Publications

The chicken embryo as a model for developmental genomics
Jimenez NA, Simoes-Costa M
Developmental Biology, 2026
Changes in cellular composition shape the inductive properties of Hensen's Node DOI
Kanno TY, Rothstein M, Simoes-Costa M
Nature Communications, Vol. 16, pp. 7824, 2025
A modular enhancer mediates SCRT2 repression of ISLET1 in the spinal cord
Botezelli VS, Kanno TY, Liau ES et al.
Developmental Biology, 2025
Isocitrate dehydrogenase 1 primes group-3 medulloblastomas for cuproptosis DOI
Dang D, Deogharkar A, McKolay J et al.
Cancer Cell, Vol. 43, pp. 1159-1174, 2025
TGF-β signaling controls neural crest developmental plasticity via SMAD2/3 DOI
Rothstein M, Azambuja AP, Kanno TY, Breen C, Simoes-Costa M
Developmental Cell, Vol. 60, pp. 1686-1701, 2025
Gag proteins encoded by endogenous retroviruses are required for zebrafish development DOI
Chang NC, Wells JN, Wang AY et al.
PNAS, Vol. 122, pp. e2411446122, 2025
Spatial patterning of the epigenome during vertebrate gastrulation
Azambuja AP, Rothstein M, Kanno TY, Simoes-Costa M
Nature Communications, 2025
ASCL1 promotes Scrt2 expression in the neural tube DOI
Goes CP, Botezelli VS, De La Cruz SM et al.
Frontiers in Cell and Developmental Biology, Vol. 12, pp. 1324584, 2024
Histone lactylation couples cellular metabolism with developmental gene regulatory networks DOI
Merkuri F, Rothstein M, Simoes-Costa M
Nature Communications, Vol. 15, pp. 90, 2024
On the evolutionary origins and regionalization of the neural crest DOI
Rothstein M, Simoes-Costa M
Seminars in Cell & Developmental Biology, Vol. 138, pp. 28-35, 2023
ChIP-Seq Protocol for In Vitro Cell Differentiation Systems book chapter
Copeland J, Merkuri F, Simoes-Costa M
DNA-Protein Interactions: Methods and Protocols, pp. 49-58, 2022
Pluripotency factors are repurposed to shape the epigenomic landscape of neural crest cells DOI
Hovland AS, Bhattacharya D, Azambuja AP et al.
Developmental Cell, Vol. 57, pp. 2257-2272, 2022
Micromanaging pattern formation: miRNA regulation of signaling systems in vertebrate development DOI
Copeland J, Wilson K, Simoes-Costa M
FEBS Journal, Vol. 289, pp. 5166-5175, 2022
The connectome of neural crest enhancers reveals regulatory features of signaling systems DOI
Azambuja AP, Simoes-Costa M
Developmental Cell, Vol. 56, pp. 1268-1282, 2021
Neural crest metabolism: At the crossroads of development and disease DOI
Bhattacharya D, Khan B, Simoes-Costa M
Developmental Biology, Vol. 475, pp. 245-255, 2021
Post-transcriptional tuning of FGF signaling mediates neural crest induction DOI
Copeland J, Simoes-Costa M
PNAS, Vol. 117, pp. 33305-33316, 2020
Scratch2, a snail superfamily member, is regulated by miR-125b DOI
Goes CP, Vieceli FM, De La Cruz SM et al.
Frontiers in Cell and Developmental Biology, Vol. 8, pp. 769, 2020
Metabolic reprogramming promotes neural crest migration via Yap/Tead signaling DOI
Bhattacharya D, Azambuja AP, Simoes-Costa M
Developmental Cell, Vol. 53, pp. 199-211, 2020
Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification DOI
Rothstein M, Simoes-Costa M
Genome Research, Vol. 30, pp. 35-48, 2020
Network architecture and regulatory logic in neural crest development DOI
Hovland AS, Rothstein M, Simoes-Costa M
WIREs Systems Biology and Medicine, Vol. 12, pp. e1468, 2020
Identifying protein-DNA and protein-protein interactions in avian embryos book chapter
Azambuja AP, Simoes-Costa M
Vertebrate Embryogenesis: Embryological, Cellular, and Genetic Methods, pp. 99-110, 2019
Evolution of the new head by gradual acquisition of neural crest regulatory circuits DOI
Martik ML, Gandhi S, Uy BR et al.
Nature, Vol. 574, pp. 675-678, 2019
Control of neural crest multipotency by Wnt signaling and the Lin28/let-7 axis DOI
Bhattacharya D, Rothstein M, Azambuja AP, Simoes-Costa M
eLife, Vol. 7, pp. e40556, 2018
The molecular basis of neural crest axial identity DOI
Rothstein M, Bhattacharya D, Simoes-Costa M
Developmental Biology, Vol. 444, pp. S170-S180, 2018
A systems-level approach reveals new gene regulatory modules in the developing ear DOI
Chen J, Tambalo M, Barembaum M et al.
Development, Vol. 144, pp. 1531-1543, 2017
The neural crest migrating into the twenty-first century DOI
Bronner ME, Simões-Costa M
Current Topics in Developmental Biology, Vol. 116, pp. 115-134, 2016
Reprogramming of avian neural crest axial identity and cell fate DOI
Simoes-Costa M, Bronner ME
Science, Vol. 352, pp. 1570-1573, 2016
Evolutionarily conserved role for SoxC genes in neural crest specification and neuronal differentiation DOI
Uy BR, Simoes-Costa M, Koo DES et al.
Developmental Biology, Vol. 397, pp. 282-292, 2015
Axud1 integrates Wnt signaling and transcriptional inputs to drive neural crest formation DOI
Simões-Costa M, Stone M, Bronner ME
Developmental Cell, Vol. 34, pp. 544-554, 2015
Evolution of vertebrates as viewed from the crest DOI
Green SA, Simoes-Costa M, Bronner ME
Nature, Vol. 520, pp. 474-482, 2015
Establishing neural crest identity: a gene regulatory recipe DOI
Simões-Costa M, Bronner ME
Development, Vol. 142, pp. 242-257, 2015
DNA methyltransferase 3B regulates duration of neural crest production via repression of Sox10 DOI
Hu N, Strobl-Mazzulla PH, Simoes-Costa M et al.
PNAS, Vol. 111, pp. 17911-17916, 2014
Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network DOI
Simões-Costa M, Tan-Cabugao J, Antoshechkin I et al.
Genome Research, Vol. 24, pp. 281-290, 2014
Expression and function of transcription factor cMyb during cranial neural crest development DOI
Betancur P, Simões-Costa M, Sauka-Spengler T, Bronner ME
Mechanisms of Development, Vol. 132, pp. 38-43, 2014
Insights into neural crest development and evolution from genomic analysis DOI
Simões-Costa M, Bronner ME
Genome Research, Vol. 23, pp. 1069-1080, 2013
The transcription factor chicken Scratch2 is expressed in a subset of early postmitotic neural progenitors DOI
Vieceli FM, Simões-Costa M, Turri JA et al.
Gene Expression Patterns, Vol. 13, pp. 189-196, 2013
Dynamic and differential regulation of stem cell factor FoxD3 in the neural crest is Encrypted in the genome DOI
Simões-Costa MS, McKeown SJ, Tan-Cabugao J et al.
PLoS Genetics, Vol. 8, pp. e1003142, 2012