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Items: 1 to 20 of 215

1.

Genetic Architecture of a Rice Nested Association Mapping Population.

Fragoso CA, Moreno M, Wang Z, Heffelfinger C, Arbelaez LJ, Aguirre JA, Franco N, Romero LE, Labadie K, Zhao H, Dellaporta SL, Lorieux M.

G3 (Bethesda). 2017 Jun 7;7(6):1913-1926. doi: 10.1534/g3.117.041608.

2.

Dysregulation of B Cell Repertoire Formation in Myasthenia Gravis Patients Revealed through Deep Sequencing.

Vander Heiden JA, Stathopoulos P, Zhou JQ, Chen L, Gilbert TJ, Bolen CR, Barohn RJ, Dimachkie MM, Ciafaloni E, Broering TJ, Vigneault F, Nowak RJ, Kleinstein SH, O'Connor KC.

J Immunol. 2017 Feb 15;198(4):1460-1473. doi: 10.4049/jimmunol.1601415. Epub 2017 Jan 13.

PMID:
28087666
3.

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG.

BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):333.

4.

A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data.

Cui A, Di Niro R, Vander Heiden JA, Briggs AW, Adams K, Gilbert T, O'Connor KC, Vigneault F, Shlomchik MJ, Kleinstein SH.

J Immunol. 2016 Nov 1;197(9):3566-3574. Epub 2016 Oct 5.

PMID:
27707999
5.

Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience.

McDougal RA, Morse TM, Carnevale T, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hines ML.

J Comput Neurosci. 2017 Feb;42(1):1-10. doi: 10.1007/s10827-016-0623-7. Epub 2016 Sep 15. Review.

PMID:
27629590
6.

Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON.

Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schürmann F, Hines ML.

Neural Comput. 2016 Oct;28(10):2063-90. doi: 10.1162/NECO_a_00876. Epub 2016 Aug 24.

PMID:
27557104
7.

Genome of Diaporthe sp. provides insights into the potential inter-phylum transfer of a fungal sesquiterpenoid biosynthetic pathway.

de Sena Filho JG, Quin MB, Spakowicz DJ, Shaw JJ, Kucera K, Dunican B, Strobel SA, Schmidt-Dannert C.

Fungal Biol. 2016 Aug;120(8):1050-1063. doi: 10.1016/j.funbio.2016.04.001. Epub 2016 Apr 12.

8.

Random close packing in protein cores.

Gaines JC, Smith WW, Regan L, O'Hern CS.

Phys Rev E. 2016 Mar;93(3):032415. doi: 10.1103/PhysRevE.93.032415. Epub 2016 Mar 28.

PMID:
27078398
9.

Reproducibility in Computational Neuroscience Models and Simulations.

McDougal RA, Bulanova AS, Lytton WW.

IEEE Trans Biomed Eng. 2016 Oct;63(10):2021-35. doi: 10.1109/TBME.2016.2539602. Epub 2016 Mar 8.

PMID:
27046845
10.

Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells.

Rubelt F, Bolen CR, McGuire HM, Vander Heiden JA, Gadala-Maria D, Levin M, Euskirchen GM, Mamedov MR, Swan GE, Dekker CL, Cowell LG, Kleinstein SH, Davis MM.

Nat Commun. 2016 Mar 23;7:11112. doi: 10.1038/ncomms11112.

11.

Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex.

Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW.

Neuroscience. 2016 Mar 1;316:344-66. doi: 10.1016/j.neuroscience.2015.12.043. Epub 2015 Dec 31.

12.

Classification of radiology reports for falls in an HIV study cohort.

Bates J, Fodeh SJ, Brandt CA, Womack JA.

J Am Med Inform Assoc. 2016 Apr;23(e1):e113-7. doi: 10.1093/jamia/ocv155. Epub 2015 Nov 13.

13.

Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing.

Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JN, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC.

Integr Biol (Camb). 2015 Dec;7(12):1587-97. doi: 10.1039/c5ib00169b. Epub 2015 Oct 20.

14.

Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation.

Di Niro R, Lee SJ, Vander Heiden JA, Elsner RA, Trivedi N, Bannock JM, Gupta NT, Kleinstein SH, Vigneault F, Gilbert TJ, Meffre E, McSorley SJ, Shlomchik MJ.

Immunity. 2015 Jul 21;43(1):120-31. doi: 10.1016/j.immuni.2015.06.013. Epub 2015 Jul 14.

15.

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.

Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH.

Bioinformatics. 2015 Oct 15;31(20):3356-8. doi: 10.1093/bioinformatics/btv359. Epub 2015 Jun 10.

16.

ModelView for ModelDB: Online Presentation of Model Structure.

McDougal RA, Morse TM, Hines ML, Shepherd GM.

Neuroinformatics. 2015 Oct;13(4):459-70. doi: 10.1007/s12021-015-9269-2.

17.

Noninvasive analysis of the sputum transcriptome discriminates clinical phenotypes of asthma.

Yan X, Chu JH, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL, Barnes KC, London SJ, Gilliland F, Weiss ST, Raby BA, Cohn L, Chupp GL.

Am J Respir Crit Care Med. 2015 May 15;191(10):1116-25. doi: 10.1164/rccm.201408-1440OC.

18.

Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model.

Neymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW.

Neural Comput. 2015 Apr;27(4):898-924. doi: 10.1162/NECO_a_00712. Epub 2015 Mar 3.

19.

Integrative Analysis of "-Omics" Data Using Penalty Functions.

Zhao Q, Shi X, Huang J, Liu J, Li Y, Ma S.

Wiley Interdiscip Rev Comput Stat. 2015 Jan-Feb;7(1):99-108.

20.

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.

Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH.

Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):E862-70. doi: 10.1073/pnas.1417683112. Epub 2015 Feb 9.

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