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Mouse Neocortical Transcriptome

PsychENCODE

XSAnno

Lun MP, Johnson MB, Broadbelt KG, Watanabe M, Kang Y, Chau KF, Springel MW, Malesz A, Sousa AMM, Pletikos M, Adelita T, Calicchio ML, Zhang Y, Holtzman MJ, Lidov HGW, Sestan N, Steen H, Monuki E, Lehtinen MK (2015) Spatially heterogeneous choroid plexus transcriptomes encode positional identity and contribute to regional CSF production. J Neurosci 35: 4903– 4916.
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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 (2015) The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun 6: 6404.
[PubMed] [PDF] [Data 1] [Data 2] [Data 3] [Data 4]

Shibata M, Gulden FO, Sestan N (2014) From trans to cis: transcriptional regulatory networks in neocortical development. Trends Genet 31, 77-87.
[PubMed] [PDF]

Mishra-Gorur K, Çaglayan AO, Schaffer AE, Chabu C, Henegariu O, Vonhoff F, Akgümüs GT, Nishimura S, Han W, Tu S, Baran B, Gümüs H, Dilber C, Zaki MS, Hossni HA, Rivière JB, Kayserili H, Spencer EG, Rosti RÖ, Schroth J, Per H, Çaglar C, Çaglar Ç, Dölen D, Baranoski JF, Kumandas S, Minja FJ, Erson-Omay EZ, Mane SM, Lifton RP, Xu T, Keshishian H, Dobyns WB, Chi NC, Sestan N, Louvi A, Bilgüvar K, Yasuno K, Gleeson JG, Günel M (2014) Mutations in KATNB1 cause complex cerebral malformations by disrupting asymmetrically dividing neural progenitors. Neuron 84, 1226-1239.
[PubMed] [PDF]

Ouyang A, Jeon T, Sunkin SM, Pletikos M, Sedmak G, Sestan N, Lein ES, Huang H (2014) Spatial mapping of structural and connectional imaging data for the developing human brain with diffusion tensor imaging. Methods [Epub ahead of print].
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Caglayan OA, Baranoski JF, Aktar F, Han W, Tuysuz B, Guzel A, Guclu B, Kaymakcalan H, Aktekin B, Akgumus GT, Murray PB, Erson Omay ZEE, Caglar CC, Bakircioglu M, Sakalar YB, Guzel E, Demir N, Tuncer O, Senturk S, Ekici B, Minja FJ, Sestan N, Yasuno K , Bilguvar K, Caksen H, Gunel M (2014) Brain malformations associated with Knobloch syndrome – Review of literature, expanding clinical spectrum and identification of novel mutations. Pediatric Neurol 51, 806-813.
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Gulden F, Sestan N (2014) Building a bigger brain. Nature 515, 206-207.
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Lee FS, Heimer H, Giedd JN, Lein ES, Sestan N, Weinberger DR, Casey BJ (2014) Mental health. Adolescent mental health--opportunity and obligation. Science 346, 547-559.
[PubMed] [PDF]

Sousa AMM, Meyer KA, Sestan N (2014) Molecular and Cellular Mechanisms of Human Brain Development and Evolution. In The Cognitive Neurosciences , 5th edition. Gazzaniga MS, Mangun GR, Eds., The MIT Press, pp. 67-74.
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Gupta AR, Pirruccello M, Cheng F, Kang HJ, Fernandez TV, Baskin JM, Choi M, Liu L, Ercan-Sencicek AG, Murdoch JD, Klei L, Neale BM, Franjic D, Daly MJ, Lifton RP, De Camilli P, Zhao H, Sestan N, State MW (2014) Rare deleterious mutations of the gene EFR3A in autism spectrum disorders. In Mol Autism 5, 31. doi: 10.1186/2040-2392-5-31.
[PubMed] [PDF]

Lennington JB, Coppola G, Kataoka-Sasaki Y, Fernandez TV, Palejev D, Li Y, Huttner A, Pletikos M, Sestan N, Leckman JF, Vaccarino FM (2014) Transcriptome analysis of the human striatum in Tourette syndrome. Biol Psychiatry [Epub ahead of print].
[PubMed] [PDF]

Zhu Y, Li M, Sousa AMM, Sestan N (2014) XSAnno: A framework for building ortholog models in cross-species transcriptome comparisons. BMC Genomics [Epub ahead of print].
[PubMed] [PDF]

Gulhan Ercan-Sencicek A, Jambi S, Franjic D, Nishimura S, Li M, El-Fishawy P, Morgan TM, Sanders SJ, Bilguvar K, Suri M, Johnson MH, Gupta AR, Yuksel Z, Mane S, Grigorenko E, Picciotto M, Alberts AS, Gunel M, Sestan N, State MW (2014) Homozygous loss of DIAPH1 is a novel cause of microcephaly in humans. Eur J Hum Genet [Epub ahead of print]
[PubMed] [PDF] [Data]

Carlyle BC, Nairn AC, Wang M, Yang Y, Jin LE, Simen AA, Ramos BP, Bordner KA, Craft GE, Davies P, Pletikos M, Sestan N, Arnsten AFT, Paspalas CD (2014) cAMP-PKA phosphorylation of tau confers risk for degeneration in aging association cortex. Proc Natl Acad Sci USA 111, 5036-5041.
[PubMed] [PDF]

Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, Caldejon S, Carey A, Cuhaciyan C, Dalley RA, Dee N, Dolbeare TA, Facer BA, Feng D, Fliss TP, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Howard RE, Jochim JM, Kuan CL, Lau C, Lee CK, Lee F, Lemon TA, Lesnar P, McMurray B, Mastan N, Mosqueda N, Naluai-Cecchini T, Ngo NK, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry SE, Stevens A, Pletikos M, Reding M, Roll K, Sandman D, Sarreal M, Shapouri S, Shapovalova NV, Shen EH, Sjoquist N, Slaughterbeck CR, Smith M, Sodt AJ, Williams D, Zöllei L, Fischl B, Gerstein MB, Geschwind DH, Glass IA, Hawrylycz MJ, Hevner RF, Huang H, Jones AR, Knowles JA, Levitt P, Phillips JW, Sestan N, Wohnoutka P, Dang C, Bernard A, Hohmann JG, Lein ES (2014) Transcriptional landscape of the prenatal human brain. Nature
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Liu L, Lei J, Sanders SJ, Willsey JA, Kou Y, Cicek EA, Klei L, Lu C, He X, Li M, Muhle RA, Avi Ma'ayan A, Noonan JP, Sestan N, McFadden K, State MW, Buxbaum JD, Devlin B, Roeder K (2014) DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics. Mol Autism [Epub ahead of print].
[PubMed] [PDF]

Tebbenkamp AT, Willsey AJ, State MW, Sestan N (2014) The developmental transcriptome of the human brain: implications for neurodevelopmental disorders. Curr Opin Neurol 27, 149-156.
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Fertuzinhos S, Li M, Kawasawa YI, Ivic V, Franjic D, Singh D, Crair MC, Sestan N (2014) Laminar and temporal expression dynamics of coding and noncoding RNAs in the mouse neocortex. Cell Rep 6, 1-13.
[PubMed] [PDF]

Bae B, Tietjen I, Atabay KD, Evrony GD, Johnson MB, Asare E, Wang PP, AY Murayama, Im K, Lisgo SN, Overman L, Sestan N, Chang BS, Barkovich AJ, Grant PE, Topçu M, Politsky J, Okano H, Piao X, Walsh CA (2014) Evolutionarily dynamic alternative splicing of GPR56 regulates regional cerebral cortical patterning. Science 343, 764-768.
[PubMed] [PDF] [Movie 1] [Movie 2]

Robichaux MA, Chenaux G, Ho HY, Soskis MJ, Dravis C, Kwan KY, Sestan N, Greenberg ME, Henkemeyer M, Cowan CW (2014) EphB receptor forward signaling regulates area-specific reciprocal thalamic and cortical axon pathfinding. Proc Natl Acad Sci USA Jan 22. [Epub ahead of print]
[PubMed] [PDF]

Pletikos M, Sousa AAM, Sedmak S, Meyer KA, Zhu Y, Cheng F, Li M, Kawasawa YM, Sestan N (2014) Temporal specification and bilaterality of human neocortical topographic gene expression. Neuron 81, 321-332.
[PubMed] [PDF] [Data]

Xie M, Li M, Vilborg A, Lee N, Shu MD, Yartseva V, Sestan N, Steitz JA (2013) Mammalian 5'-capped microRNA precursors that generate a single microRNA. Cell 155, 1568–1580.
[PubMed] [PDF] [Data]

Han W, Sestan N (2013) Cortical projection neurons: sprung from the same root. Neuron 80, 1103-1105.
[PubMed] [PDF]

Willsey JA, 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 GA, Gockley J, Gupta A, Han W, He X, Hoffman E, Klei L, Lei J,Li 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 (2013) Co-expression networks implicate human mid-fetal deep cortical projection neurons in the pathogenesis of autism. Cell 155, 997–1007.
[PubMed] [PDF] [Data 1] [Data 2] [Data 3] [Data 4] [Data 5]

Miller JA, Nathanson J, Franjic D, Shim S, Dalley RA, Shapouri S, Smith KA, Sunkin SM, Bernard A, Bennett JL, Lee CK, Hawrylycz MJ, Jones AR, Amaral DG, Sestan N, Gage FH and Lein ES (2013) Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. Development 140, 4633-4644.
[PubMed] [PDF]

Li H, Fertuzinhos S, Mohns E, Hnasko TS, Verhage M, Edwards R, Sestan N, Crair MC (2013) Laminar and columnar development of barrel cortex relies on thalamocortical neurotransmission. Neuron 79, 970-86.
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Ruusuvuori E, Huebner AK, Kirilkin I, Yukin AY, Blaesse P, Helmy M, Jung Kang H, El Muayed M, Hennings JC, Voipio J, Sestan N, Hübner CA, Kaila K (2013) Neuronal carbonic anhydrase VII provides GABAergic excitatory drive to exacerbate febrile seizures. EMBO J 32, 2275-2286.
[PubMed] [PDF] [Review Files]

Radmanesh F, Caglayan AO, Silhavy JL, Yilmaz C, Cantagrel V, Omar T, Rosti B, Kaymakcalan H, Gabriel S, Li M, Sestan N, Bilguvar K, Dobyns WB, Zaki MS, Gunel M, Gleeson JG (2013) Mutations in LAMB1 cause cobblestone brain malformation without muscular or ocular abnormalities.Am J Hum Genet 92, 468-474.
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Miller DJ, Duka T, Stimpson CD, Schapiro SJ, Baze WB, McArthur MJ, Fobbs AJ, Sousa AM, Sestan N, Wildman DE, Lipovich L, Kuzawa CW, Hof PR, Sherwood CC (2012) Prolonged myelination in human neocortical evolution. Proc Natl Acad Sci U S A 109, 16480-16485.
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State M, Sestan N (2012) The emerging biology of autism spectrum disorders. Science 337, 1301-1303.
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Huang H, Jeon T, Sedmak G, Pletikos M, Vasung L, Xu X, Yarowsky P, Richards LJ, Kostovic I, Sestan N, Mori S. (2012) Coupling diffusion imaging with histological and gene expression analysis to examine the dynamics of cortical areas across the fetal period of human brain development. Cereb Cortex [Epub ahead of print].
[PubMed] [PDF]

Shim S, Kwan KY, Li M, Lefebvre V, Sestan N (2012) Cis-regulatory control of corticospinal system development and evolution. Nature 486, 74-79.
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Kwan KY, Lam MMS, Johnson MB, Dube U, Shim S, Rasin MR, Sousa AMM, Fertuzinhos S, Chen JG, Arellano JI, Chan DW, Pletikos M, Vasung L, Rowitch DH, Huang EJ, Schwartz ML, Willemsen R, Oostra BA, Rakic P, Heffer M, Kostovic I, Judas M, Sestan N (2012) Species-dependent post-transcriptional regulation of NOS1 by FMRP in the developing cerebral cortex. Cell 149, 895-911.
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Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, Dilullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Günel M, Roeder K, Geschwind DH, Devlin B, State MW. (2012) De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485, 237-241.
[PubMed] [PDF] [Data 1] [Data 2]

Kwan KY, Sestan N, Anton ES (2012) Transcriptional co-regulation of neuronal migration and laminar identity in the neocortex. Development 139, 1535-1546.
[PubMed] [PDF]

Kang HJ, Kawasawa YI, Cheng F, Zhu Y, Xu X, Li M, Sousa AM, Pletikos M, Meyer KA, Sedmak G, Guennel T, Shin Y, Johnson MB, Krsnik Z, Mayer S, Fertuzinhos S, Umlauf S, Lisgo SN, Vortmeyer A, Weinberger DR, Mane S, Hyde TM, Huttner A, Reimers M, Kleinman JE, Sestan N (2011) Spatio-temporal transcriptome of the human brain. Nature 478, 483-489.
[PubMed] [PDF] [Data]

Barak T, Kwan KY, Louvi A, Demirbilek V, Saygi S, Tüysüz B, Choi M, Boyaci H, Doerschner K, Zhu Y, Kaymakçalan H, Yilmaz S, Bakircioglu M, Caglayan AO, Oztürk AK, Yasuno K, Brunken WJ, Atalar E, Yalçinkaya C, Dinçer A, Bronen RA, Mane S,Ozçelik T, Lifton RP, Sestan N, Bilgüvar K, Günel M (2011) Recessive LAMC3 mutations cause malformations of occipital cortical development. Nat Genet 108, 43, 590-594.
[PubMed] [PDF] [Movie 1] [Movie 2] [Movie 3] [Movie 4] [Movie 5]

Han W, Kwan KY, Shim S, Lam MM, Shin Y, Xu X, Zhu Y, Li M, Sestan N (2011) TBR1 directly represses Fezf2 to control the laminar origin and development of the corticospinal tract. Proc Natl Acad Sci U S A 108, 3041-3046.
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Bilgüvar K, Oztürk AK, Louvi A, Kwan KY, Choi M, Tatll B, Yalnlzoglu D, Tüysüz B, Caglayan AO, G?kben S, Kaymakçalan H, Barak T, Baklrcloglu M, Yasuno K, Ho W, Sanders S, Zhu Y, Yllmaz S, Dinçer A, Johnson MH, Bronen RA, Koçer N, Per H, Mane S, Pamir MN, Yalçlnkaya C, Kumandas S, Topçu M, Ozmen M, Sestan N, Lifton RP, State MW, Günel M (2010) Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature 467, 207-210.
[PubMed] [PDF] [Movie 1] [Movie 2] [Movie 3] [Movie 4] [Movie 5] [Movie 6]

Ros H, Sachdev RNS, Yu Y, Sestan N, McCormick DA (2009) Neocortical networks entrain neuronal circuits in cerebellar cortex. J Neurosci 29, 10309-10320.
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Johnson MB, Imamura Kawasawa Y, Mason CE, Krsnik Z, Coppola G, Bogdanovic D, Geschwind DH, Mane SM, State MW, Sestan N (2009) Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron 62, 494-509.
[PubMed] [PDF] [Data]

Fertuzinhos S, Krsnik Z, Imamura Kawasawa Y, Rasin MR, Kwan KY, Chen JG, Judas M, Hayashi M, Sestan N (2009) Selective depletion of molecularly defined cortical interneurons in human holoprosencephaly with severe striatal hypoplasia. Cereb Cortex 19, 2196-2207
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Stillman AA, Krsnik Z, Sun J, Rasin MR, State MW, Sestan N, Louvi A (2009) Developmentally regulated and evolutionarily conserved expression of SLITRK1 in brain circuits implicated in Tourette syndrome. J Comp Neurol 513, 21-37.
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Hashimoto-Torii K, Torii M, Sarkisian MR, Bartley CM, Shen J, Radtke F, Gridley T, Sestan N, Rakic P (2008) Interaction between Reelin and Notch signaling regulates neuronal migration in the cerebral cortex. Neuron 60, 273-284.
[PubMed] [PDF]

Kwan KY, Lam MMS, Krsnik Z, Imamura Kawasawa Y, Lefebvre V, Sestan N (2008) SOX5 postmitotically regulates migration, postmigratory differentiation, and projections of subplate and deep-layer neocortical neurons. Proc Natl Acad Sci USA 105, 16021-16026.
[PubMed] [PDF]

Britanova O, de Juan Romero C, Cheung A, Kwan KY, Schwark M, Gyorgy A, Vogel T, Akopov S, Mitkovski M, Agoston D, Sestan N, Moln?r Z, Tarabykin V (2008) Satb2 is a postmitotic determinant for upper-layer neuron specification in the neocortex. Neuron 57, 378–392.
[PubMed] [PDF]

Breunig JJ, Silbereis J, Vaccarino FM, Sestan N, Rakic P (2007) Notch regulates cell fate and dendrite morphology of newborn neurons in the postnatal dentate gyrus. Proc Natl Acad Sci USA 104, 20558–20563.
[PubMed] [PDF]

Rasin MR, Gazula VR, Breunig JJ, Kwan KY, Johnson MB, Liu-Chen S, Li HS, Jan LY, Jan YN, Rakic P, Sestan N (2007) Numb and Numbl are required for maintenance of cadherin-based adhesion and polarity of neural progenitors. Nature Neurosci 10, 819-827.
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Brandt N, Franke K, Rasin MR, Baumgart J, Vogt J, Khrulev S, Hassel B, Pohl EE, Sestan N, Nitsch R, Schumacher S (2007) The neural EGF family member CALEB/NGC mediates dendritic tree and spine complexity. EMBO J 104, 6828-6833.
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Kuo CT, Mirzadeh Z, Soriano-Navarro M, Rasin MR, Wang D, Shen J, Sestan N, Garcia-Verdugo J, Alvarez-Buylla A, Jan LY, Jan YN (2006) Postnatal deletion of Numb/Numblike reveals repair and remodeling capacity in the subventricular neurogenic niche. Cell 127, 1253-1264.
[PubMed] [PDF]

Smith KM, Ohkubo Y, Maragnoli ME, Rasin M-R, Schwartz ML, Sestan N, Vaccarino FM (2006) Midline radial glia translocation and corpus callosum formation require FGF signaling. Nature Neurosci 9, 787-797.
[PubMed] [PDF]

Chen JG, Rasin MR, Kwan KY, Sestan N (2005) Zfp312 transcription factor is required for subcortical projections and dendritic morphology of deep layer pyramidal neurons of the cerebral cortex. Pro c Natl Acad Sci USA 102,17792-17797.
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Abelson JF, Kwan KY, O'Roak BJ, Baek DY, Stillman AA, Morgan TM, Mathews CA, Pauls DL, Rasin MR, Gunel M, Davis NR, Ercan-Sencicek AG, Guez DH, Spertus JA, Leckman JF, Dure LS 4th, Kurlan R, Singer HS, Gilbert DL, Farhi A, Louvi A, Lifton RP, Sestan N, State MW (2005) Sequence variations in SLITRK1 are associated with Tourette’s syndrome. Science 310, 317-320.
[PubMed] [PDF]

Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P, Constantine-Paton M, Horvitz RH (2004) Developmental profile of microRNA expression in the mammalian brain. Genome Biol 5, R68.1-68.13.
[PubMed] [PDF]

Schmid RS, McGrath B, Berechid BE, Boyles B, Marchionni M, Sestan N, Anton ES (2003) Neuregulin 1-ErbB2 signaling is required for the establishment and transformation of radial glia in cerebral cortex. Proc Natl Acad Sci USA 100, 4251-4256.
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Roncarati R, Sestan N, Scheinfeld MH, Berechid BE, Lopez PA, Meucci O, McGlade JC, Rakic P, D’Adamio L (2002) The gamma-secretase-generated intracellular domain of beta-amyloid precursor protein binds Numb and inhibits Notch signaling. Proc Natl Acad Sci USA 90, 7102-7107.
[PubMed] [PDF]

Sestan N, Rakic P (2002) Notch signaling in the brain: More than just a developmental story. In Notch from Neurodevelopment to Neurodegeneration: Keeping the Fate. Fondation IPSEN. Israel A, De Strooper B, Checler F and Christen Y, Eds., Springer, Berlin, pp. 19-40.
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Sestan N, Rakic P, Donoghue MJ (2001) Independent parcellation of the embryonic visual cortex and thalamus revealed by combinatorial Eph/ephrin gene expression. Curr Biol 1, 39-43.
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Sestan N, Artavanis-Tsakonas S, Rakic P (1999) Contact-dependent inhibition of cortical neurite growth mediated by Notch signaling. Science 286, 741-746.
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Judas M, Sestan N, Kostovic I (1999) Nitrinergic neurons in the developing and adult human telencephalon: transient and permanent patterns of expression in comparison to other mammals. Microsc Res Tech 45, 401-419.
[PubMed] [PDF]

Qi H, Rand MD, Wu X, Sestan N, Wang W, Rakic P, Xu T, Artavanis-Tsakonas S (1999) Processing of the Notch ligand Delta by the metalloprotease Kuzbanian. Science 283, 91-94.
[PubMed] [PDF]

Sestan N, Kostovic I (1994) Histochemical localization of nitric oxide synthase in the CNS. Trends Neurosci 17, 105-106.
[PubMed] [PDF]

Sajin B, Sestan N, Dmitrovic B (1992) Compartmentalization of NADPH-diaphorase staining in the developing human striatum. Neurosci Lett 140, 117-120.
[PubMed] [PDF]