Gandal MJ, Sutton GJ, Hormozdiari F, Lu D, Lee C, Eskin E, Voineagu I, Ernst J, Geschwind DH.

Nature. 2016; 538(7626):523-527. NIHMSID: NIHMS833424

PMID: 27760116 PMCID: PMC5358922

Advancing the understanding of autism disease mechanisms through genetics.

de la Torre-Ubieta L, Won H, Stein JL, Geschwind DH.

Nature medicine. 2016; 22(4):345-61. NIHMSID: NIHMS821081

PMID: 27050589 PMCID: PMC5072455

A quantitative framework to evaluate modeling of cortical development by neural stem cells.

Stein JL, de la Torre-Ubieta L*, Tian Y, Parikshak NN, Hernández IA, Marchetto MC, Baker DK, Lu D, Hinman CR, Lowe JK, Wexler EM, Muotri AR, Gage FH, Kosik KS, Geschwind DH.

Neuron. 2014; 83(1):69-86. 

PMID: 24991955 PMCID: PMC4277209

Neuron Cover Article. 

FoxO6 regulates memory consolidation and synaptic function.

Salih DA, Rashid AJ, Colas D, de la Torre-Ubieta L, Zhu RP, Morgan AA, Santo EE, Ucar D, Devarajan K, Cole CJ, Madison DV, Shamloo M, Butte AJ, Bonni A, Josselyn SA, Brunet A.

Genes & development. 2012; 26(24):2780-801.

PMID: 23222102 PMCID: PMC3533081

Transcriptional regulation of neuronal polarity and morphogenesis in the mammalian brain.

de la Torre-Ubieta L, Bonni A.

Neuron. 2011; 72(1):22-40. NIHMSID: NIHMS328099

PMID: 21982366 PMCID: PMC3391704

A FOXO-Pak1 transcriptional pathway controls neuronal polarity.

de la Torre-Ubieta L, Gaudillière B, Yang Y, Ikeuchi Y, Yamada T, DiBacco S, Stegmüller J, Schüller U, Salih DA, Rowitch D, Brunet A, Bonni A.

Genes & development. 2010; 24(8):799-813.

PMID: 20395366 PMCID: PMC2854394