Publications (ORCID: 0000-0002-0894-5696)
Preprint & Manuscripts in preparation
Tidball A*., Niu W*, Ma, Q, Takla, TN, Walker, JC, Margolis, JL, Mojica-Perez, SP, Chopra, R., Shakkottai, VG., Li, JZ, and Parent, JM: Self-Organizing Single-Rosette Brain Organoids From Human Pluripotent Stem Cells. bioRxiv 2022.02.28.482350; doi: https://doi.org/10.1101/2022.02.28.482350 (submitted to Stem Cell Report) (*Equal contribution).
Mojica-Perez SP, Stokes K, Jaklic D, Parent JM, and Niu W: Efficient and precise single- cell clonal selection of human pluripotent stem cells (Corresponding author; submitted to STAR Protocol, in minor revision).
Peer-Reviewed Publications
2022 Deng L, Mojica-Perez SP, Parent JM, and Niu W: Loss of POGZ Alters Neural Differentiation of Human Embryonic Stem Cells. Molecular and Cellular Neuroscience 120: 103727. https://doi.org/10.1016/j.mcn.2022.103727. (Corresponding author)
2020 Niu W, Parent JM: Modeling Genetic Epilepsies In A Dish. Developmental Dynamics 2020;249:56–75. https://doi.org/10.1002/dvdy.79
2015 Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP: The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun. 6: 6404, 2015. PM25752243/PMC4355952.
2014 Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M: Regulatory analysis of the C. Elegans genome with spatiotemporal resolution. Nature. 512(7515): 400-405. PM25164749.
2014 Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M: Comparative analysis of regulatory information and circuits across distant species. Nature. 512 (7515): 453-456. PM25164757.
2013 Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW: Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell. 155(5): 997-1007. PM24267886
2013 Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V: Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biol. 14(1): R5. PM23347407.
2013 Fontrodona L, Porta-de-la-Riva M, Morán T, Niu W, Díaz M, Aristizábal-Corrales D, Villanueva A, Schwartz Jr S, Reinke V, Cerón J: RSR-2, the Caenorhabditis elegans Ortholog of Human Spliceosomal Component SRm300/SRRM2, Regulates Development by Influencing the Transcriptional Machinery. PLoS Genet. 9(6): e1003543,. PM23754964.
2012 Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M, Preston E, Zinke A, Enst S, Teichgraber T, Janette J, Reis K, Janosch S, Schloissnig S, Ejsmont RK, Slightam C, Xu X, Kim SK, Reinke V, Stewart AF, Snyder M, Waterston RH, Hyman AA: A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 150(4): 855- 866. PM22901814.
2011 Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M: Construction and analysis of an integrated regulatory network derived from High- Throughput sequencing data. PLoS Comput Biol. 7(11): e1002190. PM22125477.
2011 Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V: Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. 21(2): 245-254. PM21177963. (modENCODE special issue, Cover story).
2010 Gerstein MB, Lu ZJ*, Van Nostrand EL*, Cheng C*, Arshinoff BI*, Liu T*, Yip KY*, Robilotto R*, Rechtsteiner A*, Ikegami K*, Alves P*, Chateigner A*, Perry M*, Morris M*, Auerbach RK*, Feng X*, Leng J*, Vielle A*, Niu W*, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller 3rd DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, , Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH: Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 330(6012): 1775-1787. PM21177976. *: Equal contribution. (Cover story)
2010 Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M: Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 6(2): e1000848, 2010. PM20174564.
2010 Lei H, Fukushige T, Niu W, Sarov M, Reinke V, Krause M: A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques. PLoS One. 5(12): e15898, 2010. PM21209968.
2008 Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM: Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast. J Proteome Res. 8(1): 6-19, 2008. PM19053807.
2008 Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM: Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. PLoS Genet. 4(7): e1000120, 2008. PM18617996.
2008 Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM: Group II intron protein localization and insertion sites are affected by polyphosphate. PLoS Biol. 6(6): 1306-1320, 2008. PM18593213.
2006 Narayanaswamy R*, Niu W*, Scouras AD*, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM: Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes. Genome Biol. 7(1): R6, 2006. PM16507139. *: Equal contribution.
2002 Niu W, and Zhang D: Evolution of 5S rRNA genes in Ophiopogon xylorrrhizus Wang et Dai and O. sylvicola Wang et Tang (Convallariaceae). Acta Botanica Sinica 44(3): 329-336.
Book Chapters
2014 Brdlik CM, Niu W, Snyder M.: Chromatin Immunoprecipitation and Multiplex Sequencing (ChIP-Seq) to Identify Global Transcription Factor Binding Sites in the Nematode Caenorhabditis elegans. Laboratory Methods in Enzymology, Edited by Jon Lorsch, Elsevier Inc. 7, 89-111.
2011 Niu W, Hart GT, Marcotte EM: High-throughput immunofluorescence microscopy using yeast spheroplast cell-based microarrays. Methods in molecular biology (Clifton, N.J.) 706: 83-95. PM21104056.
Tidball A*., Niu W*, Ma, Q, Takla, TN, Walker, JC, Margolis, JL, Mojica-Perez, SP, Chopra, R., Shakkottai, VG., Li, JZ, and Parent, JM: Self-Organizing Single-Rosette Brain Organoids From Human Pluripotent Stem Cells. bioRxiv 2022.02.28.482350; doi: https://doi.org/10.1101/2022.02.28.482350 (submitted to Stem Cell Report) (*Equal contribution).
Mojica-Perez SP, Stokes K, Jaklic D, Parent JM, and Niu W: Efficient and precise single- cell clonal selection of human pluripotent stem cells (Corresponding author; submitted to STAR Protocol, in minor revision).
Peer-Reviewed Publications
2022 Deng L, Mojica-Perez SP, Parent JM, and Niu W: Loss of POGZ Alters Neural Differentiation of Human Embryonic Stem Cells. Molecular and Cellular Neuroscience 120: 103727. https://doi.org/10.1016/j.mcn.2022.103727. (Corresponding author)
2020 Niu W, Parent JM: Modeling Genetic Epilepsies In A Dish. Developmental Dynamics 2020;249:56–75. https://doi.org/10.1002/dvdy.79
2015 Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP: The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun. 6: 6404, 2015. PM25752243/PMC4355952.
2014 Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M: Regulatory analysis of the C. Elegans genome with spatiotemporal resolution. Nature. 512(7515): 400-405. PM25164749.
2014 Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M: Comparative analysis of regulatory information and circuits across distant species. Nature. 512 (7515): 453-456. PM25164757.
2013 Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW: Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell. 155(5): 997-1007. PM24267886
2013 Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V: Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biol. 14(1): R5. PM23347407.
2013 Fontrodona L, Porta-de-la-Riva M, Morán T, Niu W, Díaz M, Aristizábal-Corrales D, Villanueva A, Schwartz Jr S, Reinke V, Cerón J: RSR-2, the Caenorhabditis elegans Ortholog of Human Spliceosomal Component SRm300/SRRM2, Regulates Development by Influencing the Transcriptional Machinery. PLoS Genet. 9(6): e1003543,. PM23754964.
2012 Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M, Preston E, Zinke A, Enst S, Teichgraber T, Janette J, Reis K, Janosch S, Schloissnig S, Ejsmont RK, Slightam C, Xu X, Kim SK, Reinke V, Stewart AF, Snyder M, Waterston RH, Hyman AA: A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 150(4): 855- 866. PM22901814.
2011 Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M: Construction and analysis of an integrated regulatory network derived from High- Throughput sequencing data. PLoS Comput Biol. 7(11): e1002190. PM22125477.
2011 Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V: Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. 21(2): 245-254. PM21177963. (modENCODE special issue, Cover story).
2010 Gerstein MB, Lu ZJ*, Van Nostrand EL*, Cheng C*, Arshinoff BI*, Liu T*, Yip KY*, Robilotto R*, Rechtsteiner A*, Ikegami K*, Alves P*, Chateigner A*, Perry M*, Morris M*, Auerbach RK*, Feng X*, Leng J*, Vielle A*, Niu W*, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller 3rd DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, , Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH: Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 330(6012): 1775-1787. PM21177976. *: Equal contribution. (Cover story)
2010 Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M: Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 6(2): e1000848, 2010. PM20174564.
2010 Lei H, Fukushige T, Niu W, Sarov M, Reinke V, Krause M: A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques. PLoS One. 5(12): e15898, 2010. PM21209968.
2008 Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM: Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast. J Proteome Res. 8(1): 6-19, 2008. PM19053807.
2008 Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM: Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. PLoS Genet. 4(7): e1000120, 2008. PM18617996.
2008 Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM: Group II intron protein localization and insertion sites are affected by polyphosphate. PLoS Biol. 6(6): 1306-1320, 2008. PM18593213.
2006 Narayanaswamy R*, Niu W*, Scouras AD*, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM: Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes. Genome Biol. 7(1): R6, 2006. PM16507139. *: Equal contribution.
2002 Niu W, and Zhang D: Evolution of 5S rRNA genes in Ophiopogon xylorrrhizus Wang et Dai and O. sylvicola Wang et Tang (Convallariaceae). Acta Botanica Sinica 44(3): 329-336.
Book Chapters
2014 Brdlik CM, Niu W, Snyder M.: Chromatin Immunoprecipitation and Multiplex Sequencing (ChIP-Seq) to Identify Global Transcription Factor Binding Sites in the Nematode Caenorhabditis elegans. Laboratory Methods in Enzymology, Edited by Jon Lorsch, Elsevier Inc. 7, 89-111.
2011 Niu W, Hart GT, Marcotte EM: High-throughput immunofluorescence microscopy using yeast spheroplast cell-based microarrays. Methods in molecular biology (Clifton, N.J.) 706: 83-95. PM21104056.