Naqvi Lab Quantitative principles of gene regulation in development and disease

Selected Publications (*equal contribution, ‡co-corresponding)

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage
Sahin Naqvi‡, Seungsoo Kim*, Saman Tabatabaee*, Anusri Pampari, Anshul Kundaje, Jonathan K. Pritchard‡, Joanna Wysocka‡
bioRxiv   ·   29 May 2024   ·   doi:10.1101/2024.05.28.596078
Precise modulation of transcription factor levels identifies features underlying dosage sensitivity
Sahin Naqvi, Seungsoo Kim, Hanne Hoskens, Harry S. Matthews, Richard A. Spritz, ..., Benedikt Hallgrímsson, Tomek Swigut, Peter Claes, Jonathan K. Pritchard‡, Joanna Wysocka‡
Nature Genetics   ·   06 Apr 2023   ·   doi:10.1038/s41588-023-01366-2
Shared heritability of human face and brain shape
Sahin Naqvi*‡, Yoeri Sleyp*, Hanne Hoskens, Karlijne Indencleef, Jeffrey P. Spence, ..., Jonathan K. Pritchard, Stefan Sunaert, Hilde Peeters, Joanna Wysocka‡, Peter Claes‡
Nature Genetics   ·   05 Apr 2021   ·   doi:10.1038/s41588-021-00827-w
GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background
Nasa Sinnott-Armstrong*‡, Sahin Naqvi*, Manuel Rivas, Jonathan K Pritchard‡
eLife   ·   15 Feb 2021   ·   doi:10.7554/eLife.58615
Conservation, acquisition, and functional impact of sex-biased gene expression in mammals
Sahin Naqvi, Alexander K. Godfrey, Jennifer F. Hughes, Mary L. Goodheart, Richard N. Mitchell, David C. Page
Science   ·   19 Jul 2019   ·   doi:10.1126/science.aaw7317

All Publications (*equal contribution, ‡co-corresponding)

2024

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage
Sahin Naqvi‡, Seungsoo Kim*, Saman Tabatabaee*, Anusri Pampari, Anshul Kundaje, Jonathan K. Pritchard‡, Joanna Wysocka‡
bioRxiv   ·   29 May 2024   ·   doi:10.1101/2024.05.28.596078
DNA-guided transcription factor cooperativity shapes face and limb mesenchyme
Seungsoo Kim, Ekaterina Morgunova*, Sahin Naqvi*, Maram Bader, Mervenaz Koska, ..., Christy Luong, Angela Pogson, Peter Claes, Jussi Taipale, Joanna Wysocka
Cell   ·   01 Feb 2024   ·   doi:10.1016/j.cell.2023.12.032

2023

Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape
Seppe Goovaerts, Hanne Hoskens, Ryan J. Eller, Noah Herrick, Anthony M. Musolf, ..., Mark D. Shriver, Joanna Wysocka, Susan Walsh, Seth M. Weinberg, Peter Claes
Nature Communications   ·   16 Nov 2023   ·   doi:10.1038/s41467-023-43237-8
Systematic differences in discovery of genetic effects on gene expression and complex traits
Hakhamanesh Mostafavi, Jeffrey P. Spence, Sahin Naqvi, Jonathan K. Pritchard
Nature Genetics   ·   19 Oct 2023   ·   doi:10.1038/s41588-023-01529-1
A genome-wide genetic screen uncovers determinants of human pigmentation
Vivek K. Bajpai, Tomek Swigut, Jaaved Mohammed*, Sahin Naqvi*, Martin Arreola, Josh Tycko, Tayne C. Kim, Jonathan K. Pritchard, Michael C. Bassik, Joanna Wysocka
Science   ·   11 Aug 2023   ·   doi:10.1126/science.ade6289
Precise modulation of transcription factor levels identifies features underlying dosage sensitivity
Sahin Naqvi, Seungsoo Kim, Hanne Hoskens, Harry S. Matthews, Richard A. Spritz, ..., Benedikt Hallgrímsson, Tomek Swigut, Peter Claes, Jonathan K. Pritchard‡, Joanna Wysocka‡
Nature Genetics   ·   06 Apr 2023   ·   doi:10.1038/s41588-023-01366-2

2022

Decoding the Human Face: Progress and Challenges in Understanding the Genetics of Craniofacial Morphology
Sahin Naqvi*, Hanne Hoskens*, Franziska Wilke, Seth M. Weinberg, John R. Shaffer, Susan Walsh, Mark D. Shriver, Joanna Wysocka‡, Peter Claes‡
Annual Review of Genomics and Human Genetics   ·   31 Aug 2022   ·   doi:10.1146/annurev-genom-120121-102607
Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks
Jacob W. Freimer, Oren Shaked, Sahin Naqvi, Nasa Sinnott-Armstrong, Arwa Kathiria, ..., Amy F. Chen, Jessica T. Cortez, William J. Greenleaf, Jonathan K. Pritchard, Alexander Marson
Nature Genetics   ·   11 Jul 2022   ·   doi:10.1038/s41588-022-01106-y

2021

Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations
Chenxing Liu, Myoung Keun Lee, Sahin Naqvi, Hanne Hoskens, Dongjing Liu, ..., Susan Walsh, Mark D. Shriver, Peter Claes, Seth M. Weinberg, John R. Shaffer
PLOS Genetics   ·   19 Aug 2021   ·   doi:10.1371/journal.pgen.1009695
3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies
Hanne Hoskens, Dongjing Liu, Sahin Naqvi, Myoung Keun Lee, Ryan J. Eller, ..., Mark D. Shriver, John R. Shaffer, Hilde Peeters, Seth M. Weinberg, Peter Claes
PLOS Genetics   ·   13 May 2021   ·   doi:10.1371/journal.pgen.1009528
Shared heritability of human face and brain shape
Sahin Naqvi*‡, Yoeri Sleyp*, Hanne Hoskens, Karlijne Indencleef, Jeffrey P. Spence, ..., Jonathan K. Pritchard, Stefan Sunaert, Hilde Peeters, Joanna Wysocka‡, Peter Claes‡
Nature Genetics   ·   05 Apr 2021   ·   doi:10.1038/s41588-021-00827-w
Human–chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution
David Gokhman, Rachel M. Agoglia, Maia Kinnebrew, Wei Gordon, Danqiong Sun, ..., Honghao Zhang, Yuji Mishina, Joanna Wysocka, Rajat Rohatgi, Hunter B. Fraser
Nature Genetics   ·   17 Mar 2021   ·   doi:10.1038/s41588-021-00804-3
GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background
Nasa Sinnott-Armstrong*‡, Sahin Naqvi*, Manuel Rivas, Jonathan K Pritchard‡
eLife   ·   15 Feb 2021   ·   doi:10.7554/eLife.58615

2020

Insights into the genetic architecture of the human face
Julie D. White*‡, Karlijne Indencleef*, Sahin Naqvi, Ryan J. Eller, Hanne Hoskens, ..., Joanna Wysocka, Susan Walsh, Seth M. Weinberg, Mark D. Shriver, Peter Claes‡
Nature Genetics   ·   07 Dec 2020   ·   doi:10.1038/s41588-020-00741-7
Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
Alexander K. Godfrey, Sahin Naqvi, Lukáš Chmátal, Joel M. Chick, Richard N. Mitchell, Steven P. Gygi, Helen Skaletsky, David C. Page
Genome Research   ·   27 May 2020   ·   doi:10.1101/gr.261248.120

2019

Conservation, acquisition, and functional impact of sex-biased gene expression in mammals
Sahin Naqvi, Alexander K. Godfrey, Jennifer F. Hughes, Mary L. Goodheart, Richard N. Mitchell, David C. Page
Science   ·   19 Jul 2019   ·   doi:10.1126/science.aaw7317

2018

Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
Sahin Naqvi, Daniel W. Bellott, Kathy S. Lin, David C. Page
Genome Research   ·   15 Feb 2018   ·   doi:10.1101/gr.230433.117

2013

Chemical Sensing by Nonequilibrium Cooperative Receptors
Monica Skoge, Sahin Naqvi, Yigal Meir, Ned S. Wingreen
Physical Review Letters   ·   11 Jun 2013   ·   doi:10.1103/PhysRevLett.110.248102