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Items: 1 to 50 of 114

1.

Framework for advancing rigorous research.

Koroshetz WJ, Behrman S, Brame CJ, Branchaw JL, Brown EN, Clark EA, Dockterman D, Elm JJ, Gay PL, Green KM, Hsi S, Kaplitt MG, Kolber BJ, Kolodkin AL, Lipscombe D, MacLeod MR, McKinney CC, Munafò MR, Oakley B, Olimpo JT, Percie du Sert N, Raman IM, Riley C, Shelton AL, Uzzo SM, Crawford DC, Silberberg SD.

Elife. 2020 Mar 4;9. pii: e55915. doi: 10.7554/eLife.55915.

2.

Development and evaluation of a harmonized whole body physiologically based pharmacokinetic (PBPK) model for flutamide in rats and its extrapolation to humans.

Sharma RP, Kumar V, Schuhmacher M, Kolodkin A, Westerhoff HV.

Environ Res. 2020 Mar;182:108948. doi: 10.1016/j.envres.2019.108948. Epub 2019 Nov 26.

PMID:
31841869
3.

Binary Fate Choice between Closely Related Interneuronal Types Is Determined by a Fezf1-Dependent Postmitotic Transcriptional Switch.

Peng YR, James RE, Yan W, Kay JN, Kolodkin AL, Sanes JR.

Neuron. 2020 Feb 5;105(3):464-474.e6. doi: 10.1016/j.neuron.2019.11.002. Epub 2019 Dec 4.

PMID:
31812516
4.

Semaphorin 2b Regulates Sleep-Circuit Formation in the Drosophila Central Brain.

Xie X, Tabuchi M, Corver A, Duan G, Wu MN, Kolodkin AL.

Neuron. 2019 Oct 23;104(2):322-337.e14. doi: 10.1016/j.neuron.2019.07.019. Epub 2019 Sep 26.

PMID:
31564592
5.

Editorial Overview: Developmental neuroscience (2018).

Kolodkin AL, López-Bendito G.

Curr Opin Neurobiol. 2018 Dec;53:iii-vi. doi: 10.1016/j.conb.2018.10.010. No abstract available.

PMID:
30449415
6.

Genetic access to neurons in the accessory optic system reveals a role for Sema6A in midbrain circuitry mediating motion perception.

Lilley BN, Sabbah S, Hunyara JL, Gribble KD, Al-Khindi T, Xiong J, Wu Z, Berson DM, Kolodkin AL.

J Comp Neurol. 2019 Jan 1;527(1):282-296. doi: 10.1002/cne.24507. Epub 2018 Nov 11.

7.

Neuropilin-2/PlexinA3 Receptors Associate with GluA1 and Mediate Sema3F-Dependent Homeostatic Scaling in Cortical Neurons.

Wang Q, Chiu SL, Koropouli E, Hong I, Mitchell S, Easwaran TP, Hamilton NR, Gustina AS, Zhu Q, Ginty DD, Huganir RL, Kolodkin AL.

Neuron. 2017 Dec 6;96(5):1084-1098.e7. doi: 10.1016/j.neuron.2017.10.029. Epub 2017 Nov 16.

8.

Varicose and cheerio collaborate with pebble to mediate semaphorin-1a reverse signaling in Drosophila.

Jeong S, Yang DS, Hong YG, Mitchell SP, Brown MP, Kolodkin AL.

Proc Natl Acad Sci U S A. 2017 Sep 26;114(39):E8254-E8263. doi: 10.1073/pnas.1713010114. Epub 2017 Sep 11.

9.

The laminar organization of the Drosophila ellipsoid body is semaphorin-dependent and prevents the formation of ectopic synaptic connections.

Xie X, Tabuchi M, Brown MP, Mitchell SP, Wu MN, Kolodkin AL.

Elife. 2017 Jun 20;6. pii: e25328. doi: 10.7554/eLife.25328.

10.

Netrin-Mediated Axon Guidance to the CNS Midline Revisited.

Hand RA, Kolodkin AL.

Neuron. 2017 May 17;94(4):691-693. doi: 10.1016/j.neuron.2017.05.012.

11.

Establishing Wiring Specificity in Visual System Circuits: From the Retina to the Brain.

Zhang C, Kolodkin AL, Wong RO, James RE.

Annu Rev Neurosci. 2017 Jul 25;40:395-424. doi: 10.1146/annurev-neuro-072116-031607. Epub 2017 Apr 26. Review.

PMID:
28460185
12.

Wiring visual systems: common and divergent mechanisms and principles.

Kolodkin AL, Hiesinger PR.

Curr Opin Neurobiol. 2017 Feb;42:128-135. doi: 10.1016/j.conb.2016.12.006. Epub 2017 Jan 5. Review.

13.

Ryk controls remapping of motor cortex during functional recovery after spinal cord injury.

Hollis ER 2nd, Ishiko N, Yu T, Lu CC, Haimovich A, Tolentino K, Richman A, Tury A, Wang SH, Pessian M, Jo E, Kolodkin A, Zou Y.

Nat Neurosci. 2016 May;19(5):697-705. doi: 10.1038/nn.4282. Epub 2016 Apr 11.

14.

Sculpting neural circuits by axon and dendrite pruning.

Riccomagno MM, Kolodkin AL.

Annu Rev Cell Dev Biol. 2015;31:779-805. doi: 10.1146/annurev-cellbio-100913-013038. Epub 2015 Oct 2. Review.

15.

Axon Dynamics during Neocortical Laminar Innervation.

Hand RA, Khalid S, Tam E, Kolodkin AL.

Cell Rep. 2015 Jul 14;12(2):172-82. doi: 10.1016/j.celrep.2015.06.026. Epub 2015 Jul 2.

16.

Functional assembly of accessory optic system circuitry critical for compensatory eye movements.

Sun LO, Brady CM, Cahill H, Al-Khindi T, Sakuta H, Dhande OS, Noda M, Huberman AD, Nathans J, Kolodkin AL.

Neuron. 2015 May 20;86(4):971-984. doi: 10.1016/j.neuron.2015.03.064. Epub 2015 May 7.

17.

Semaphorin 5A inhibits synaptogenesis in early postnatal- and adult-born hippocampal dentate granule cells.

Duan Y, Wang SH, Song J, Mironova Y, Ming GL, Kolodkin AL, Giger RJ.

Elife. 2014 Oct 14;3. doi: 10.7554/eLife.04390.

18.

Dlg5 regulates dendritic spine formation and synaptogenesis by controlling subcellular N-cadherin localization.

Wang SH, Celic I, Choi SY, Riccomagno M, Wang Q, Sun LO, Mitchell SP, Vasioukhin V, Huganir RL, Kolodkin AL.

J Neurosci. 2014 Sep 17;34(38):12745-61. doi: 10.1523/JNEUROSCI.1280-14.2014.

19.

Macromolecular networks and intelligence in microorganisms.

Westerhoff HV, Brooks AN, Simeonidis E, García-Contreras R, He F, Boogerd FC, Jackson VJ, Goncharuk V, Kolodkin A.

Front Microbiol. 2014 Jul 22;5:379. doi: 10.3389/fmicb.2014.00379. eCollection 2014.

20.

Semaphorins and the dynamic regulation of synapse assembly, refinement, and function.

Koropouli E, Kolodkin AL.

Curr Opin Neurobiol. 2014 Aug;27:1-7. doi: 10.1016/j.conb.2014.02.005. Epub 2014 Mar 2. Review.

21.

Cas adaptor proteins organize the retinal ganglion cell layer downstream of integrin signaling.

Riccomagno MM, Sun LO, Brady CM, Alexandropoulos K, Seo S, Kurokawa M, Kolodkin AL.

Neuron. 2014 Feb 19;81(4):779-86. doi: 10.1016/j.neuron.2014.01.036.

22.

Function of the Drosophila receptor guanylyl cyclase Gyc76C in PlexA-mediated motor axon guidance.

Chak K, Kolodkin AL.

Development. 2014 Jan;141(1):136-47. doi: 10.1242/dev.095968. Epub 2013 Nov 27.

23.

On and off retinal circuit assembly by divergent molecular mechanisms.

Sun LO, Jiang Z, Rivlin-Etzion M, Hand R, Brady CM, Matsuoka RL, Yau KW, Feller MB, Kolodkin AL.

Science. 2013 Nov 1;342(6158):1241974. doi: 10.1126/science.1241974.

24.

MEGF8 is a modifier of BMP signaling in trigeminal sensory neurons.

Engelhard C, Sarsfield S, Merte J, Wang Q, Li P, Beppu H, Kolodkin AL, Sucov HM, Ginty DD.

Elife. 2013 Sep 17;2:e01160. doi: 10.7554/eLife.01160.

25.

Optimization of stress response through the nuclear receptor-mediated cortisol signalling network.

Kolodkin A, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant N.

Nat Commun. 2013;4:1792. doi: 10.1038/ncomms2799.

26.

Sema6B, Sema6C, and Sema6D expression and function during mammalian retinal development.

Matsuoka RL, Sun LO, Katayama K, Yoshida Y, Kolodkin AL.

PLoS One. 2013 Apr 30;8(4):e63207. doi: 10.1371/journal.pone.0063207. Print 2013.

27.

SnapShot: Axon guidance II.

Kolodkin AL, Pasterkamp RJ.

Cell. 2013 Apr 25;153(3):722.e1. doi: 10.1016/j.cell.2013.04.004. No abstract available.

28.

SnapShot: Axon Guidance.

Pasterkamp RJ, Kolodkin AL.

Cell. 2013 Apr 11;153(2):494, 494e1-2. doi: 10.1016/j.cell.2013.03.031. No abstract available.

29.

Cbl-associated protein regulates assembly and function of two tension-sensing structures in Drosophila.

Bharadwaj R, Roy M, Ohyama T, Sivan-Loukianova E, Delannoy M, Lloyd TE, Zlatic M, Eberl DF, Kolodkin AL.

Development. 2013 Feb 1;140(3):627-38. doi: 10.1242/dev.085100.

30.

The coordinate regulation of sensory afferent CNS targeting and CNS longitudinal tract organization in Drosophila during neural development.

Wu Z, Andreone BJ, Kolodkin AL.

J Peripher Nerv Syst. 2012 Dec;17 Suppl 3:34-7. doi: 10.1111/j.1529-8027.2012.00429.x. Review.

31.

The Control of semaphorin-1a-mediated reverse signaling by opposing pebble and RhoGAPp190 functions in drosophila.

Jeong S, Juhaszova K, Kolodkin AL.

Neuron. 2012 Nov 21;76(4):721-34. doi: 10.1016/j.neuron.2012.09.018.

32.

Computing life: Add logos to biology and bios to physics.

Kolodkin A, Simeonidis E, Westerhoff HV.

Prog Biophys Mol Biol. 2013 Apr;111(2-3):69-74. doi: 10.1016/j.pbiomolbio.2012.10.003. Epub 2012 Oct 24.

PMID:
23103359
33.

The extracellular matrix proteoglycan perlecan facilitates transmembrane semaphorin-mediated repulsive guidance.

Cho JY, Chak K, Andreone BJ, Wooley JR, Kolodkin AL.

Genes Dev. 2012 Oct 1;26(19):2222-35. doi: 10.1101/gad.193136.112.

34.

Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence.

Kolodkin A, Simeonidis E, Balling R, Westerhoff HV.

Front Physiol. 2012 Jul 23;3:291. doi: 10.3389/fphys.2012.00291. eCollection 2012.

35.

The RacGAP β2-Chimaerin selectively mediates axonal pruning in the hippocampus.

Riccomagno MM, Hurtado A, Wang H, Macopson JG, Griner EM, Betz A, Brose N, Kazanietz MG, Kolodkin AL.

Cell. 2012 Jun 22;149(7):1594-606. doi: 10.1016/j.cell.2012.05.018.

36.

Autism spectrum disorder susceptibility gene TAOK2 affects basal dendrite formation in the neocortex.

de Anda FC, Rosario AL, Durak O, Tran T, Gräff J, Meletis K, Rei D, Soda T, Madabhushi R, Ginty DD, Kolodkin AL, Tsai LH.

Nat Neurosci. 2012 Jun 10;15(7):1022-31. doi: 10.1038/nn.3141.

37.

Guidance-cue control of horizontal cell morphology, lamination, and synapse formation in the mammalian outer retina.

Matsuoka RL, Jiang Z, Samuels IS, Nguyen-Ba-Charvet KT, Sun LO, Peachey NS, Chédotal A, Yau KW, Kolodkin AL.

J Neurosci. 2012 May 16;32(20):6859-68. doi: 10.1523/JNEUROSCI.0267-12.2012.

38.

The p150(Glued) CAP-Gly domain regulates initiation of retrograde transport at synaptic termini.

Lloyd TE, Machamer J, O'Hara K, Kim JH, Collins SE, Wong MY, Sahin B, Imlach W, Yang Y, Levitan ES, McCabe BD, Kolodkin AL.

Neuron. 2012 Apr 26;74(2):344-60. doi: 10.1016/j.neuron.2012.02.026.

39.

Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting.

Sweeney LB, Chou YH, Wu Z, Joo W, Komiyama T, Potter CJ, Kolodkin AL, Garcia KC, Luo L.

Neuron. 2011 Dec 8;72(5):734-47. doi: 10.1016/j.neuron.2011.09.026.

40.

Class 5 transmembrane semaphorins control selective Mammalian retinal lamination and function.

Matsuoka RL, Chivatakarn O, Badea TC, Samuels IS, Cahill H, Katayama K, Kumar SR, Suto F, Chédotal A, Peachey NS, Nathans J, Yoshida Y, Giger RJ, Kolodkin AL.

Neuron. 2011 Aug 11;71(3):460-73. doi: 10.1016/j.neuron.2011.06.009.

41.

Emergence of the silicon human and network targeting drugs.

Kolodkin A, Boogerd FC, Plant N, Bruggeman FJ, Goncharuk V, Lunshof J, Moreno-Sanchez R, Yilmaz N, Bakker BM, Snoep JL, Balling R, Westerhoff HV.

Eur J Pharm Sci. 2012 Jul 16;46(4):190-7. doi: 10.1016/j.ejps.2011.06.006. Epub 2011 Jun 16.

PMID:
21704158
42.

A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS.

Wu Z, Sweeney LB, Ayoob JC, Chak K, Andreone BJ, Ohyama T, Kerr R, Luo L, Zlatic M, Kolodkin AL.

Neuron. 2011 Apr 28;70(2):281-98. doi: 10.1016/j.neuron.2011.02.050.

43.

Transmembrane semaphorin signalling controls laminar stratification in the mammalian retina.

Matsuoka RL, Nguyen-Ba-Charvet KT, Parray A, Badea TC, Chédotal A, Kolodkin AL.

Nature. 2011 Feb 10;470(7333):259-63. doi: 10.1038/nature09675.

44.

Design principles of nuclear receptor signaling: how complex networking improves signal transduction.

Kolodkin AN, Bruggeman FJ, Plant N, Moné MJ, Bakker BM, Campbell MJ, van Leeuwen JP, Carlberg C, Snoep JL, Westerhoff HV.

Mol Syst Biol. 2010 Dec 21;6:446. doi: 10.1038/msb.2010.102.

45.

Mechanisms and molecules of neuronal wiring: a primer.

Kolodkin AL, Tessier-Lavigne M.

Cold Spring Harb Perspect Biol. 2011 Jun 1;3(6). pii: a001727. doi: 10.1101/cshperspect.a001727. Review.

46.

A forward genetic screen in mice identifies Sema3A(K108N), which binds to neuropilin-1 but cannot signal.

Merte J, Wang Q, Vander Kooi CW, Sarsfield S, Leahy DJ, Kolodkin AL, Ginty DD.

J Neurosci. 2010 Apr 21;30(16):5767-75. doi: 10.1523/JNEUROSCI.5061-09.2010.

47.

Secreted semaphorins control spine distribution and morphogenesis in the postnatal CNS.

Tran TS, Rubio ME, Clem RL, Johnson D, Case L, Tessier-Lavigne M, Huganir RL, Ginty DD, Kolodkin AL.

Nature. 2009 Dec 24;462(7276):1065-9. doi: 10.1038/nature08628. Epub 2009 Dec 13.

48.

A genetic pathway composed of Sox14 and Mical governs severing of dendrites during pruning.

Kirilly D, Gu Y, Huang Y, Wu Z, Bashirullah A, Low BC, Kolodkin AL, Wang H, Yu F.

Nat Neurosci. 2009 Dec;12(12):1497-505. doi: 10.1038/nn.2415. Epub 2009 Nov 1.

49.

Semaphorin 3F is a bifunctional guidance cue for dopaminergic axons and controls their fasciculation, channeling, rostral growth, and intracortical targeting.

Kolk SM, Gunput RA, Tran TS, van den Heuvel DM, Prasad AA, Hellemons AJ, Adolfs Y, Ginty DD, Kolodkin AL, Burbach JP, Smidt MP, Pasterkamp RJ.

J Neurosci. 2009 Oct 7;29(40):12542-57. doi: 10.1523/JNEUROSCI.2521-09.2009.

50.

Systems biology towards life in silico: mathematics of the control of living cells.

Westerhoff HV, Kolodkin A, Conradie R, Wilkinson SJ, Bruggeman FJ, Krab K, van Schuppen JH, Hardin H, Bakker BM, Moné MJ, Rybakova KN, Eijken M, van Leeuwen HJ, Snoep JL.

J Math Biol. 2009 Jan;58(1-2):7-34. doi: 10.1007/s00285-008-0160-8. Epub 2008 Feb 16.

PMID:
18278498

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