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Items: 1 to 20 of 43

1.

Correlation of preterm infant illness severity with placental histology.

Chisholm KM, Heerema-McKenney A, Tian L, Rajani AK, Saria S, Koller D, Penn AA.

Placenta. 2016 Mar;39:61-9. doi: 10.1016/j.placenta.2016.01.012. Epub 2016 Jan 16.

2.

Parameter Estimation and Energy Minimization for Region-Based Semantic Segmentation.

Kumar MP, Turki H, Preston D, Koller D.

IEEE Trans Pattern Anal Mach Intell. 2015 Jul;37(7):1373-86. doi: 10.1109/TPAMI.2014.2372766.

PMID:
26352446
3.

Sharing and Specificity of Co-expression Networks across 35 Human Tissues.

Pierson E; GTEx Consortium, Koller D, Battle A, Mostafavi S, Ardlie KG, Getz G, Wright FA, Kellis M, Volpi S, Dermitzakis ET.

PLoS Comput Biol. 2015 May 13;11(5):e1004220. doi: 10.1371/journal.pcbi.1004220. eCollection 2015 May.

4.

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation.

Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, Koller D.

Mol Syst Biol. 2014 Dec 23;10:770. doi: 10.15252/msb.20145524.

5.

Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains.

Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, Mathis D, Benoist C; Immunological Genome Consortium.

J Immunol. 2014 Nov 1;193(9):4485-96. doi: 10.4049/jimmunol.1401280. Epub 2014 Sep 29.

6.

Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements.

Jackson KJ, Liu Y, Roskin KM, Glanville J, Hoh RA, Seo K, Marshall EL, Gurley TC, Moody MA, Haynes BF, Walter EB, Liao HX, Albrecht RA, García-Sastre A, Chaparro-Riggers J, Rajpal A, Pons J, Simen BB, Hanczaruk B, Dekker CL, Laserson J, Koller D, Davis MM, Fire AZ, Boyd SD.

Cell Host Microbe. 2014 Jul 9;16(1):105-14. doi: 10.1016/j.chom.2014.05.013. Epub 2014 Jun 26.

7.

Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes.

Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL.

Science. 2014 May 2;344(6183):519-23. doi: 10.1126/science.1249547.

8.

High-resolution antibody dynamics of vaccine-induced immune responses.

Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden JA, Kelton W, Taek Jung S, Liu Y, Laserson J, Chari R, Lee JH, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein SH, Church GM.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4928-33. doi: 10.1073/pnas.1323862111. Epub 2014 Mar 17.

9.

Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires.

Wang C, Liu Y, Xu LT, Jackson KJ, Roskin KM, Pham TD, Laserson J, Marshall EL, Seo K, Lee JY, Furman D, Koller D, Dekker CL, Davis MM, Fire AZ, Boyd SD.

J Immunol. 2014 Jan 15;192(2):603-11. doi: 10.4049/jimmunol.1301384. Epub 2013 Dec 11.

10.

The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies.

Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, Simen BB, St John EP, Chan-Hui PY, Swiderek K, Kleinstein SH, Alter G, Seaman MS, Chakraborty AK, Koller D, Wilson IA, Church GM, Burton DR, Poignard P.

PLoS Pathog. 2013;9(11):e1003754. doi: 10.1371/journal.ppat.1003754. Epub 2013 Nov 21. Erratum in: PLoS Pathog. 2013 Dec;9(12). doi:10.1371/annotation/f1f8c791-61e9-45c6-a455-92c6dadf9f06. Kleinstein, Stephen H [corrected to Kleinstein, Steven H].

11.

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.

Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D.

Genome Res. 2014 Jan;24(1):14-24. doi: 10.1101/gr.155192.113. Epub 2013 Oct 3.

12.

Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge.

Mostafavi S, Battle A, Zhu X, Urban AE, Levinson D, Montgomery SB, Koller D.

PLoS One. 2013 Jul 18;8(7):e68141. doi: 10.1371/journal.pone.0068141. Print 2013.

13.

Convergent antibody signatures in human dengue.

Parameswaran P, Liu Y, Roskin KM, Jackson KK, Dixit VP, Lee JY, Artiles KL, Zompi S, Vargas MJ, Simen BB, Hanczaruk B, McGowan KR, Tariq MA, Pourmand N, Koller D, Balmaseda A, Boyd SD, Harris E, Fire AZ.

Cell Host Microbe. 2013 Jun 12;13(6):691-700. doi: 10.1016/j.chom.2013.05.008.

14.

The transcriptional landscape of αβ T cell differentiation.

Mingueneau M, Kreslavsky T, Gray D, Heng T, Cruse R, Ericson J, Bendall S, Spitzer MH, Nolan GP, Kobayashi K, von Boehmer H, Mathis D, Benoist C; Immunological Genome Consortium, Best AJ, Knell J, Goldrath A, Joic V, Koller D, Shay T, Regev A, Cohen N, Brennan P, Brenner M, Kim F, Nageswara Rao T, Wagers A, Heng T, Ericson J, Rothamel K, Ortiz-Lopez A, Mathis D, Benoist C, Bezman NA, Sun JC, Min-Oo G, Kim CC, Lanier LL, Miller J, Brown B, Merad M, Gautier EL, Jakubzick C, Randolph GJ, Monach P, Blair DA, Dustin ML, Shinton SA, Hardy RR, Laidlaw D, Collins J, Gazit R, Rossi DJ, Malhotra N, Sylvia K, Kang J, Kreslavsky T, Fletcher A, Elpek K, Bellemare-Pelletier A, Malhotra D, Turley S.

Nat Immunol. 2013 Jun;14(6):619-32. doi: 10.1038/ni.2590. Epub 2013 May 5.

15.

Identification of transcriptional regulators in the mouse immune system.

Jojic V, Shay T, Sylvia K, Zuk O, Sun X, Kang J, Regev A, Koller D; Immunological Genome Project Consortium, Best AJ, Knell J, Goldrath A, Joic V, Koller D, Shay T, Regev A, Cohen N, Brennan P, Brenner M, Kim F, Rao TN, Wagers A, Heng T, Ericson J, Rothamel K, Ortiz-Lopez A, Mathis D, Benoist C, Bezman NA, Sun JC, Min-Oo G, Kim CC, Lanier LL, Miller J, Brown B, Merad M, Gautier EL, Jakubzick C, Randolph GJ, Monach P, Blair DA, Dustin ML, Shinton SA, Hardy RR, Laidlaw D, Collins J, Gazit R, Rossi DJ, Malhotra N, Sylvia K, Kang J, Kreslavsky T, Fletcher A, Elpek K, Bellemarte-Pelletier A, Malhotra D, Turley S.

Nat Immunol. 2013 Jun;14(6):633-43. doi: 10.1038/ni.2587. Epub 2013 Apr 28.

16.

Apoptosis and other immune biomarkers predict influenza vaccine responsiveness.

Furman D, Jojic V, Kidd B, Shen-Orr S, Price J, Jarrell J, Tse T, Huang H, Lund P, Maecker HT, Utz PJ, Dekker CL, Koller D, Davis MM.

Mol Syst Biol. 2013 Apr 16;9:659. doi: 10.1038/msb.2013.15. Erratum in: Mol Syst Biol. 2014;10:750. Mol Syst Biol. 2013;9:680.

17.

Conservation and divergence in the transcriptional programs of the human and mouse immune systems.

Shay T, Jojic V, Zuk O, Rothamel K, Puyraimond-Zemmour D, Feng T, Wakamatsu E, Benoist C, Koller D, Regev A; ImmGen Consortium.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2946-51. doi: 10.1073/pnas.1222738110. Epub 2013 Feb 4.

18.

Imputing gene expression from selectively reduced probe sets.

Donner Y, Feng T, Benoist C, Koller D.

Nat Methods. 2012 Nov;9(11):1120-5. doi: 10.1038/nmeth.2207. Epub 2012 Oct 14.

19.

Systematic analysis of breast cancer morphology uncovers stromal features associated with survival.

Beck AH, Sangoi AR, Leung S, Marinelli RJ, Nielsen TO, van de Vijver MJ, West RB, van de Rijn M, Koller D.

Sci Transl Med. 2011 Nov 9;3(108):108ra113. doi: 10.1126/scitranslmed.3002564.

20.

Genovo: de novo assembly for metagenomes.

Laserson J, Jojic V, Koller D.

J Comput Biol. 2011 Mar;18(3):429-43. doi: 10.1089/cmb.2010.0244.

PMID:
21385045

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