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Items: 15

1.

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing.

Laks E, McPherson A, Zahn H, Lai D, Steif A, Brimhall J, Biele J, Wang B, Masud T, Ting J, Grewal D, Nielsen C, Leung S, Bojilova V, Smith M, Golovko O, Poon S, Eirew P, Kabeer F, Ruiz de Algara T, Lee SR, Taghiyar MJ, Huebner C, Ngo J, Chan T, Vatrt-Watts S, Walters P, Abrar N, Chan S, Wiens M, Martin L, Scott RW, Underhill TM, Chavez E, Steidl C, Da Costa D, Ma Y, Coope RJN, Corbett R, Pleasance S, Moore R, Mungall AJ, Mar C, Cafferty F, Gelmon K, Chia S; CRUK IMAXT Grand Challenge Team, Marra MA, Hansen C, Shah SP, Aparicio S.

Cell. 2019 Nov 14;179(5):1207-1221.e22. doi: 10.1016/j.cell.2019.10.026.

PMID:
31730858
2.

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses.

O'Flanagan CH, Campbell KR, Zhang AW, Kabeer F, Lim JLP, Biele J, Eirew P, Lai D, McPherson A, Kong E, Bates C, Borkowski K, Wiens M, Hewitson B, Hopkins J, Pham J, Ceglia N, Moore R, Mungall AJ, McAlpine JN; CRUK IMAXT Grand Challenge Team, Shah SP, Aparicio S.

Genome Biol. 2019 Oct 17;20(1):210. doi: 10.1186/s13059-019-1830-0.

3.

Images from the surface of asteroid Ryugu show rocks similar to carbonaceous chondrite meteorites.

Jaumann R, Schmitz N, Ho TM, Schröder SE, Otto KA, Stephan K, Elgner S, Krohn K, Preusker F, Scholten F, Biele J, Ulamec S, Krause C, Sugita S, Matz KD, Roatsch T, Parekh R, Mottola S, Grott M, Michel P, Trauthan F, Koncz A, Michaelis H, Lange C, Grundmann JT, Maibaum M, Sasaki K, Wolff F, Reill J, Moussi-Soffys A, Lorda L, Neumann W, Vincent JB, Wagner R, Bibring JP, Kameda S, Yano H, Watanabe S, Yoshikawa M, Tsuda Y, Okada T, Yoshimitsu T, Mimasu Y, Saiki T, Yabuta H, Rauer H, Honda R, Morota T, Yokota Y, Kouyama T.

Science. 2019 Aug 23;365(6455):817-820. doi: 10.1126/science.aaw8627.

PMID:
31439797
4.

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers.

Campbell KR, Steif A, Laks E, Zahn H, Lai D, McPherson A, Farahani H, Kabeer F, O'Flanagan C, Biele J, Brimhall J, Wang B, Walters P, Consortium I, Bouchard-Côté A, Aparicio S, Shah SP.

Genome Biol. 2019 Mar 12;20(1):54. doi: 10.1186/s13059-019-1645-z.

5.

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

Leung K, Klaus A, Lin BK, Laks E, Biele J, Lai D, Bashashati A, Huang YF, Aniba R, Moksa M, Steif A, Mes-Masson AM, Hirst M, Shah SP, Aparicio S, Hansen CL.

Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):8484-9. doi: 10.1073/pnas.1520964113. Epub 2016 Jul 13.

6.

Clonal genotype and population structure inference from single-cell tumor sequencing.

Roth A, McPherson A, Laks E, Biele J, Yap D, Wan A, Smith MA, Nielsen CB, McAlpine JN, Aparicio S, Bouchard-Côté A, Shah SP.

Nat Methods. 2016 Jul;13(7):573-6. doi: 10.1038/nmeth.3867. Epub 2016 May 16.

PMID:
27183439
7.

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

McPherson A, Roth A, Laks E, Masud T, Bashashati A, Zhang AW, Ha G, Biele J, Yap D, Wan A, Prentice LM, Khattra J, Smith MA, Nielsen CB, Mullaly SC, Kalloger S, Karnezis A, Shumansky K, Siu C, Rosner J, Chan HL, Ho J, Melnyk N, Senz J, Yang W, Moore R, Mungall AJ, Marra MA, Bouchard-Côté A, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP.

Nat Genet. 2016 Jul;48(7):758-67. doi: 10.1038/ng.3573. Epub 2016 May 16.

PMID:
27182968
8.

COMETARY SCIENCE. The landing(s) of Philae and inferences about comet surface mechanical properties.

Biele J, Ulamec S, Maibaum M, Roll R, Witte L, Jurado E, Muñoz P, Arnold W, Auster HU, Casas C, Faber C, Fantinati C, Finke F, Fischer HH, Geurts K, Güttler C, Heinisch P, Herique A, Hviid S, Kargl G, Knapmeyer M, Knollenberg J, Kofman W, Kömle N, Kührt E, Lommatsch V, Mottola S, Pardo de Santayana R, Remetean E, Scholten F, Seidensticker KJ, Sierks H, Spohn T.

Science. 2015 Jul 31;349(6247):aaa9816. doi: 10.1126/science.aaa9816.

9.

Philae's first look. Philae's First Days on the Comet. Introduction.

Bibring JP, Taylor MG, Alexander C, Auster U, Biele J, Finzi AE, Goesmann F, Klingelhoefer G, Kofman W, Mottola S, Seidensticker KJ, Spohn T, Wright I.

Science. 2015 Jul 31;349(6247):493. doi: 10.1126/science.aac5116. Epub 2015 Jul 30. No abstract available.

PMID:
26228139
10.

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.

Eirew P, Steif A, Khattra J, Ha G, Yap D, Farahani H, Gelmon K, Chia S, Mar C, Wan A, Laks E, Biele J, Shumansky K, Rosner J, McPherson A, Nielsen C, Roth AJ, Lefebvre C, Bashashati A, de Souza C, Siu C, Aniba R, Brimhall J, Oloumi A, Osako T, Bruna A, Sandoval JL, Algara T, Greenwood W, Leung K, Cheng H, Xue H, Wang Y, Lin D, Mungall AJ, Moore R, Zhao Y, Lorette J, Nguyen L, Huntsman D, Eaves CJ, Hansen C, Marra MA, Caldas C, Shah SP, Aparicio S.

Nature. 2015 Feb 19;518(7539):422-6. doi: 10.1038/nature13952. Epub 2014 Nov 26.

11.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.

Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, Melnyk N, McPherson A, Bashashati A, Laks E, Biele J, Ding J, Le A, Rosner J, Shumansky K, Marra MA, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP.

Genome Res. 2014 Nov;24(11):1881-93. doi: 10.1101/gr.180281.114. Epub 2014 Jul 24.

12.

PyClone: statistical inference of clonal population structure in cancer.

Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, Ha G, Aparicio S, Bouchard-Côté A, Shah SP.

Nat Methods. 2014 Apr;11(4):396-8. doi: 10.1038/nmeth.2883. Epub 2014 Mar 16.

13.

Fibrinogen genes and myocardial infarction: a haplotype analysis.

Koch W, Hoppmann P, Biele J, Mueller JC, Schömig A, Kastrati A.

Arterioscler Thromb Vasc Biol. 2008 Apr;28(4):758-63. doi: 10.1161/ATVBAHA.107.157842. Epub 2008 Jan 17.

PMID:
18202324
14.

Polarization Lidar: Correction of instrumental effects.

Biele J, Beyerle G, Baumgarten G.

Opt Express. 2000 Dec 4;7(12):427-35.

PMID:
19407894
15.

A sample-size-optimal Bayesian procedure for sequential pharmaceutical trials.

Cressie N, Biele J.

Biometrics. 1994 Sep;50(3):700-11.

PMID:
7981396

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