Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage

Authors: Naqvi, Sahin ^{1, 2, 3, 4, 9, ∗}, Kim, Seungsoo ^{1, 5, 8}, Tabatabaee, Saman ^{1, 8}, Pampari, Anusri ⁶, Kundaje, Anshul ^{2, 6}, Pritchard, Jonathan K. ^{2, 7, ∗∗}, Wysocka, Joanna ^{1, 5, ∗∗∗}

Source: In Cell Genomics 12 March 2025 5(3)

DNA-guided transcription factor cooperativity shapes face and limb mesenchyme

Authors: Kim, Seungsoo, Morgunova, Ekaterina, Naqvi, Sahin, Goovaerts, Seppe, Bader, Maram, Koska, Mervenaz, Popov, Alexander, Luong, Christy, Pogson, Angela, Swigut, Tomek, Claes, Peter, Taipale, Jussi, Wysocka, Joanna

Source: In Cell 1 February 2024 187(3):692-711

Mammalian germ cells are determined after PGC colonization of the nascent gonad

Authors: Nicholls, Peter K., Schorle, Hubert, Naqvi, Sahin, Hu, Yueh-Chiang, Fan, Yuting, Carmell, Michelle A., Dobrinski, Ina, Watson, Adrienne L., Carlson, Daniel F., Fahrenkrug, Scott C., Page, David C.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 Dec . 116(51), 25677-25687.

Access URL: https://www.jstor.org/stable/26863912

Conservation, acquisition, and functional impact of sex-biased gene expression in mammals

Authors: Naqvi, Sahin, Godfrey, Alexander K., Hughes, Jennifer F., Goodheart, Mary L., Mitchell, Richard N., Page, David C.

Source: Science, 2019 Jul . 365(6450), 249-249.

Access URL: https://www.jstor.org/stable/26782161

Chemical sensing by nonequilibrium cooperative receptors

Authors: Skoge, Monica, Naqvi, Sahin, Meir, Yigal, Wingreen, Ned S.

Source: PRL 110, 248102 (2013)

Subject Terms: Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1307.2930

Quantitative analysis of Y-Chromosome gene expression across 36 human tissues

Authors: Godfrey, Alexander K., Naqvi, Sahin, Chmátal, Lukáš, Chick, Joel M., Mitchell, Richard N., Gygi, Steven P., Skaletsky, Helen, Page, David C.

Source: Genome research. 30(6):860-873

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN624723397&indx=1&recIds=ETOCRN624723397

Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution

Authors: Naqvi, Sahin, Bellott, Daniel W., Lin, Kathy S., Page, David C.

Source: Genome research. 28(4):474-483

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN615549044&indx=1&recIds=ETOCRN615549044

Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations.

Authors: Liu, Chenxing¹, Lee, Myoung Keun², Naqvi, Sahin^3,4, Hoskens, Hanne^5,6, Liu, Dongjing¹, White, Julie D.⁷, Indencleef, Karlijne^5,8, Matthews, Harold^5,6,9, Eller, Ryan J.¹⁰, Li, Jiarui^5,8, Mohammed, Jaaved^3,11, Swigut, Tomek^3,11, Richmond, Stephen¹², Manyama, Mange¹³, Hallgrímsson, Benedikt¹⁴, Spritz, Richard A.¹⁵, Feingold, Eleanor¹, Marazita, Mary L.^1,2, Wysocka, Joanna^3,11,16, Walsh, Susan¹⁰

Source: PLoS Genetics; 8/19/2021, Vol. 17 Issue 8, p1-21, 21p

3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies.

Authors: Hoskens, Hanne^1,2, hanne.hoskens@kuleuven.be, Liu, Dongjing³, Naqvi, Sahin^4,5, Lee, Myoung Keun⁶, Eller, Ryan J.⁷, Indencleef, Karlijne^2,8,9, White, Julie D.¹⁰, Li, Jiarui^2,8, Larmuseau, Maarten H. D.^1,11,12, Hens, Greet⁹, Wysocka, Joanna^4,13,14, Walsh, Susan⁷, Richmond, Stephen¹⁵, Shriver, Mark D.¹⁰, Shaffer, John R.^3,6, Peeters, Hilde¹, Weinberg, Seth M.^3,6,16, Claes, Peter^1,2,8,17, hanne.hoskens@kuleuven.be

Source: PLoS Genetics; 5/13/2021, Vol. 17 Issue 5, p1-28, 28p

Precise modulation of transcription factor levels identifies features underlying dosage sensitivity

Authors: Naqvi, Sahin, Kim, Seungsoo, Hoskens, Hanne, Matthews, Harold S., Spritz, Richard A., Klein, Ophir D., Hallgrímsson, Benedikt, Swigut, Tomek, Claes, Peter, Pritchard, Jonathan K., Wysocka, Joanna

Source: Nature Genetics; May 2023, Vol. 55 Issue: 5 p841-851, 11p

Systematic differences in discovery of genetic effects on gene expression and complex traits

Authors: Mostafavi, Hakhamanesh, Spence, Jeffrey P., Naqvi, Sahin, Pritchard, Jonathan K.

Source: Nature Genetics; 20230101, Issue: Preprints p1-10, 10p

Decoding the Human Face: Progress and Challenges in Understanding the Genetics of Craniofacial Morphology.

Authors: Naqvi, Sahin^1,2 (AUTHOR) naqvi@stanford.edu, Hoskens, Hanne^3,4 (AUTHOR) hanne.hoskens@kuleuven.be, Wilke, Franziska⁵ (AUTHOR) fwilke@iu.edu, Weinberg, Seth M.^6,7,8 (AUTHOR) smwst46@pitt.edu, Shaffer, John R.^6,7 (AUTHOR), Walsh, Susan⁵ (AUTHOR), Shriver, Mark D.⁹ (AUTHOR) mds17@psu.edu, Wysocka, Joanna^1,10,11 (AUTHOR), Claes, Peter^3,4,12,13 (AUTHOR)

Source: Annual Review of Genomics & Human Genetics. 2022, Vol. 23 Issue 1, p383-412. 28p.

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

Authors: Freimer, Jacob W., Shaked, Oren, Naqvi, Sahin, Sinnott-Armstrong, Nasa, Kathiria, Arwa, Garrido, Christian M., Chen, Amy F., Cortez, Jessica T., Greenleaf, William J., Pritchard, Jonathan K., Marson, Alexander

Source: Nature Genetics; 20220101, Issue: Preprints p1-12, 12p

The Intersection of the Genetic Architectures of Orofacial Clefts and Normal Facial Variation.

Authors: Indencleef, Karlijne, Hoskens, Hanne, Lee, Myoung Keun, White, Julie D., Liu, Chenxing, Eller, Ryan J., Naqvi, Sahin, Wehby, George L., Moreno Uribe, Lina M., Hecht, Jacqueline T., Long, Ross E., Christensen, Kaare, Deleyiannis, Frederic W., Walsh, Susan, Shriver, Mark D., Richmond, Stephen, Wysocka, Joanna, Peeters, Hilde, Shaffer, John R., Marazita, Mary L.

Source: Frontiers in Genetics; 2/22/2021, Vol. 11, pN.PAG-N.PAG, 14p

Subject Terms: CLEFT lip, CLEFT palate, LOCUS (Genetics), GENES, THREE-dimensional imaging

GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background.

Authors: Sinnott-Armstrong, Nasa¹ nasa@stanford.edu, Naqvi, Sahin^1,2, Rivas, Manuel³, Pritchard, Jonathan K.^1,4 pritch@stanford.edu

Source: eLife. 2/15/2021, p1-35. 35p.

Subject Terms: *GENOME-wide association studies, *TESTOSTERONE regulation, *GENES, *HERITABILITY, *TESTOSTERONE

Geographic Terms: UNITED Kingdom

Human–chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution

Authors: Gokhman, David, Agoglia, Rachel M., Kinnebrew, Maia, Gordon, Wei, Sun, Danqiong, Bajpai, Vivek K., Naqvi, Sahin, Chen, Coral, Chan, Anthony, Chen, Chider, Petrov, Dmitri A., Ahituv, Nadav, Zhang, Honghao, Mishina, Yuji, Wysocka, Joanna, Rohatgi, Rajat, Fraser, Hunter B.

Source: Nature Genetics; April 2021, Vol. 53 Issue: 4 p467-476, 10p

Shared heritability of human face and brain shape

Authors: Naqvi, Sahin, Sleyp, Yoeri, Hoskens, Hanne, Indencleef, Karlijne, Spence, Jeffrey P., Bruffaerts, Rose, Radwan, Ahmed, Eller, Ryan J., Richmond, Stephen, Shriver, Mark D., Shaffer, John R., Weinberg, Seth M., Walsh, Susan, Thompson, James, Pritchard, Jonathan K., Sunaert, Stefan, Peeters, Hilde, Wysocka, Joanna, Claes, Peter

Source: Nature Genetics; 20210101, Issue: Preprints p1-10, 10p

Insights into the genetic architecture of the human face

Authors: White, Julie D., Indencleef, Karlijne, Naqvi, Sahin, Eller, Ryan J., Hoskens, Hanne, Roosenboom, Jasmien, Lee, Myoung Keun, Li, Jiarui, Mohammed, Jaaved, Richmond, Stephen, Quillen, Ellen E., Norton, Heather L., Feingold, Eleanor, Swigut, Tomek, Marazita, Mary L., Peeters, Hilde, Hens, Greet, Shaffer, John R., Wysocka, Joanna, Walsh, Susan, Weinberg, Seth M., Shriver, Mark D., Claes, Peter

Source: Nature Genetics; January 2021, Vol. 53 Issue: 1 p45-53, 9p

A genome-wide genetic screen uncovers determinants of human pigmentation.

Authors: Bajpai, Vivek K., Swigut, Tomek, Mohammed, Jaaved, Naqvi, Sahin, Arreola, Martin, Tycko, Josh, Kim, Tayne C., Pritchard, Jonathan K., Bassik, Michael C., Wysocka, Joanna, wysocka@stanford.edu

Source: Science; 8/11/2023, Vol. 381 Issue 6658, p646-646, 1p, 1 Diagram

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