Kinkade JA, Seetharam AS, Sachdev S, Bivens NJ, Phinney BS, Grigorean G, Roberts RM, Tuteja G, Rosenfeld CS. Extracellular vesicles from mouse trophoblast cells: Effects on neural progenitor cells and potential participants in the placenta-brain axis. Biol Reprod. 2024 Feb 10;110(2):310-328. doi: 10.1093/biolre/ioad146. PMID: 37883444; PMCID: PMC10873279.
Iqbal K, Dominguez EM, Nixon B, Moreno-Irusta A, Crnkovich B, Scott RL, Vu HTH, Tuteja G, Vivian JL, Soares MJ. Conditionally mutant animal model for investigating the invasive trophoblast cell lineage. Development. 2024 Jan 15;151(2):dev202239. doi: 10.1242/dev.202239. Epub 2024 Jan 17. PMID: 38112206; PMCID: PMC10820817.
Vu HTH, Scott RL, Iqbal K, Soares MJ, Tuteja G. Core conserved transcriptional regulatory networks define the invasive trophoblast cell lineage. Development. 2023 Aug 1;150(15):dev201826. doi: 10.1242/dev.201826. Epub 2023 Jul 31. PMID: 37417811; PMCID: PMC10445752.
Vu HTH, Zhang Y, Tuteja G, Dorman KS. Unsupervised contrastive peak caller for ATAC-seq. Genome Res. 2023 Jul;33(7):1133-1144. doi: 10.1101/gr.277677.123. Epub 2023 May 22. PMID: 37217250.
Yu W, Chakravarthi VP, Borosha S, Dilower I, Lee EB, Ratri A, Starks RR, Fields PE, Wolfe MW, Faruque MO, Tuteja G, Rumi MAK. Transcriptional regulation of Satb1 in mouse trophoblast stem cells. Front Cell Dev Biol. 2022 Dec 14;10:918235. doi: 10.3389/fcell.2022.918235. PMID: 36589740; PMCID: PMC9795202.
Vu HT, Kaur H, Kies KR, Starks RR, Tuteja G. Identifying novel regulators of placental development using time-series transcriptome data. Life Sci Alliance. 2022 Dec 13;6(2):e202201788. doi: 10.26508/lsa.202201788. PMID: 36622342; PMCID: PMC9748866.
Scott RL, Vu HTH, Jain A, Iqbal K, Tuteja G, Soares MJ. Conservation at the uterine-placental interface. Proc Natl Acad Sci U S A. 2022 Oct 11;119(41):e2210633119. doi: 10.1073/pnas.2210633119. Epub 2022 Oct 3. PMID: 36191208; PMCID: PMC9565169.
Seetharam AS, Vu HTH, Choi S, Khan T, Sheridan MA, Ezashi T, Roberts RM, Tuteja G. The product of BMP-directed differentiation protocols for human primed pluripotent stem cells is placental trophoblast and not amnion. Stem Cell Reports. 2022 Jun 14;17(6):1289-1302. doi: 10.1016/j.stemcr.2022.04.014. Epub 2022 May 19. PMID: 35594861; PMCID: PMC9214062.
Adu-Gyamfi EA, Rosenfeld CS, Tuteja G. The impact of bisphenol A on the placenta. Biol Reprod. 2022 May 17;106(5):826-834. doi: 10.1093/biolre/ioac001. PMID: 35020819; PMCID: PMC9113501.
Tuteja G, Soares MJ. Editorial: Multi-Omics Approaches to Study Placental Development and Disease. Front Cell Dev Biol. 2021 Nov 8;9:798966. doi: 10.3389/fcell.2021.798966. PMID: 34820389; PMCID: PMC8606685.
Starks RR, Kaur H, Tuteja G. Mapping cis-regulatory elements in the midgestation mouse placenta. Sci Rep. 2021 Nov 16;11(1):22331. doi: 10.1038/s41598-021-01664-x. PMID: 34785717; PMCID: PMC8595355.
Khan T, Seetharam AS, Zhou J, Bivens NJ, Schust DJ, Ezashi T, Tuteja G, Roberts RM. Single Nucleus RNA Sequence (snRNAseq) Analysis of the Spectrum of Trophoblast Lineages Generated From Human Pluripotent Stem Cells in vitro. Front Cell Dev Biol. 2021 Jul 21;9:695248. doi: 10.3389/fcell.2021.695248. PMID: 34368143; PMCID: PMC8334858.
Starks RR, Abu Alhasan R, Kaur H, Pennington KA, Schulz LC, Tuteja G (2020). Transcription factor PLAGL1 is Associated with Angiogenic Gene Expression in the Placenta. Int J Mol Sci. 2020 Nov 6;21(21):8317. doi: 10.3390/ijms21218317.
Jain A, Tuteja G (2020). PlacentaCellEnrich: A tool to characterize gene sets using placenta cell-specific gene enrichment analysis. Placenta.
2020 Oct 27;103:164-171. doi: 10.1016/j.placenta.2020.10.029.
Green MT, Martin RE, Kinkade JA, Schmidt RR, Bivens NJ, Tuteja G, Mao J, Rosenfeld CS (2020). Maternal oxycodone treatment causes pathophysiological changes in the mouse placenta. Placenta. Oct;100:96-110. doi: 10.1016/j.placenta.2020.08.006.
Jiude Mao, Ashish Jain, Nancy D Denslow, Mohammad-Zaman Nouri, Sixue Chen, Tingting Wang, Ning Zhu, Jin Koh, Saurav J Sarma, Barbara W Sumner, Zhentian Lei, Lloyd W Sumner, Nathan J Bivens, R Michael Roberts*, Geetu Tuteja*, Cheryl S Rosenfeld* (2020).
Bisphenol A and Bisphenol S Disruptions of the Mouse Placenta and Potential Effects on the Placenta-Brain Axis. PNAS; doi: 10.1073/pnas.1919563117.
*co-corresponding authors
Abdulghani M, Song G, Kaur H, Walley JW, Tuteja G (2019). Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development. Journal of Proteome Research. Apr 15. doi: 10.1021/acs.jproteome.8b00970.
Starks RR, Biswas A, Jain A, Tuteja G (2019). Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks. Epigenetics & Chromatin. Feb 22;12(1):16. doi: 10.1186/s13072-019-0260-2.
Sheridan MA, Yang Y, Jain A, Lyons AS, Yang P, Brahmasani SR, Dai A, Tian Y, Ellersieck MR, Tuteja G, Schust DJ, Schulz LC, Ezashi T, Roberts RM (2019). Early onset preeclampsia in a model for human placental trophoblast. PNAS; pii: 201816150. doi: 10.1073/pnas.1816150116.
Jain A, Tuteja G (2018). TissueEnrich: Tissue-specific gene enrichment analysis. Bioinformatics; In Press. doi: 10.1093/bioinformatics/bty890.
Abdulghani M, Jain A, Tuteja G (2018). Genome-wide identification of enhancer elements in the placenta.
Placenta; pii: S0143-4004(18)30642-8. doi: 10.1016/j.placenta.2018.09.003.
Jain A, Ezashi T, Roberts RM, Tuteja G (2017). Deciphering transcriptional regulation in human embryonic stem cells specified towards a trophoblast fate. Scientific Reports; 7(1):17257; doi: 10.1038/s41598-017-17614-5.
Albrecht C, Baker JC, Blundell C, Chavez SL, Carbone L, Chamley L, Hannibal RL, Illsley N, Kurre P, Laurent LC, McKenzie C, Morales-Prieto D, Pantham P, Paquette A, Powell K, Price N, Rao BM, Sadovsky Y, Salomon C, Tuteja G, Wilson S, O'Tierney-Ginn PF (2016). IFPA meeting 2016 workshop report I: Genomic communication, bioinformatics, trophoblast biology and transport systems. Placenta; doi: 10.1016/j.placenta.2017.01.103.
Tuteja G, Chung T, Bejerano G (2015). Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network. Placenta; doi:10.1016/j.placenta.2015.11.001.
Tuteja G, Moreira KE, Wenger AM, Chung T, Chen J, Bejerano G (2014). Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data. PLoS Computational Biology; 10(1): e1003449.
Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G (2013). The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. PLoS Genetics; 9(8):e1003728.
Tuteja G, Cheng E, Papadakis H, Bejerano G (2012). PESNPdb: A comprehensive database of SNPs studied in association with pre-eclampsia. Placenta; 33(12):1055-1057.
Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W, Kaestner KH (2012). Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell; 151(7):1608-1616.
Li Z, Tuteja G, Schug J, Kaestner KH (2012). Foxa1 and Foxa2 are essential for sexual dimorphism in liver cancer. Cell; 148(1):72-83.
Tuteja G (2012). DNA-protein Interaction analysis (ChIP-Seq). In Bioinformatics for Next Generation Sequencing. Springer; 127-149.
Li Z, Schug J, Tuteja G, White P, Kaestner KH (2011). The nucleosome map of the mammalian liver. Nat Struct Mol Biol; 18(6):742-6.
Soccio RE*, Tuteja G*, Everett L, Lazar MA, Kaestner KH (2011). Species-specific strategies underlying conserved functions of metabolic transcription factors. Mol Endocrinol; 25(4):694-706.
* Contributed equally to this work
Lefterova MI, Steger DJ, Zhuo D, Qatanani M, Mullican SE, Tuteja G, Manduchi E, Grant GR, and Lazar MA (2010). Cell Specific Determinants of PPARg Function in Adipocytes and Macrophages. Mol. Cell. Biol.; 24(10):1035-44.
Le Lay J, Tuteja G, White P, Dhir R, Ahima R, Kaestner KH (2009). CRTC2 Contributes to the Transcriptional Response to Fasting in the Liver but is Not Required for the Maintenance of Glucose Homeostasis. Cell Metabolism; 10(1):55-62.
Tuteja G, White P, Schug, J, Kaestner KH (2009). Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Research; 37(17):e113.
Li Z, White P, Tuteja G, Sackett S, Kaestner KH (2009). Foxa1 and Foxa2 control bile duct development. Journal of Clinical Investigation; 119(6):1537-1545.
Tuteja G, Jensen ST, White P, Kaestner KH (2008). Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site. Nucleic Acids Research; 36(12):4149-57.
Tuteja G, Kaestner KH (2007). Forkhead transcription factors II. Cell. 131(1):192.
Tuteja G, Kaestner KH (2007). Forkhead transcription factors I. Cell. 130(6):1160.
Iqbal K, Dominguez EM, Nixon B, Moreno-Irusta A, Crnkovich B, Scott RL, Vu HTH, Tuteja G, Vivian JL, Soares MJ. Conditionally mutant animal model for investigating the invasive trophoblast cell lineage. Development. 2024 Jan 15;151(2):dev202239. doi: 10.1242/dev.202239. Epub 2024 Jan 17. PMID: 38112206; PMCID: PMC10820817.
Vu HTH, Scott RL, Iqbal K, Soares MJ, Tuteja G. Core conserved transcriptional regulatory networks define the invasive trophoblast cell lineage. Development. 2023 Aug 1;150(15):dev201826. doi: 10.1242/dev.201826. Epub 2023 Jul 31. PMID: 37417811; PMCID: PMC10445752.
Vu HTH, Zhang Y, Tuteja G, Dorman KS. Unsupervised contrastive peak caller for ATAC-seq. Genome Res. 2023 Jul;33(7):1133-1144. doi: 10.1101/gr.277677.123. Epub 2023 May 22. PMID: 37217250.
Yu W, Chakravarthi VP, Borosha S, Dilower I, Lee EB, Ratri A, Starks RR, Fields PE, Wolfe MW, Faruque MO, Tuteja G, Rumi MAK. Transcriptional regulation of Satb1 in mouse trophoblast stem cells. Front Cell Dev Biol. 2022 Dec 14;10:918235. doi: 10.3389/fcell.2022.918235. PMID: 36589740; PMCID: PMC9795202.
Vu HT, Kaur H, Kies KR, Starks RR, Tuteja G. Identifying novel regulators of placental development using time-series transcriptome data. Life Sci Alliance. 2022 Dec 13;6(2):e202201788. doi: 10.26508/lsa.202201788. PMID: 36622342; PMCID: PMC9748866.
Scott RL, Vu HTH, Jain A, Iqbal K, Tuteja G, Soares MJ. Conservation at the uterine-placental interface. Proc Natl Acad Sci U S A. 2022 Oct 11;119(41):e2210633119. doi: 10.1073/pnas.2210633119. Epub 2022 Oct 3. PMID: 36191208; PMCID: PMC9565169.
Seetharam AS, Vu HTH, Choi S, Khan T, Sheridan MA, Ezashi T, Roberts RM, Tuteja G. The product of BMP-directed differentiation protocols for human primed pluripotent stem cells is placental trophoblast and not amnion. Stem Cell Reports. 2022 Jun 14;17(6):1289-1302. doi: 10.1016/j.stemcr.2022.04.014. Epub 2022 May 19. PMID: 35594861; PMCID: PMC9214062.
Adu-Gyamfi EA, Rosenfeld CS, Tuteja G. The impact of bisphenol A on the placenta. Biol Reprod. 2022 May 17;106(5):826-834. doi: 10.1093/biolre/ioac001. PMID: 35020819; PMCID: PMC9113501.
Tuteja G, Soares MJ. Editorial: Multi-Omics Approaches to Study Placental Development and Disease. Front Cell Dev Biol. 2021 Nov 8;9:798966. doi: 10.3389/fcell.2021.798966. PMID: 34820389; PMCID: PMC8606685.
Starks RR, Kaur H, Tuteja G. Mapping cis-regulatory elements in the midgestation mouse placenta. Sci Rep. 2021 Nov 16;11(1):22331. doi: 10.1038/s41598-021-01664-x. PMID: 34785717; PMCID: PMC8595355.
Khan T, Seetharam AS, Zhou J, Bivens NJ, Schust DJ, Ezashi T, Tuteja G, Roberts RM. Single Nucleus RNA Sequence (snRNAseq) Analysis of the Spectrum of Trophoblast Lineages Generated From Human Pluripotent Stem Cells in vitro. Front Cell Dev Biol. 2021 Jul 21;9:695248. doi: 10.3389/fcell.2021.695248. PMID: 34368143; PMCID: PMC8334858.
Starks RR, Abu Alhasan R, Kaur H, Pennington KA, Schulz LC, Tuteja G (2020). Transcription factor PLAGL1 is Associated with Angiogenic Gene Expression in the Placenta. Int J Mol Sci. 2020 Nov 6;21(21):8317. doi: 10.3390/ijms21218317.
Jain A, Tuteja G (2020). PlacentaCellEnrich: A tool to characterize gene sets using placenta cell-specific gene enrichment analysis. Placenta.
2020 Oct 27;103:164-171. doi: 10.1016/j.placenta.2020.10.029.
Green MT, Martin RE, Kinkade JA, Schmidt RR, Bivens NJ, Tuteja G, Mao J, Rosenfeld CS (2020). Maternal oxycodone treatment causes pathophysiological changes in the mouse placenta. Placenta. Oct;100:96-110. doi: 10.1016/j.placenta.2020.08.006.
Jiude Mao, Ashish Jain, Nancy D Denslow, Mohammad-Zaman Nouri, Sixue Chen, Tingting Wang, Ning Zhu, Jin Koh, Saurav J Sarma, Barbara W Sumner, Zhentian Lei, Lloyd W Sumner, Nathan J Bivens, R Michael Roberts*, Geetu Tuteja*, Cheryl S Rosenfeld* (2020).
Bisphenol A and Bisphenol S Disruptions of the Mouse Placenta and Potential Effects on the Placenta-Brain Axis. PNAS; doi: 10.1073/pnas.1919563117.
*co-corresponding authors
Abdulghani M, Song G, Kaur H, Walley JW, Tuteja G (2019). Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development. Journal of Proteome Research. Apr 15. doi: 10.1021/acs.jproteome.8b00970.
Starks RR, Biswas A, Jain A, Tuteja G (2019). Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks. Epigenetics & Chromatin. Feb 22;12(1):16. doi: 10.1186/s13072-019-0260-2.
Sheridan MA, Yang Y, Jain A, Lyons AS, Yang P, Brahmasani SR, Dai A, Tian Y, Ellersieck MR, Tuteja G, Schust DJ, Schulz LC, Ezashi T, Roberts RM (2019). Early onset preeclampsia in a model for human placental trophoblast. PNAS; pii: 201816150. doi: 10.1073/pnas.1816150116.
Jain A, Tuteja G (2018). TissueEnrich: Tissue-specific gene enrichment analysis. Bioinformatics; In Press. doi: 10.1093/bioinformatics/bty890.
Abdulghani M, Jain A, Tuteja G (2018). Genome-wide identification of enhancer elements in the placenta.
Placenta; pii: S0143-4004(18)30642-8. doi: 10.1016/j.placenta.2018.09.003.
Jain A, Ezashi T, Roberts RM, Tuteja G (2017). Deciphering transcriptional regulation in human embryonic stem cells specified towards a trophoblast fate. Scientific Reports; 7(1):17257; doi: 10.1038/s41598-017-17614-5.
Albrecht C, Baker JC, Blundell C, Chavez SL, Carbone L, Chamley L, Hannibal RL, Illsley N, Kurre P, Laurent LC, McKenzie C, Morales-Prieto D, Pantham P, Paquette A, Powell K, Price N, Rao BM, Sadovsky Y, Salomon C, Tuteja G, Wilson S, O'Tierney-Ginn PF (2016). IFPA meeting 2016 workshop report I: Genomic communication, bioinformatics, trophoblast biology and transport systems. Placenta; doi: 10.1016/j.placenta.2017.01.103.
Tuteja G, Chung T, Bejerano G (2015). Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network. Placenta; doi:10.1016/j.placenta.2015.11.001.
Tuteja G, Moreira KE, Wenger AM, Chung T, Chen J, Bejerano G (2014). Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data. PLoS Computational Biology; 10(1): e1003449.
Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G (2013). The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. PLoS Genetics; 9(8):e1003728.
Tuteja G, Cheng E, Papadakis H, Bejerano G (2012). PESNPdb: A comprehensive database of SNPs studied in association with pre-eclampsia. Placenta; 33(12):1055-1057.
Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W, Kaestner KH (2012). Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell; 151(7):1608-1616.
Li Z, Tuteja G, Schug J, Kaestner KH (2012). Foxa1 and Foxa2 are essential for sexual dimorphism in liver cancer. Cell; 148(1):72-83.
Tuteja G (2012). DNA-protein Interaction analysis (ChIP-Seq). In Bioinformatics for Next Generation Sequencing. Springer; 127-149.
Li Z, Schug J, Tuteja G, White P, Kaestner KH (2011). The nucleosome map of the mammalian liver. Nat Struct Mol Biol; 18(6):742-6.
Soccio RE*, Tuteja G*, Everett L, Lazar MA, Kaestner KH (2011). Species-specific strategies underlying conserved functions of metabolic transcription factors. Mol Endocrinol; 25(4):694-706.
* Contributed equally to this work
Lefterova MI, Steger DJ, Zhuo D, Qatanani M, Mullican SE, Tuteja G, Manduchi E, Grant GR, and Lazar MA (2010). Cell Specific Determinants of PPARg Function in Adipocytes and Macrophages. Mol. Cell. Biol.; 24(10):1035-44.
Le Lay J, Tuteja G, White P, Dhir R, Ahima R, Kaestner KH (2009). CRTC2 Contributes to the Transcriptional Response to Fasting in the Liver but is Not Required for the Maintenance of Glucose Homeostasis. Cell Metabolism; 10(1):55-62.
Tuteja G, White P, Schug, J, Kaestner KH (2009). Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Research; 37(17):e113.
Li Z, White P, Tuteja G, Sackett S, Kaestner KH (2009). Foxa1 and Foxa2 control bile duct development. Journal of Clinical Investigation; 119(6):1537-1545.
Tuteja G, Jensen ST, White P, Kaestner KH (2008). Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site. Nucleic Acids Research; 36(12):4149-57.
Tuteja G, Kaestner KH (2007). Forkhead transcription factors II. Cell. 131(1):192.
Tuteja G, Kaestner KH (2007). Forkhead transcription factors I. Cell. 130(6):1160.