PUBLICATIONS
2025
Martin CJ, Calarco JA. Spatio-temporal protein interaction analysis using bimolecular fluorescence complementation in C. elegans. bioRxiv 2025.02.28.640866; doi: https://doi.org/10.1101/2025.02.28.640866
Calarco JA, Taylor SR, Miller DM 3rd. Detecting gene expression in Caenorhabditis elegans. Genetics. 2025 Jan 8;229(1):1-108. doi: 10.1093/genetics/iyae167.
2024
Laver JD#, Duncan M, Calarco JA#. A global view of the RNA-binding and regulatory protein landscape in Caenorhabditis elegans. bioRxiv 2024.11.07.622524; doi: https://doi.org/10.1101/2024.11.07.622524
Pan P, Zhang P, Premachandran S, Peng R, Wang S, Fan Q, Sun Y, Calarco JA#, Liu X#. High-Resolution Imaging and Morphological Phenotyping of C. elegans through Stable Robotic Sample Rotation and Artificial Intelligence-Based 3-Dimensional Reconstruction. Research (Wash D C). 2024 Oct 30;7:0513. doi: 10.34133/research.0513. eCollection 2024.
Pan P, Zoberman M, Zhang P, Premachandran S, Bhatnagar S, Pilaka-Akella PP, Sun W, Li C, Martin C, Xu P, Zhang Z, Li R, Hung W, Tang H, MacGillivray K, Yu B, Zuo R, Pe K, Qin Z, Wang S, Li A, Derry WB, Zhen M, Saltzman AL, Calarco JA#, Liu X#. Robotic microinjection enables large-scale transgenic studies of Caenorhabditis elegans. Nat Commun. 2024 Oct 14;15(1):8848. doi: 10.1038/s41467-024-53108-5.
2023
Pan P, Qin Z, Sun W, Zhou Y,Wang S, Song P, Wang Y, Ru C, Wang X, Calarco JA, Liu X. A spiral microfluidic device for rapid sorting, trapping, and long-term live imaging of Caenorhabditis elegans embryos. Microsyst Nanoeng 9, 17 2023. doi: 10.1038/s41378-023-00485-4.
Harris N, Bates S, Zhuang Z, Bernstein M, Stonemetz J, Hill T, Yu YV, Calarco JA, Sengupta P. Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity. Curr Biol. 2023 Apr 24;33(8):1487-1501.e7. doi: 10.1016/j.cub.2023.02.073. Epub 2023 Mar 27.
2022
Wu S, Li Y, Roy C, Wang Y, Mulcahy B, Li W, Calarco JA, Hung W, Zhen M. Two Muscle-Specific and Direct Transcriptional Targets of DAF-16/FOXO Activated by Reduced Insulin/IGF-1 Signaling. bioRxiv 2022.12.09.519372; doi: https://doi.org/10.1101/2022.12.09.519372.
Calarco JA, Pilaka-Akella PP. Two-Color Fluorescent Reporters for Analysis of Alternative Splicing. Methods Mol Biol. 2022;2537:211-229. doi: 10.1007/978-1-0716-2521-7_13.
Martin CJ, Calarco JA. Approaches for CRISPR/Cas9 Genome Editing in C. elegans.
Methods Mol Biol. 2022;2468:215-237. doi: 10.1007/978-1-0716-2181-3_11.
Liu H, Wu T, Canales XG, Wu M, Choi MK, Duan F, Calarco JA, Zhang Y. Forgetting generates a novel state that is reactivatable. Sci Adv. 2022 Feb 11;8(6):eabi9071. doi: 10.1126/sciadv.abi9071.
2021
Calarco JA. A Genetic Interaction Screening Approach in C. elegans. Methods Mol Biol. 2021;2381:79-95. doi: 10.1007/978-1-0716-1740-3_4.
Skowron P, Farooq H, Cavalli FMG, Morrissy AS, Ly M, Hendrikse LD, Wang EY, Djambazian H, Zhu H, Mungall KL, Trinh QM, Zheng T, Dai S, Stucklin ASG, Vladoiu MC, Fong V, Holgado BL, Nor C, Wu X, Abd-Rabbo D, Bérubé P, Wang YC, Luu B, Suarez RA, Rastan A, Gillmor AH, Lee JJY, Zhang XY, Daniels C, Dirks P, Malkin D, Bouffet E, Tabori U, Loukides J, Doz FP, Bourdeaut F, Delattre OO, Masliah-Planchon J, Ayrault O, Kim SK, Meyronet D, Grajkowska WA, Carlotti CG, de Torres C, Mora J, Eberhart CG, Van Meir EG, Kumabe T, French PJ, Kros JM, Jabado N, Lach B, Pollack IF, Hamilton RL, Rao AAN, Giannini C, Olson JM, Bognár L, Klekner A, Zitterbart K, Phillips JJ, Thompson RC, Cooper MK, Rubin JB, Liau LM, Garami M, Hauser P, Li KKW, Ng HK, Poon WS, Yancey Gillespie G, Chan JA, Jung S, McLendon RE, Thompson EM, Zagzag D, Vibhakar R, Ra YS, Garre ML, Schüller U, Shofuda T, Faria CC, López-Aguilar E, Zadeh G, Hui CC, Ramaswamy V, Bailey SD, Jones SJ, Mungall AJ, Moore RA, Calarco JA, Stein LD, Bader GD, Reimand J, Ragoussis J, Weiss WA, Marra MA, Suzuki H, Taylor MD.
The transcriptional landscape of Shh medulloblastoma. Nat Commun. 2021 Mar 19;12(1):1749. doi: 10.1038/s41467-021-21883-0.
2020
Koterniak B, Pilaka PP, Gracida X, Schneider LM, Pritišanac I, Zhang Y, Calarco JA.
Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans. Genome Res. Dec;30(12):1766-1780. doi: 10.1101/gr.267328.120.
Pan P, Laver JD, Qin Z, Zhou Y, Peng R, Zhao L, Xie H, Calarco JA, Liu X.
On‐Chip Rotation of Caenorhabditis elegans Using Microfluidic Vortices. Adv. Mater. Technol. 2020, 2000575. https://doi.org/10.1002/admt.202000575
2019
Suzuki H, Kumar SA, Shuai S, Diaz-Navarro A, Gutierrez-Fernandez A, De Antonellis P, Cavalli FMG, Juraschka K, Farooq H, Shibahara I, Vladoiu MC, Zhang J, Abeysundara N, Przelicki D, Skowron P, Gauer N, Luu B, Daniels C, Wu X, Forget A, Momin A, Wang J, Dong W, Kim SK, Grajkowska WA, Jouvet A, Fèvre-Montange M, Garrè ML, Rao AAN, Giannini C, Kros JM, French PJ, Jabado N, Ng HK, Poon WS, Eberhart CG, Pollack IF, Olson JM, Weiss WA, Kumabe T, López-Aguilar E, Lach B, Massimino M, Van Meir EG, Rubin JB, Vibhakar R, Chambless LB, Kijima N, Klekner A, Bognár L, Chan JA, Faria CC, Ragoussis J, Pfister SM, Goldenberg A, Wechsler-Reya RJ, Bailey SD, Garzia L, Morrissy AS, Marra MA, Huang X, Malkin D, Ayrault O, Ramaswamy V, Puente XS, Calarco JA, Stein L, Taylor MD. (2019).
Recurrent non-coding U1-snRNA mutations drive cryptic splicing in Shh medulloblastoma. Nature. 2019 Oct 9. doi: 10.1038/s41586-019-1650-0.
Thompson M., Bixby R., Dalton R., Vandenburg A., Calarco J.A., Norris A.D. (2019). Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors. Elife. 2019 Jul 19;8. pii: e46726. doi: 10.7554/eLife.46726.
Calarco J.A., Samuel A.D.T. (2019).
Imaging whole nervous systems: insights into behavior from worms to fish. Nat Methods. 2019 Jan;16(1):14-15. doi: 10.1038/s41592-018-0276-8.
2018
Gonatopoulos-Pournatzis T., Wu M., Braunschweig U., Roth J., Han H., Best A.J., Raj B., Aregger M., O'Hanlon D., Ellis J.D., Calarco J.A., Moffat J., Gingras A.C., Blencowe B.J. (2018).
Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons. Mol Cell. 2018 Nov 1;72(3):510-524.e12. doi: 10.1016/j.molcel.2018.10.008.
Chitturi J., Hung W., Rahman A.M.A., Wu M., Lim M.A., Calarco J., Baran R., Huang X., Dennis J.W., Zhen M. (2018).
The UBR-1 ubiquitin ligase regulates glutamate metabolism to generate coordinated motor pattern in Caenorhabditis elegans. PLoS Genet. 2018 Apr 12;14(4):e1007303. doi: 10.1371/journal.pgen.1007303. eCollection 2018 Apr.
Calarco J.A., Norris A.D. (2018).
Synthetic Genetic Interaction (CRISPR-SGI) Profiling in Caenorhabditis elegans. Bio Protoc. 2018 Mar 5;8(5). pii: e2756. doi: 10.21769/BioProtoc.2756.
2017
Gracida X, Dion M.F., Harris G., Zhang, Y., Calarco, J.A. (2017).
An Elongin-Cullin-SOCS Box Complex Regulates Stress-Induced Serotonergic Neuromodulation. Cell Rep. 2017 Dec 12;21(11):3089-3101. doi: 10.1016/j.celrep.2017.11.042.
Norris A.D., Gracida X., Calarco J.A. (2017).
CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitness. Elife. 2017 Jul 18;6. pii: e28129. doi: 10.7554/eLife.28129.
#Gracida X., #Calarco J.A. (2017).
Cell type-specific transcriptome profiling in C. elegans using the Translating Ribosome Affinity Purification technique. Methods. 2017 Jun 22. pii: S1046-2023(16)30433-9. doi: 10.1016/j.ymeth.2017.06.023.
Lee, K.S., Iwanir, S., Kopito, R.B., Scholz, M., Calarco, J.A., Biron, D., Levine, E. (2017).
Serotonin-dependent kinetics of feeding bursts underlie a graded response to food availability in C. elegans. Nat Commun. Feb 1;8:14221. doi: 10.1038/ncomms14221.
2016
Lim, M.A., Chitturi, J., Laskova, V., Meng, J., Findeis, D., Wiekenberg, A., Mulcahy, B., Luo, L., Li, Y., Lu, Y., Hung, W., Qu, Y., Ho, C.Y., Holmyard, D., Ji, N., McWhirter, R., Samuel, A.D., Miller, D.M., Schnabel, R., #Calarco, J.A., #Zhen, M. (2016).
Neuroendocrine modulation sustains the C. elegans forward motor state. Elife. Nov 18;5. pii: e19887. doi: 10.7554/eLife.19887.
*Gracida, X., *Norris, A.D., Calarco J.A. (2016).
Regulation of tissue-specific alternative splicing: C. elegans as a model system. Adv Exp Med Biol. 907:229-61. doi: 10.1007/978-3-319-29073-7_10.
2015
Calarco J.A., Friedland, A.E. (2015).
Creating genome modifications in C. elegans using the CRISPR/Cas9 system. Methods Mol Biol. 1327:59-74. doi: 10.1007/978-1-4939-2842-2_6.
*Norris A.D., *Kim H.M., #Colaiácovo M.P., #Calarco J.A. (2015).
Efficient genome editing in C. elegans with a toolkit of dual marker selection cassettes. Genetics. 2015 Jul 30. pii: genetics.115.180679.
2014
Shen Y., Zhang J., Calarco J.A., Zhang Y. (2014).
EOL-1, the homolog of the mammalian Dom3Z, regulates olfactory learning in C. elegans. J Neurosci 34(40):13364-70.
Norris A.D., Gao S., Norris M.L., Ray D., Ramani A.K., Fraser A.G., Morris Q., Hughes T.R., #Zhen M., #Calarco J.A. (2014).
A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types. Mol Cell 54(6):946-59.
2013
Tzur Y.B., Friedland A.E., Nadarajan S., Church G.M., #Calarco J.A., #Colaiácovo MP. (2013).
Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system. Genetics 195(3):1181-5.
Friedland A.E., Tzur Y.B., Esvelt K.M., Colaiácovo M.P., #Church G.M., #Calarco J.A. (2013).
Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 10(8):741-3.
Calarco J.A. (2013).
'Cryptic' exons reveal some of their secrets. Elife 2:e00476.
2012
Norris A.D, Calarco J.A. (2012).
Emerging Roles of Alternative Pre-mRNA Splicing Regulation in Neuronal Development and Function. Front Neurosci Aug 21;6:122.
Ellis J.D., Barrios-Rodiles M., Colak R., Irimia M., Kim T., Calarco J.A., Wang X., Pan Q., O'Hanlon D., Kim P.M., Wrana J.L., Blencowe B.J. (2012). Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell 46(6):884-92.
#Po, M.D., #Calarco, J.A., #Zhen, M. (2012).
Releasing the inner inhibition for axon regeneration. Neuron 73(2):207-9.
2011
#Calarco, J.A., Zhen, M., Blencowe, B.J. (2011).
Networking in a global world: making connections when neural splicing regulators meet their target transcripts. RNA 17(5):775-91.
#,*Ramani, A.K., #,*Calarco, J.A., Pan, Q., Mavandadi, S., Wang, Y., Nelson, A.C., Lee, L.J., Morris, Q., Blencowe, B.J., #Zhen, M., #Fraser, A.G. (2011). Genome-wide analysis of alternative splicing in C. elegans. Genome Res 21(2):342-8.
2010
*Barash, Y., *Calarco, J. A., Pan, Q., Gao, W.,Wang, X., Shai, O., Blencowe, B. J., Frey, B. J. (2010).
Deciphering the Splicing Code. Nature 465(7294):53-9. (See comment in Nature 465(7294):45-6)
2009
*Khanna, M., *Van Bakel, H., Tang, X., Calarco, J. A., Babak, T., Guo, G., Emili, A., Greenblatt, J. F., Hughes, T. R., Krogan, N. J., and Blencowe, B. J. (2009).
A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA 15(12):2174-85.
Calarco, J. A., Superina, S., O'Hanlon, D., Gabut, M., Raj, B., Pan, Q., Skalska, U., Clarke, L., Gelinas, D., van der Kooy, D., et al. (2009).
Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell 138, 898-910. (Selected as must read by Faculty of 1000)
2007
*Calarco, J. A., *Xing, Y., *Caceres, M., Calarco, J. P., Xiao, X., Pan, Q., Lee, C., Preuss, T. M., and Blencowe, B. J. (2007).
Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev 21, 2963-2975. (Highlighted in Cell, Leading Edge Genetics Select, January 25 2008)
*Calarco, J.A., *Saltzman, A.L., Ip J.Y., Blencowe, B.J. (2007).
Technologies for the global discovery and analysis of alternative splicing. Adv Exp Med Biol. 2007;623:64-84.
2006
Wang, Y., Gracheva, E. O., Richmond, J., Kawano, T., Couto, J. M., Calarco, J. A., Vijayaratnam, V., Jin, Y., and Zhen, M. (2006).
The C2H2 zinc-finger protein SYD-9 is a putative posttranscriptional regulator for synaptic transmission. Proc Natl Acad Sci USA 103, 10450-10455.
*Cartegni, L., *Hastings, M. L., Calarco, J. A., de Stanchina, E., and Krainer, A. R. (2006).
Determinants of exon 7 splicing in the spinal muscular atrophy genes, SMN1 and SMN2. Am J Hum Genet 78, 63-77.
2005
*Rosonina, E., *Ip, J. Y., Calarco, J. A., Bakowski, M. A., Emili, A., McCracken, S., Tucker, P., Ingles, C. J., and Blencowe, B. J. (2005).
Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol Cell Biol 25, 6734-6746.
*denotes co-first authors
#denotes co-corresponding authors
Martin CJ, Calarco JA. Spatio-temporal protein interaction analysis using bimolecular fluorescence complementation in C. elegans. bioRxiv 2025.02.28.640866; doi: https://doi.org/10.1101/2025.02.28.640866
Calarco JA, Taylor SR, Miller DM 3rd. Detecting gene expression in Caenorhabditis elegans. Genetics. 2025 Jan 8;229(1):1-108. doi: 10.1093/genetics/iyae167.
2024
Laver JD#, Duncan M, Calarco JA#. A global view of the RNA-binding and regulatory protein landscape in Caenorhabditis elegans. bioRxiv 2024.11.07.622524; doi: https://doi.org/10.1101/2024.11.07.622524
Pan P, Zhang P, Premachandran S, Peng R, Wang S, Fan Q, Sun Y, Calarco JA#, Liu X#. High-Resolution Imaging and Morphological Phenotyping of C. elegans through Stable Robotic Sample Rotation and Artificial Intelligence-Based 3-Dimensional Reconstruction. Research (Wash D C). 2024 Oct 30;7:0513. doi: 10.34133/research.0513. eCollection 2024.
Pan P, Zoberman M, Zhang P, Premachandran S, Bhatnagar S, Pilaka-Akella PP, Sun W, Li C, Martin C, Xu P, Zhang Z, Li R, Hung W, Tang H, MacGillivray K, Yu B, Zuo R, Pe K, Qin Z, Wang S, Li A, Derry WB, Zhen M, Saltzman AL, Calarco JA#, Liu X#. Robotic microinjection enables large-scale transgenic studies of Caenorhabditis elegans. Nat Commun. 2024 Oct 14;15(1):8848. doi: 10.1038/s41467-024-53108-5.
2023
Pan P, Qin Z, Sun W, Zhou Y,Wang S, Song P, Wang Y, Ru C, Wang X, Calarco JA, Liu X. A spiral microfluidic device for rapid sorting, trapping, and long-term live imaging of Caenorhabditis elegans embryos. Microsyst Nanoeng 9, 17 2023. doi: 10.1038/s41378-023-00485-4.
Harris N, Bates S, Zhuang Z, Bernstein M, Stonemetz J, Hill T, Yu YV, Calarco JA, Sengupta P. Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity. Curr Biol. 2023 Apr 24;33(8):1487-1501.e7. doi: 10.1016/j.cub.2023.02.073. Epub 2023 Mar 27.
2022
Wu S, Li Y, Roy C, Wang Y, Mulcahy B, Li W, Calarco JA, Hung W, Zhen M. Two Muscle-Specific and Direct Transcriptional Targets of DAF-16/FOXO Activated by Reduced Insulin/IGF-1 Signaling. bioRxiv 2022.12.09.519372; doi: https://doi.org/10.1101/2022.12.09.519372.
Calarco JA, Pilaka-Akella PP. Two-Color Fluorescent Reporters for Analysis of Alternative Splicing. Methods Mol Biol. 2022;2537:211-229. doi: 10.1007/978-1-0716-2521-7_13.
Martin CJ, Calarco JA. Approaches for CRISPR/Cas9 Genome Editing in C. elegans.
Methods Mol Biol. 2022;2468:215-237. doi: 10.1007/978-1-0716-2181-3_11.
Liu H, Wu T, Canales XG, Wu M, Choi MK, Duan F, Calarco JA, Zhang Y. Forgetting generates a novel state that is reactivatable. Sci Adv. 2022 Feb 11;8(6):eabi9071. doi: 10.1126/sciadv.abi9071.
2021
Calarco JA. A Genetic Interaction Screening Approach in C. elegans. Methods Mol Biol. 2021;2381:79-95. doi: 10.1007/978-1-0716-1740-3_4.
Skowron P, Farooq H, Cavalli FMG, Morrissy AS, Ly M, Hendrikse LD, Wang EY, Djambazian H, Zhu H, Mungall KL, Trinh QM, Zheng T, Dai S, Stucklin ASG, Vladoiu MC, Fong V, Holgado BL, Nor C, Wu X, Abd-Rabbo D, Bérubé P, Wang YC, Luu B, Suarez RA, Rastan A, Gillmor AH, Lee JJY, Zhang XY, Daniels C, Dirks P, Malkin D, Bouffet E, Tabori U, Loukides J, Doz FP, Bourdeaut F, Delattre OO, Masliah-Planchon J, Ayrault O, Kim SK, Meyronet D, Grajkowska WA, Carlotti CG, de Torres C, Mora J, Eberhart CG, Van Meir EG, Kumabe T, French PJ, Kros JM, Jabado N, Lach B, Pollack IF, Hamilton RL, Rao AAN, Giannini C, Olson JM, Bognár L, Klekner A, Zitterbart K, Phillips JJ, Thompson RC, Cooper MK, Rubin JB, Liau LM, Garami M, Hauser P, Li KKW, Ng HK, Poon WS, Yancey Gillespie G, Chan JA, Jung S, McLendon RE, Thompson EM, Zagzag D, Vibhakar R, Ra YS, Garre ML, Schüller U, Shofuda T, Faria CC, López-Aguilar E, Zadeh G, Hui CC, Ramaswamy V, Bailey SD, Jones SJ, Mungall AJ, Moore RA, Calarco JA, Stein LD, Bader GD, Reimand J, Ragoussis J, Weiss WA, Marra MA, Suzuki H, Taylor MD.
The transcriptional landscape of Shh medulloblastoma. Nat Commun. 2021 Mar 19;12(1):1749. doi: 10.1038/s41467-021-21883-0.
2020
Koterniak B, Pilaka PP, Gracida X, Schneider LM, Pritišanac I, Zhang Y, Calarco JA.
Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans. Genome Res. Dec;30(12):1766-1780. doi: 10.1101/gr.267328.120.
Pan P, Laver JD, Qin Z, Zhou Y, Peng R, Zhao L, Xie H, Calarco JA, Liu X.
On‐Chip Rotation of Caenorhabditis elegans Using Microfluidic Vortices. Adv. Mater. Technol. 2020, 2000575. https://doi.org/10.1002/admt.202000575
2019
Suzuki H, Kumar SA, Shuai S, Diaz-Navarro A, Gutierrez-Fernandez A, De Antonellis P, Cavalli FMG, Juraschka K, Farooq H, Shibahara I, Vladoiu MC, Zhang J, Abeysundara N, Przelicki D, Skowron P, Gauer N, Luu B, Daniels C, Wu X, Forget A, Momin A, Wang J, Dong W, Kim SK, Grajkowska WA, Jouvet A, Fèvre-Montange M, Garrè ML, Rao AAN, Giannini C, Kros JM, French PJ, Jabado N, Ng HK, Poon WS, Eberhart CG, Pollack IF, Olson JM, Weiss WA, Kumabe T, López-Aguilar E, Lach B, Massimino M, Van Meir EG, Rubin JB, Vibhakar R, Chambless LB, Kijima N, Klekner A, Bognár L, Chan JA, Faria CC, Ragoussis J, Pfister SM, Goldenberg A, Wechsler-Reya RJ, Bailey SD, Garzia L, Morrissy AS, Marra MA, Huang X, Malkin D, Ayrault O, Ramaswamy V, Puente XS, Calarco JA, Stein L, Taylor MD. (2019).
Recurrent non-coding U1-snRNA mutations drive cryptic splicing in Shh medulloblastoma. Nature. 2019 Oct 9. doi: 10.1038/s41586-019-1650-0.
Thompson M., Bixby R., Dalton R., Vandenburg A., Calarco J.A., Norris A.D. (2019). Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors. Elife. 2019 Jul 19;8. pii: e46726. doi: 10.7554/eLife.46726.
Calarco J.A., Samuel A.D.T. (2019).
Imaging whole nervous systems: insights into behavior from worms to fish. Nat Methods. 2019 Jan;16(1):14-15. doi: 10.1038/s41592-018-0276-8.
2018
Gonatopoulos-Pournatzis T., Wu M., Braunschweig U., Roth J., Han H., Best A.J., Raj B., Aregger M., O'Hanlon D., Ellis J.D., Calarco J.A., Moffat J., Gingras A.C., Blencowe B.J. (2018).
Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons. Mol Cell. 2018 Nov 1;72(3):510-524.e12. doi: 10.1016/j.molcel.2018.10.008.
Chitturi J., Hung W., Rahman A.M.A., Wu M., Lim M.A., Calarco J., Baran R., Huang X., Dennis J.W., Zhen M. (2018).
The UBR-1 ubiquitin ligase regulates glutamate metabolism to generate coordinated motor pattern in Caenorhabditis elegans. PLoS Genet. 2018 Apr 12;14(4):e1007303. doi: 10.1371/journal.pgen.1007303. eCollection 2018 Apr.
Calarco J.A., Norris A.D. (2018).
Synthetic Genetic Interaction (CRISPR-SGI) Profiling in Caenorhabditis elegans. Bio Protoc. 2018 Mar 5;8(5). pii: e2756. doi: 10.21769/BioProtoc.2756.
2017
Gracida X, Dion M.F., Harris G., Zhang, Y., Calarco, J.A. (2017).
An Elongin-Cullin-SOCS Box Complex Regulates Stress-Induced Serotonergic Neuromodulation. Cell Rep. 2017 Dec 12;21(11):3089-3101. doi: 10.1016/j.celrep.2017.11.042.
Norris A.D., Gracida X., Calarco J.A. (2017).
CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitness. Elife. 2017 Jul 18;6. pii: e28129. doi: 10.7554/eLife.28129.
#Gracida X., #Calarco J.A. (2017).
Cell type-specific transcriptome profiling in C. elegans using the Translating Ribosome Affinity Purification technique. Methods. 2017 Jun 22. pii: S1046-2023(16)30433-9. doi: 10.1016/j.ymeth.2017.06.023.
Lee, K.S., Iwanir, S., Kopito, R.B., Scholz, M., Calarco, J.A., Biron, D., Levine, E. (2017).
Serotonin-dependent kinetics of feeding bursts underlie a graded response to food availability in C. elegans. Nat Commun. Feb 1;8:14221. doi: 10.1038/ncomms14221.
2016
Lim, M.A., Chitturi, J., Laskova, V., Meng, J., Findeis, D., Wiekenberg, A., Mulcahy, B., Luo, L., Li, Y., Lu, Y., Hung, W., Qu, Y., Ho, C.Y., Holmyard, D., Ji, N., McWhirter, R., Samuel, A.D., Miller, D.M., Schnabel, R., #Calarco, J.A., #Zhen, M. (2016).
Neuroendocrine modulation sustains the C. elegans forward motor state. Elife. Nov 18;5. pii: e19887. doi: 10.7554/eLife.19887.
*Gracida, X., *Norris, A.D., Calarco J.A. (2016).
Regulation of tissue-specific alternative splicing: C. elegans as a model system. Adv Exp Med Biol. 907:229-61. doi: 10.1007/978-3-319-29073-7_10.
2015
Calarco J.A., Friedland, A.E. (2015).
Creating genome modifications in C. elegans using the CRISPR/Cas9 system. Methods Mol Biol. 1327:59-74. doi: 10.1007/978-1-4939-2842-2_6.
*Norris A.D., *Kim H.M., #Colaiácovo M.P., #Calarco J.A. (2015).
Efficient genome editing in C. elegans with a toolkit of dual marker selection cassettes. Genetics. 2015 Jul 30. pii: genetics.115.180679.
2014
Shen Y., Zhang J., Calarco J.A., Zhang Y. (2014).
EOL-1, the homolog of the mammalian Dom3Z, regulates olfactory learning in C. elegans. J Neurosci 34(40):13364-70.
Norris A.D., Gao S., Norris M.L., Ray D., Ramani A.K., Fraser A.G., Morris Q., Hughes T.R., #Zhen M., #Calarco J.A. (2014).
A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types. Mol Cell 54(6):946-59.
2013
Tzur Y.B., Friedland A.E., Nadarajan S., Church G.M., #Calarco J.A., #Colaiácovo MP. (2013).
Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system. Genetics 195(3):1181-5.
Friedland A.E., Tzur Y.B., Esvelt K.M., Colaiácovo M.P., #Church G.M., #Calarco J.A. (2013).
Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 10(8):741-3.
Calarco J.A. (2013).
'Cryptic' exons reveal some of their secrets. Elife 2:e00476.
2012
Norris A.D, Calarco J.A. (2012).
Emerging Roles of Alternative Pre-mRNA Splicing Regulation in Neuronal Development and Function. Front Neurosci Aug 21;6:122.
Ellis J.D., Barrios-Rodiles M., Colak R., Irimia M., Kim T., Calarco J.A., Wang X., Pan Q., O'Hanlon D., Kim P.M., Wrana J.L., Blencowe B.J. (2012). Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell 46(6):884-92.
#Po, M.D., #Calarco, J.A., #Zhen, M. (2012).
Releasing the inner inhibition for axon regeneration. Neuron 73(2):207-9.
2011
#Calarco, J.A., Zhen, M., Blencowe, B.J. (2011).
Networking in a global world: making connections when neural splicing regulators meet their target transcripts. RNA 17(5):775-91.
#,*Ramani, A.K., #,*Calarco, J.A., Pan, Q., Mavandadi, S., Wang, Y., Nelson, A.C., Lee, L.J., Morris, Q., Blencowe, B.J., #Zhen, M., #Fraser, A.G. (2011). Genome-wide analysis of alternative splicing in C. elegans. Genome Res 21(2):342-8.
2010
*Barash, Y., *Calarco, J. A., Pan, Q., Gao, W.,Wang, X., Shai, O., Blencowe, B. J., Frey, B. J. (2010).
Deciphering the Splicing Code. Nature 465(7294):53-9. (See comment in Nature 465(7294):45-6)
2009
*Khanna, M., *Van Bakel, H., Tang, X., Calarco, J. A., Babak, T., Guo, G., Emili, A., Greenblatt, J. F., Hughes, T. R., Krogan, N. J., and Blencowe, B. J. (2009).
A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA 15(12):2174-85.
Calarco, J. A., Superina, S., O'Hanlon, D., Gabut, M., Raj, B., Pan, Q., Skalska, U., Clarke, L., Gelinas, D., van der Kooy, D., et al. (2009).
Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell 138, 898-910. (Selected as must read by Faculty of 1000)
2007
*Calarco, J. A., *Xing, Y., *Caceres, M., Calarco, J. P., Xiao, X., Pan, Q., Lee, C., Preuss, T. M., and Blencowe, B. J. (2007).
Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev 21, 2963-2975. (Highlighted in Cell, Leading Edge Genetics Select, January 25 2008)
*Calarco, J.A., *Saltzman, A.L., Ip J.Y., Blencowe, B.J. (2007).
Technologies for the global discovery and analysis of alternative splicing. Adv Exp Med Biol. 2007;623:64-84.
2006
Wang, Y., Gracheva, E. O., Richmond, J., Kawano, T., Couto, J. M., Calarco, J. A., Vijayaratnam, V., Jin, Y., and Zhen, M. (2006).
The C2H2 zinc-finger protein SYD-9 is a putative posttranscriptional regulator for synaptic transmission. Proc Natl Acad Sci USA 103, 10450-10455.
*Cartegni, L., *Hastings, M. L., Calarco, J. A., de Stanchina, E., and Krainer, A. R. (2006).
Determinants of exon 7 splicing in the spinal muscular atrophy genes, SMN1 and SMN2. Am J Hum Genet 78, 63-77.
2005
*Rosonina, E., *Ip, J. Y., Calarco, J. A., Bakowski, M. A., Emili, A., McCracken, S., Tucker, P., Ingles, C. J., and Blencowe, B. J. (2005).
Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol Cell Biol 25, 6734-6746.
*denotes co-first authors
#denotes co-corresponding authors