Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Ana Uzquiano*, Amanda J. Kedaigle*, Martina Pigoni, Bruna Paulsen, Xian Adiconis, Kwanho Kim, Tyler Faits, Surya Nagaraja, Noelia Antón-Bolaños, Chiara Gerhardinger, Ashley Tucewicz, Evan Murray, Xin Jin, Jason Buenrostro, Fei Chen, Silvia Velasco, Aviv Regev, Joshua Z. Levin, Paola Arlotta. Cell, 2022.
Autism genes converge on asynchronous development of shared neuron classes. Bruna Paulsen*, Silvia Velasco*, Amanda J. Kedaigle*, Martina Pigoni*, Giorgia Quadrato, Anthony Deo, Xian Adiconis, Ana Uzquiano, Rafaela Sartore, Sung Min Yang, Sean K. Simmons, Panagiotis Symvoulidis, Kwanho Kim, Kalliopi Tsafou, Archana Podury, Catherine Abbate, Ashley Tucewicz, Samantha N. Smith, Alexandre Albanese, Lindy Barrett, Neville E. Sanjana, Xi Shi, Kwanghun Chung, Kasper Lage, Edward S. Boyden, Aviv Regev, Joshua Z. Levin & Paola Arlotta. Nature, 2022.
Immortalized striatal precursor neurons from Huntington’s disease patient-derived iPS cells as a platform for target identification and screening for experimental therapeutics. Sergey S Akimov, Mali Jiang, Amanda J Kedaigle, Nicolas Arbez, Leonard O Marque, Chelsy R Eddings, Paul T Ranum, Emma Whelan, Anthony Tang, Ronald Wang, Lauren R DeVine, Conover C Talbot, Jr, Robert N Cole, Tamara Ratovitski, Beverly L Davidson, Ernest Fraenkel, Christopher A Ross. Human Molecular Genetics, 2021.
Skin-resident innate lymphoid cells converge on a pathogenic effector state. Piotr Bielecki*, Samantha J. Riesenfeld*, Jan-Christian Hütter*, Elena Torlai Triglia*, Monika S. Kowalczyk, Roberto R. Ricardo-Gonzalez, Mi Lian, Maria C. Amezcua Vesely, Lina Kroehling, Hao Xu, Michal Slyper, Christoph Muus, Leif S. Ludwig, Elena Christian, Liming Tao, Amanda J. Kedaigle, Holly R. Steach, Autumn G. York, Mathias H. Skadow, Parastou Yaghoubi, Danielle Dionne, Abigail Jarret, Heather M. McGee, Caroline B. M. Porter, Paula Licona-Limón, Will Bailis, Ruaidhrí Jackson, Nicola Gagliani, Georg Gasteiger, Richard M. Locksley, Aviv Regev & Richard A. Flavell. Nature, 2021.
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Jiarui Ding, Xian Adiconis, Sean K. Simmons, Monika S. Kowalczyk, Cynthia C. Hession, Nemanja D. Marjanovic, Travis K. Hughes, Marc H. Wadsworth, Tyler Burks, Lan T. Nguyen, John Y. H. Kwon, Boaz Barak, William Ge, Amanda J. Kedaigle, Shaina Carroll, Shuqiang Li, Nir Hacohen, Orit Rozenblatt-Rosen, Alex K. Shalek, Alexandra-Chloé Villani, Aviv Regev & Joshua Z. Levin. Nature Biotechnology, 2020.
Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington's disease mice. Amanda J. Kedaigle*, Jack C. Reidling*, Ryan G. Lim*, Miriam Adam, Jie Wu, Brook Wassie, Jennifer T. Stocksdale, Malcolm S. Casale, Ernest Fraenkel, Leslie M. Thompson. Human Molecular Genetics, 2020.
ATR is a MYB regulated gene and potential therapeutic target in adenoid cystic carcinoma. Mattias K. Andersson, Giovanna Mangiapane, Paloma Tejera Nevado, Alexia Tsakaneli, Therese Carlsson, Gabriele Corda, Valentina Nieddu, Carla Abrahamian, Olesya Chayka, Lilam Rai, Michael Wick, Amanda Kedaigle, Göran Stenman & Arturo Sala. Oncogenesis, 2020.
Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Silvia Velasco, Amanda J. Kedaigle, Sean K. Simmons, Allison Nash, Marina Rocha, Giorgia Quadrato, Bruna Paulsen, Lan Nguyen, Xian Adiconis, Aviv Regev, Joshua Z. Levin, Paola Arlotta. Nature, 2019.
Individual oligodendrocytes show bias for inhibitory axons in the neocortex. Marzieh Zonouzi, Daniel Berger, Vahbiz Jokhi, Amanda J Kedaigle, Jeff Lichtman, Paola Arlotta. Cell Reports, 2019.
Bioenergetic deficits in Huntington’s disease iPSC-derived neural cells and rescue with glycolytic metabolites. Amanda J Kedaigle, Ernest Fraenkel, and the rest of the HD iPSC Consortium. Human Molecular Genetics, 2019.
Turning omics data into therapeutic insights. Amanda Kedaigle & Ernest Fraenkel. Current Opinion in Pharmacology, 2018.
Discovering altered regulation and signaling through network-based integration of transcriptomic, epigenomic and proteomic tumor data. Amanda Kedaigle and Ernest Fraenkel. Cancer Systems Biology: Methods in Molecular Biology, ed. Louise von Stechow, Springer Science, 2018.
Integrating Omics data: a new software tool and its use in implicating therapeutic targets in Huntington's disease. Amanda Kedaigle. PhD dissertation, Massachusetts Institute of Technology, 2018.
Developmental alterations in Huntington’s disease neural cells and pharmacological rescue in cells and mice. The HD iPSC Consortium, first author of MIT group Amanda Kedaigle, Theresa Gipson, Ferah Yildirim, Chris W. Ng, Pamela Milani, David E. Housman, Ernest Fraenkel. Nature Neuroscience, 2017; 20(5).
PCSF: An R-package for network-based interpretation of high-throughput data. M Akhmedov, AJ Kedaigle, RE Chong, R Montemanni, R Bertoni, E Fraenkel, I Kwee. PLoS Computational Biology, 2017; 13(7).
Huntington’s Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT- Mediated Angiogenic and Blood-Brain Barrier Deficits. Ryan G. Lim, Chris Quan, Andrea M. Reyes-Ortiz, Sarah E. Lutz, Amanda J. Kedaigle, Theresa Gipson, Jie Wu, Gad D. Vatine, Jennifer Stocksdale, Malcolm S. Casale, Clive N. Svendsen, Ernest Fraenkel, David E. Housman, Dritan Agalliu, Leslie M. Thompson. Cell Reports, 2017; 19(7).
Network-based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. Nurcan Tuncbag, Sara Gosline, Amanda Kedaigle, Anthony Soltis, Anthony Gitter, Ernest Fraenkel. PLOS Computational Biology 2016.
Studying the Lipid Binding of Patellin1 using Molecular Dynamics Simulations. Amanda Daigle with advisors Donald E. Elmore, Brian Tjaden, and Mala Radhakrishnan. Wellesley College Honors Thesis Collection. 2012 May (46).
Serotonin as an integrator of leech behavior and muscle mechanical performance. Shannon P. Gerry, Amanda J. Daigle, Kara L. Feilich, Jessica Liao, Azzara L. Oston, Calais A.D. Weber and David J. Ellerby. Zoology (Jena). 2012 Aug;115(4):255-60.
MLL- Rearranged Leukemia is Dependent on Aberrant H3K79 Methylation by DOT1L. Bernt, K.M., Zhu, N., Sinha, A., Vempati, S., Faber, J., Krivtsov, A.V., Feng, Z., Punt, N., Daigle, A., Bullinger, L., Pollock, R.M., Richon, V.M., Kung, A.L., Armstrong, S.A. Cancer Cell. 2011 Jul 12;20(1):66-78.
*These authors contributed equally
Autism genes converge on asynchronous development of shared neuron classes. Bruna Paulsen*, Silvia Velasco*, Amanda J. Kedaigle*, Martina Pigoni*, Giorgia Quadrato, Anthony Deo, Xian Adiconis, Ana Uzquiano, Rafaela Sartore, Sung Min Yang, Sean K. Simmons, Panagiotis Symvoulidis, Kwanho Kim, Kalliopi Tsafou, Archana Podury, Catherine Abbate, Ashley Tucewicz, Samantha N. Smith, Alexandre Albanese, Lindy Barrett, Neville E. Sanjana, Xi Shi, Kwanghun Chung, Kasper Lage, Edward S. Boyden, Aviv Regev, Joshua Z. Levin & Paola Arlotta. Nature, 2022.
Immortalized striatal precursor neurons from Huntington’s disease patient-derived iPS cells as a platform for target identification and screening for experimental therapeutics. Sergey S Akimov, Mali Jiang, Amanda J Kedaigle, Nicolas Arbez, Leonard O Marque, Chelsy R Eddings, Paul T Ranum, Emma Whelan, Anthony Tang, Ronald Wang, Lauren R DeVine, Conover C Talbot, Jr, Robert N Cole, Tamara Ratovitski, Beverly L Davidson, Ernest Fraenkel, Christopher A Ross. Human Molecular Genetics, 2021.
Skin-resident innate lymphoid cells converge on a pathogenic effector state. Piotr Bielecki*, Samantha J. Riesenfeld*, Jan-Christian Hütter*, Elena Torlai Triglia*, Monika S. Kowalczyk, Roberto R. Ricardo-Gonzalez, Mi Lian, Maria C. Amezcua Vesely, Lina Kroehling, Hao Xu, Michal Slyper, Christoph Muus, Leif S. Ludwig, Elena Christian, Liming Tao, Amanda J. Kedaigle, Holly R. Steach, Autumn G. York, Mathias H. Skadow, Parastou Yaghoubi, Danielle Dionne, Abigail Jarret, Heather M. McGee, Caroline B. M. Porter, Paula Licona-Limón, Will Bailis, Ruaidhrí Jackson, Nicola Gagliani, Georg Gasteiger, Richard M. Locksley, Aviv Regev & Richard A. Flavell. Nature, 2021.
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Jiarui Ding, Xian Adiconis, Sean K. Simmons, Monika S. Kowalczyk, Cynthia C. Hession, Nemanja D. Marjanovic, Travis K. Hughes, Marc H. Wadsworth, Tyler Burks, Lan T. Nguyen, John Y. H. Kwon, Boaz Barak, William Ge, Amanda J. Kedaigle, Shaina Carroll, Shuqiang Li, Nir Hacohen, Orit Rozenblatt-Rosen, Alex K. Shalek, Alexandra-Chloé Villani, Aviv Regev & Joshua Z. Levin. Nature Biotechnology, 2020.
Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington's disease mice. Amanda J. Kedaigle*, Jack C. Reidling*, Ryan G. Lim*, Miriam Adam, Jie Wu, Brook Wassie, Jennifer T. Stocksdale, Malcolm S. Casale, Ernest Fraenkel, Leslie M. Thompson. Human Molecular Genetics, 2020.
ATR is a MYB regulated gene and potential therapeutic target in adenoid cystic carcinoma. Mattias K. Andersson, Giovanna Mangiapane, Paloma Tejera Nevado, Alexia Tsakaneli, Therese Carlsson, Gabriele Corda, Valentina Nieddu, Carla Abrahamian, Olesya Chayka, Lilam Rai, Michael Wick, Amanda Kedaigle, Göran Stenman & Arturo Sala. Oncogenesis, 2020.
Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Silvia Velasco, Amanda J. Kedaigle, Sean K. Simmons, Allison Nash, Marina Rocha, Giorgia Quadrato, Bruna Paulsen, Lan Nguyen, Xian Adiconis, Aviv Regev, Joshua Z. Levin, Paola Arlotta. Nature, 2019.
Individual oligodendrocytes show bias for inhibitory axons in the neocortex. Marzieh Zonouzi, Daniel Berger, Vahbiz Jokhi, Amanda J Kedaigle, Jeff Lichtman, Paola Arlotta. Cell Reports, 2019.
Bioenergetic deficits in Huntington’s disease iPSC-derived neural cells and rescue with glycolytic metabolites. Amanda J Kedaigle, Ernest Fraenkel, and the rest of the HD iPSC Consortium. Human Molecular Genetics, 2019.
Turning omics data into therapeutic insights. Amanda Kedaigle & Ernest Fraenkel. Current Opinion in Pharmacology, 2018.
Discovering altered regulation and signaling through network-based integration of transcriptomic, epigenomic and proteomic tumor data. Amanda Kedaigle and Ernest Fraenkel. Cancer Systems Biology: Methods in Molecular Biology, ed. Louise von Stechow, Springer Science, 2018.
Integrating Omics data: a new software tool and its use in implicating therapeutic targets in Huntington's disease. Amanda Kedaigle. PhD dissertation, Massachusetts Institute of Technology, 2018.
Developmental alterations in Huntington’s disease neural cells and pharmacological rescue in cells and mice. The HD iPSC Consortium, first author of MIT group Amanda Kedaigle, Theresa Gipson, Ferah Yildirim, Chris W. Ng, Pamela Milani, David E. Housman, Ernest Fraenkel. Nature Neuroscience, 2017; 20(5).
PCSF: An R-package for network-based interpretation of high-throughput data. M Akhmedov, AJ Kedaigle, RE Chong, R Montemanni, R Bertoni, E Fraenkel, I Kwee. PLoS Computational Biology, 2017; 13(7).
Huntington’s Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT- Mediated Angiogenic and Blood-Brain Barrier Deficits. Ryan G. Lim, Chris Quan, Andrea M. Reyes-Ortiz, Sarah E. Lutz, Amanda J. Kedaigle, Theresa Gipson, Jie Wu, Gad D. Vatine, Jennifer Stocksdale, Malcolm S. Casale, Clive N. Svendsen, Ernest Fraenkel, David E. Housman, Dritan Agalliu, Leslie M. Thompson. Cell Reports, 2017; 19(7).
Network-based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. Nurcan Tuncbag, Sara Gosline, Amanda Kedaigle, Anthony Soltis, Anthony Gitter, Ernest Fraenkel. PLOS Computational Biology 2016.
Studying the Lipid Binding of Patellin1 using Molecular Dynamics Simulations. Amanda Daigle with advisors Donald E. Elmore, Brian Tjaden, and Mala Radhakrishnan. Wellesley College Honors Thesis Collection. 2012 May (46).
Serotonin as an integrator of leech behavior and muscle mechanical performance. Shannon P. Gerry, Amanda J. Daigle, Kara L. Feilich, Jessica Liao, Azzara L. Oston, Calais A.D. Weber and David J. Ellerby. Zoology (Jena). 2012 Aug;115(4):255-60.
MLL- Rearranged Leukemia is Dependent on Aberrant H3K79 Methylation by DOT1L. Bernt, K.M., Zhu, N., Sinha, A., Vempati, S., Faber, J., Krivtsov, A.V., Feng, Z., Punt, N., Daigle, A., Bullinger, L., Pollock, R.M., Richon, V.M., Kung, A.L., Armstrong, S.A. Cancer Cell. 2011 Jul 12;20(1):66-78.
*These authors contributed equally