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2021

ASHLEYS: automated quality control for single-cell Strand-seq data.
Eimer, C. and Sanders, A.D. and Korbel, J.O. and Marschall, T. and Ebert, P.
Bioinformatics : btab221. 1 April 2021 (In Press)

Construction of whole genomes from scaffolds using single cell strand-seq data.
Hills, M. and Falconer, E. and O'Neill, K. and Sanders, A.D. and Howe, K. and Guryev, V. and Lansdorp, P.M.
International Journal of Molecular Sciences 22 (7): 3617. 1 April 2021

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.
Porubsky, D. and Ebert, P. and Audano, P.A. and Vollger, M.R. and Harvey, W.T. and Marijon, P. and Ebler, J. and Munson, K.M. and Sorensen, M. and Sulovari, A. and Haukness, M. and Ghareghani, M. and Lansdorp, P.M. and Paten, B. and Devine, S.E. and Sanders, A.D. and Lee, C. and Chaisson, M.J.P. and Korbel, J.O. and Eichler, E.E. and Marschall, T.
Nature Biotechnology 39 (3): 302-308. March 2021

Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Ebert, P. and Audano, P. A. and Zhu, Q. and Rodriguez-Martin, B. and Porubsky, D. and Bonder, M.J. and Sulovari, A. and Ebler, J. and Zhou, W. and Serra Mari, R. and Yilmaz, F. and Zhao, X. and Hsieh, P.H. and Lee, J. and Kumar, S. and Lin, J. and Rausch, T. and Chen, Y. and Ren, J. and Santamarina, M. and Höps, W. and Ashraf, H. and Chuang, N.T. and Yang, X. and Munson, K.M. and Lewis, A.P. and Fairley, S. and Tallon, L.J. and Clarke, W.E. and Basile, A.O. and Byrska-Bishop, M. and Corvelo, A. and Evani, U.S. and Lu, T.Y. and Chaisson, M.J.P. and Chen, J. and Li, C. and Brand, H. and Wenger, A.M. and Ghareghani, M. and Harvey, W.T. and Raeder, B. and Hasenfeld, P. and Regier, A.A. and Abel, H.J. and Hall, I.M. and Flicek, P. and Stegle, O. and Gerstein, M.B and Tubio, J.M.C. and Mu, Z. and Li, Y.I. and Shi, X. and Hastie, A.R. and Ye, K. and Chong, Z. and Sanders, A.D. and Zody, M.C. and Talkowski, M.E. and Mills, R. E. and Devine, S.E. and Lee, C. and Korbel, J.O. and Marschall, T. and Eichler, E.E.
Science : eabf7117. 25 February 2021

2020

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.
Warren, W.C. and Harris, R.A. and Haukness, M. and Fiddes, I.T. and Murali, S.C. and Fernandes, J. and Dishuck, P.C. and Storer, J.M and Raveendran, M. and Hillier, L.W. and Porubsky, D. and Mao, Y. and Gordon, D. and Vollger, M.R. and Lewis, A.P. and Munson, K.M. and DeVogelaere, E. and Armstrong, J. and Diekhans, M. and Walker, J.A. and Tomlinson, C. and Graves-Lindsay, T.A. and Kremitzki, M. and Salama, S.R. and Audano, P.A. and Escalona, M. and Maurer, N.W. and Antonacci, F. and Mercuri, L. and Maggiolini, F.A.M. and Catacchio, C.R. and Underwood, J.G. and O'Connor, D.H. and Sanders, A.D. and Korbel, J.O. and Ferguson, B. and Kubisch, H.M. and Picker, L. and Kalin, N.H. and Rosene, D. and Levine, J. and Abbott, D.H. and Gray, S.B. and Sanchez, M.M. and Kovacs-Balint, Z.A. and Kemnitz, J.W. and Thomasy, S.M. and Roberts, J.A. and Kinnally, E.L. and Capitanio, J.P. and Skene, J.H.Pate and Platt, M. and Cole, S.A. and Green, R.E. and Ventura, M. and Wiseman, R.W. and Paten, B. and Batzer, M.A. and Rogers, J. and Eichler, E.E.
Science 370 (6523): eabc6617. 18 December 2020

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.
Maggiolini, F.A.M. and Sanders, A.D. and Shew, C.J. and Sulovari, A. and Mao, Y. and Puig, M. and Catacchio, C.R. and Dellino, M. and Palmisano, D. and Mercuri, L. and Bitonto, M. and Porubský, D. and Cáceres, M. and Eichler, E.E. and Ventura, M. and Dennis, M.Y. and Korbel, J.O. and Antonacci, F.
Genome Research 30 (11): 1680-1693. November 2020

Recurrent inversion toggling and great ape genome evolution.
Porubsky, D. and Sanders, A.D. and Höps, W. and Hsieh, P. and Sulovari, A. and Li, R. and Mercuri, L. and Sorensen, M. and Murali, S.C. and Gordon, D. and Cantsilieris, S. and Pollen, A.A. and Ventura, M. and Antonacci, F. and Marschall, T. and Korbel, J.O. and Eichler, E.E.
Nature Genetics 52 (8): 849-858. August 2020

Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads.
Vollger, M.R. and Logsdon, G.A. and Audano, P.A. and Sulovari, A. and Porubsky, D. and Peluso, P. and Wenger, A.M. and Concepcion, G.T. and Kronenberg, Z.N. and Munson, K.M. and Baker, C. and Sanders, A.D. and Spierings, D.C.J. and Lansdorp, P.M. and Surti, U. and Hunkapiller, M.W. and Eichler, E.E.
Annals of Human Genetics 84 (2): 125-140. March 2020

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.
Sanders, A.D. and Meiers, S. and Ghareghani, M. and Porubsky, D. and Jeong, H. and van Vliet, M.A.C.C. and Rausch, T. and Richter-Pechańska, P. and Kunz, J.B. and Jenni, S. and Bolognini, D. and Longo, G.M.C. and Raeder, B. and Kinanen, V. and Zimmermann, J. and Benes, V. and Schrappe, M. and Mardin, B.R. and Kulozik, A.E. and Bornhauser, B. and Bourquin, J.P. and Marschall, T. and Korbel, J.O.
Nature Biotechnology 38 (3): 343-354. March 2020

VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing.
Bolognini, D. and Sanders, A. and Korbel, J.O. and Magi, A. and Benes, V. and Rausch, T.
Bioinformatics 36 (4): 1267-1269. 15 February 2020

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data.
Porubsky, D. and Sanders, A.D. and Taudt, A. and Colomé-Tatché, M. and Lansdorp, P.M. and Guryev, V.
Bioinformatics 36 (4): 1260-1261. 15 February 2020

The effects of common structural variants on 3D chromatin structure.
Shanta, O. and Noor, A. and Sebat, J.
BMC Genomics 21 (1): 95. 30 January 2020

2019

A fully phased accurate assembly of an individual human genome.
Porubsky, D. and Ebert, P. and Audano, P.A. and Vollger, M.R. and Harvey, W.T. and Munson, K.M. and Sorensen, M. and Sulovari, A. and Haukness, M. and Ghareghani, M. and Lansdorp, P.M. and Paten, B. and Devine, S.E. and Sanders, A.D. and Lee, C. and Chaisson, M.J.P. and Korbel, J.O. and Eichler, E.E. and Marschall, T.
bioRxiv : 855049. 26 November 2019

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes.
Sanders, A.D. and Meiers, S. and Ghareghani, M. and Porubsky, D. and Jeong, H. and van Vliet, M.A.C.C. and Rausch, T. and Richter-Pechańska, P. and Kunz, J.B. and Jenni, S. and Raeder, B. and Kinanen, V. and Zimmermann, J. and Benes, V. and Schrappe, M. and Mardin, B.R. and Kulozik, A. and Bornhauser, B. and Bourquin, J.P. and Marschall, T. and Korbel, J.O.
bioRxiv : 849604. 21 November 2019

Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Chaisson, M.J.P. and Sanders, A.D. and Zhao, X. and Malhotra, A. and Porubsky, D. and Rausch, T. and Gardner, E.J. and Rodriguez, O.L. and Guo, L. and Collins, R.L. and Fan, X. and Wen, J. and Handsaker, R.E. and Fairley, S. and Kronenberg, Z.N. and Kong, X. and Hormozdiari, F. and Lee, D. and Wenger, A.M. and Hastie, A.R. and Antaki, D. and Anantharaman, T. and Audano, P.A. and Brand, H. and Cantsilieris, S. and Cao, H. and Cerveira, E. and Chen, C. and Chen, X. and Chin, C.S. and Chong, Z. and Chuang, N.T. and Lambert, C.C. and Church, D.M. and Clarke, L. and Farrell, A. and Flores, J. and Galeev, T. and Gorkin, D.U. and Gujral, M. and Guryev, V. and Heaton, W.H. and Korlach, J. and Kumar, S. and Kwon, J.Y. and Lam, E.T. and Lee, J.E. and Lee, J. and Lee, W.P. and Lee, S.P. and Li, S. and Marks, P. and Viaud-Martinez, K. and Meiers, S. and Munson, K.M. and Navarro, F.C.P. and Nelson, B.J. and Nodzak, C. and Noor, A. and Kyriazopoulou-Panagiotopoulou, S. and Pang, A.W.C. and Qiu, Y. and Rosanio, G. and Ryan, M. and Stütz, A. and Spierings, D.C.J. and Ward, A. and Welch, A.E. and Xiao, M. and Xu, W. and Zhang, C. and Zhu, Q. and Zheng-Bradley, X. and Lowy, E. and Yakneen, S. and McCarroll, S. and Jun, G. and Ding, L. and Koh, C.L. and Ren, B. and Flicek, P. and Chen, K. and Gerstein, M.B. and Kwok, P.Y. and Lansdorp, P.M. and Marth, G.T. and Sebat, J. and Shi, X. and Bashir, A. and Ye, K. and Devine, S.E. and Talkowski, M.E. and Mills, R.E. and Marschall, T. and Korbel, J.O. and Eichler, E.E. and Lee, C.
Nature Communications 10 (1): 1784. 16 April 2019

Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus.
Maggiolini, F.A.M. and Cantsilieris, S. and D'Addabbo, P. and Manganelli, M. and Coe, B.P. and Dumont, B.L. and Sanders, A.D. and Pang, A.W.C. and Vollger, M.R. and Palumbo, O. and Palumbo, P. and Accadia, M. and Carella, M. and Eichler, E.E. and Antonacci, F.
PLoS Genetics 15 (3): e1008075. 27 March 2019

2018

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization.
Ghareghani, M. and Porubskỳ, D. and Sanders, A.D. and Meiers, S. and Eichler, E.E. and Korbel, J.O. and Marschall, T.
Bioinformatics 34 (13): i115-i123. 1 July 2018

Construction of whole genomes from scaffolds using single cell strand-seq data.
Hills, M. and Falconer, E. and O’Neil, K. and Sanders, A.D. and Howe, K. and Guryev, V. and Lansdorp, P.M.
bioRxiv : 271510. 26 February 2018

Computational pan-genomics: status, promises and challenges.

Briefings in Bioinformatics 19 (1): 118-135. January 2018

2017

Dense and accurate whole-chromosome haplotyping of individual genomes.
Porubsky, D. and Garg, S. and Sanders, A.D. and Korbel, J.O. and Guryev, V. and Lansdorp, P.M. and Marschall, T.
Nature Communications 8 (1): 1293. 3 November 2017

Single-cell template strand sequencing by strand-seq enables the characterization of individual homologs.
Sanders, A.D. and Falconer, E. and Hills, M. and Spierings, D.C.J. and Lansdorp, P.M.
Nature Protocols 12 (6): 1151-1176. June 2017

2016

Characterizing polymorphic inversions in human genomes by single-cell sequencing.
Sanders, A.D. and Hills, M. and Porubský, D. and Guryev, V. and Falconer, E. and Lansdorp, P.M.
Genome Research 26 (11): 1575-1587. November 2016

Direct chromosome-length haplotyping by single-cell sequencing.
Porubský, D. and Sanders, A.D. and van Wietmarschen, N. and Falconer, E. and Hills, M. and Spierings, D.C.J. and Bevova, M.R. and Guryev, V. and Lansdorp, P.M.
Genome Research 26 (11): 1565-1574. November 2016

2015

The prognostic impact of CD163-positive macrophages in follicular lymphoma: a study from the BC Cancer Agency and the Lymphoma Study Association.
Kridel, R. and Xerri, L. and Gelas-Dore, B. and Tan, K. and Feugier, P. and Vawda, A. and Canioni, D. and Farinha, P. and Boussetta, S. and Moccia, A.A. and Brice, P. and Chavez, E.A. and Kyle, A.H. and Scott, D.W. and Sanders, A.D. and Fabiani, B. and Slack, G.W. and Minchinton, A.I. and Haioun, C. and Connors, J.M. and Sehn, L.H. and Steidl, C. and Gascoyne, R.D. and Salles, G.
Clinical Cancer Research 21 (15): 3428-3435. August 2015

2012

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.
Falconer, E. and Hills, M. and Naumann, U. and Poon, S.S.S. and Chavez, E.A. and Sanders, A.D. and Zhao, Y. and Hirst, M. and Lansdorp, P.M.
Nature Methods 9 (11): 1107-1112. November 2012

2011

Adult spinal cord radial glia display a unique progenitor phenotype.
Petit, A. and Sanders, A.D. and Kennedy, T.E. and Tetzlaff, W. and Glattfelder, K.J. and Dalley, R.A. and Puchalski, R.B. and Jones, A.R. and Roskams, A.J.
PLoS ONE 6 (9): e24538. 12 September 2011

Essential role for Ptpn11 in survival of hematopoietic stem and progenitor cells.
Chan, G. and Cheung, L.S. and Yang, W. and Milyavsky, M. and Sanders, A.D. and Gu, S. and Hong, W.X. and Liu, A.X. and Wang, X. and Barbara, M. and Sharma, T. and Gavin, J. and Kutok, J.L. and Iscove, N.N. and Shannon, K.M. and Dick, J.E. and Neel, B.G. and Braun, B.S.
Blood 117 (16): 4253-4261. 21 April 2011

This list was generated on Fri Sep 17 02:22:11 2021 CEST.
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