2012 Publications

Improving the performance of true single molecule sequencing for ancient DNA.
Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, Stiller M, Shapiro B, Zazula G,Froese D, Steinmann KE, Thompson JF, Al-Rasheid KA, Gilbert TM, Willerslev E,Orlando L.
BMC Genomics
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Single molecule sequencing of free DNA from maternal plasma for noninvasive trisomy 21 detection.
​ van den Oever JM, Balkassmi S, Verweij EJ, van Iterson M, Adama van Scheltema PN, Oepkes D, van Lith JM, Hoffer MJ, den Dunnen JT, Bakker E, Boon EM.
Clinical Chemistry

Profiling of short RNAs using Helicos single-molecule sequencing.
Kapranov P, Ozsolak F, Milos PM
Methods Molecular Biology

Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing.
Kapranov P, Chen L, Dederich D, Dong B, He J, Steinmann KE, Moore AR, Thompson JF, Milos PM, Xiao W.
Human Gene Therapy

Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations.
Thompson JF, Reifenberger JG, Giladi E, Kerouac K, Gill J, Hansen E, Kahvejian A, Kapranov P, Knope T, Lipson D, Steinmann KE, Milos PM.
Genome Research

5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary ​
Khare T, Pai S, Koncevicius K, Pal M, Kriukiene E,Liutkeviciute Z, Irimia M, Jia P, Ptak C, Xia M, Tice R, Tochigi M, Moréra S, Nazarians A, Belsham D, Wong AH, Blencowe BJ, Wang SC, Kapranov K, Kustra R, Labrie V, Klimasauskas S, and Petronis A
Nature Structural & Molecular Biology

Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts.
Magistri M, Faghihi MA, St Laurent G 3rd, Wahlestedt C
Trends Genetics

RNA Sequencing: Platform Selection, Experimental Design, and Data Interpretation
Chu Y, Corey D
Nucleic Acid Therapeutics

Transcriptional Response of Mucoid Pseudomonas aeruginosa to Human Respiratory Mucus
V. Cattoir, G. Narasimhan, D. Skurnik, H. Aschard, D. Roux, R. Ramphal, J. Jyot, S. Lory
mBio

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.
Sherstnev A, Duc C, Cole C, Zacharaki V, Hornyik C, Ozsolak F, Milos PM, Barton GJ, Simpson GG.
Nature Structural & Molecular Biology

Genome-wide identification and characterization of replication origins by deep sequencing
Xu J,Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z and Rhind N
Genome Biology
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​RNA sequencing of pancreatic circulating tumour cells implicates WNT signalling in metastasis
Yu M, Ting D, Stott S, Wittner B, Ozsolak F, Paul S, Ciciliano J, Smas M, Winokur D, Gilman A, Ulman M, Xega K, Contino G, Alagesan B, Brannigan B, Milos P, Ryan D, Sequist L, Bardeesy N, Ramaswamy S, Toner M, Maheswaran S , Haber D
Nature