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The SEQC2 epigenomi...
The SEQC2 epigenomics quality control (EpiQC) study
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- Foox, Jonathan (författare)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10021 USA.
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- Nordlund, Jessica (författare)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands
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- Lalancette, Claudia (författare)
- Univ Michigan Med, BRCF Epigen Core, Ann Arbor, MI 48109 USA.
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visa fler...
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- Gong, Ting (författare)
- Univ Hawaii, Dept Quantitat Hlth Sci, John A Burns Sch Med, Honolulu, HI 96813 USA.
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- Lacey, Michelle (författare)
- Tulane Univ, New Orleans, LA 70118 USA.
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- Lent, Samantha (författare)
- AbbVie Genom Res Ctr, 1 N Waukegan Rd, N Chicago, IL 60036 USA.
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- Langhorst, Bradley W. (författare)
- New England Biolabs Inc, Ipswich, MA 01938 USA.
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- Ponnaluri, V. K. Chaithanya (författare)
- New England Biolabs Inc, Ipswich, MA 01938 USA.
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- Williams, Louise (författare)
- New England Biolabs Inc, Ipswich, MA 01938 USA.
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- Padmanabhan, Karthik Ramaswamy (författare)
- Univ Michigan Med, BRCF Epigen Core, Ann Arbor, MI 48109 USA.
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- Cavalcante, Raymond (författare)
- Univ Michigan Med, BRCF Epigen Core, Ann Arbor, MI 48109 USA.
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- Lundmark, Anders (författare)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands
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- Butler, Daniel (författare)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.
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- Mozsary, Christopher (författare)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.
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- Gurvitch, Justin (författare)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.
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- Greally, John M. (författare)
- Albert Einstein Coll Med, Bronx, NY 10461 USA.
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- Suzuki, Masako (författare)
- Albert Einstein Coll Med, Bronx, NY 10461 USA.
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- Menor, Mark (författare)
- Univ Hawaii, Dept Quantitat Hlth Sci, John A Burns Sch Med, Honolulu, HI 96813 USA.
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- Nasu, Masaki (författare)
- Univ Hawaii, Dept Quantitat Hlth Sci, John A Burns Sch Med, Honolulu, HI 96813 USA.
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- Alonso, Alicia (författare)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.
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- Sheridan, Caroline (författare)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.;Weill Cornell Med, Div Hematol Oncol, Dept Med, Epigen Core Facil, New York, NY USA.
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- Scherer, Andreas (författare)
- EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands.;Univ Helsinki, Inst Mol Med Finland FIMM, Helsinki, Finland.
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- Bruinsma, Stephen (författare)
- Illumina Inc, Madison, WI 53705 USA.
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- Golda, Gosia (författare)
- Jagiellonian Univ, Fac Biochem Biophys & Biotechnol, Krakow, Poland.
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- Muszynska, Agata (författare)
- Jagiellonian Univ, Malopolska Ctr Biotechnol, Krakow, Poland.
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- Labaj, Pawel P. (författare)
- Jagiellonian Univ, Malopolska Ctr Biotechnol, Krakow, Poland.
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- Campbell, Matthew A. (författare)
- New England Biolabs Inc, Ipswich, MA 01938 USA.
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- Wos, Frank (författare)
- New York Genome Ctr, New York, NY 10013 USA.
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- Raine, Amanda (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för medicinska vetenskaper,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands
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- Liljedahl, Ulrika (författare)
- Uppsala universitet,Institutionen för medicinska vetenskaper,Science for Life Laboratory, SciLifeLab,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands
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- Axelsson, Tomas (författare)
- Uppsala universitet,Institutionen för medicinska vetenskaper,Science for Life Laboratory, SciLifeLab,EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands
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- Wang, Charles (författare)
- Loma Linda Univ, Ctr Genom, Sch Med, Loma Linda, CA 92350 USA.
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- Chen, Zhong (författare)
- Loma Linda Univ, Ctr Genom, Sch Med, Loma Linda, CA 92350 USA.
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- Yang, Zhaowei (författare)
- Loma Linda Univ, Ctr Genom, Sch Med, Loma Linda, CA 92350 USA.;Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Dept Allergy & Clin Immunol, State Key Lab Resp Dis,Affiliated Hosp 1, Guangzhou, Peoples R China.
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- Li, Jing (författare)
- Loma Linda Univ, Ctr Genom, Sch Med, Loma Linda, CA 92350 USA.;Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Dept Allergy & Clin Immunol, State Key Lab Resp Dis,Affiliated Hosp 1, Guangzhou, Peoples R China.
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- Yang, Xiaopeng (författare)
- Zhengzhou Univ, Dept Neurol, Affiliated Hosp 2, Zhengzhou 450014, Peoples R China.
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- Wang, Hongwei (författare)
- Univ Chicago, Dev Med, Chicago, IL 60637 USA.
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- Melnick, Ari (författare)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.
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- Guo, Shang (författare)
- Zhengzhou Univ, Affiliated Hosp 2, Shanghai 200233, Peoples R China.
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- Blume, Alexander (författare)
- Max Delbrueck Ctr Mol Med, Berlin Inst Med Syst Biol, Bioinformat & Omics Data Sci Platform, Berlin, Germany.
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- Franke, Vedran (författare)
- Max Delbrueck Ctr Mol Med, Berlin Inst Med Syst Biol, Bioinformat & Omics Data Sci Platform, Berlin, Germany.
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- Ibanez de Caceres, Inmaculada (författare)
- EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands.;IdiPAZ, Canc Epigenet Lab, INGEMM, Madrid, Spain.
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- Rodriguez-Antolin, Carlos (författare)
- EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands.;IdiPAZ, Canc Epigenet Lab, INGEMM, Madrid, Spain.
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- Rosas, Rocio (författare)
- EATRIS ERIC European Infrastruct Translat Med, De Boelelaan 1118, NL-1081 HZ Amsterdam, Netherlands.;IdiPAZ, Canc Epigenet Lab, INGEMM, Madrid, Spain.
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- Davis, Justin Wade (författare)
- AbbVie Genom Res Ctr, 1 N Waukegan Rd, N Chicago, IL 60036 USA.
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- Ishii, Jennifer (författare)
- New York Genome Ctr, New York, NY 10013 USA.
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- Megherbi, Dalila B. (författare)
- Univ Massachusetts Lowell, Francis Coll Engn, CMINDS Res Ctr, Lowell, MA 01854 USA.
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- Xiao, Wenming (författare)
- US FDA, Ctr Devices & Radiol Hlth, 10903 New Hampshire Ave, Silver Spring, MD 20993 USA.
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- Liao, Will (författare)
- New York Genome Ctr, New York, NY 10013 USA.
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- Xu, Joshua (författare)
- US FDA, Div Bioinformat & Biostat, Natl Ctr Toxicol Res, 3900 NCTR Rd, Jefferson, AR 72079 USA.
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- Hong, Huixiao (författare)
- US FDA, Div Bioinformat & Biostat, Natl Ctr Toxicol Res, 3900 NCTR Rd, Jefferson, AR 72079 USA.
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- Ning, Baitang (författare)
- US FDA, Div Bioinformat & Biostat, Natl Ctr Toxicol Res, 3900 NCTR Rd, Jefferson, AR 72079 USA.
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- Tong, Weida (författare)
- US FDA, Div Bioinformat & Biostat, Natl Ctr Toxicol Res, 3900 NCTR Rd, Jefferson, AR 72079 USA.
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- Akalin, Altuna (författare)
- Max Delbrueck Ctr Mol Med, Berlin Inst Med Syst Biol, Bioinformat & Omics Data Sci Platform, Berlin, Germany.
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- Wang, Yunliang (författare)
- Zhengzhou Univ, Affiliated Hosp 2, Shanghai 200233, Peoples R China.
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- Deng, Youping (författare)
- Univ Hawaii, Dept Quantitat Hlth Sci, John A Burns Sch Med, Honolulu, HI 96813 USA.
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- Mason, Christopher E. (författare)
- Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA.;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10021 USA.;Feil Family Brain & Mind Res Inst, New York, NY 10065 USA.;Weill Cornell Med, WorldQuant Initiat Quantitat Predict, New York, NY 10021 USA.
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Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10021 USA;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10021 USA. Molekylär medicin (creator_code:org_t)
- 2021-12-06
- 2021
- Engelska.
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://genomebiolog...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- BackgroundCytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group.ResultsEach sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.ConclusionsThe data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
Ämnesord
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
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Foox, Jonathan
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Nordlund, Jessic ...
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Lalancette, Clau ...
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Gong, Ting
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Lacey, Michelle
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Lent, Samantha
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visa fler...
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Langhorst, Bradl ...
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Ponnaluri, V. K. ...
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Williams, Louise
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Padmanabhan, Kar ...
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Cavalcante, Raym ...
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Lundmark, Anders
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Butler, Daniel
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Mozsary, Christo ...
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Gurvitch, Justin
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Greally, John M.
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Suzuki, Masako
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Menor, Mark
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Nasu, Masaki
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Alonso, Alicia
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Sheridan, Caroli ...
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Scherer, Andreas
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Bruinsma, Stephe ...
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Golda, Gosia
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Muszynska, Agata
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Labaj, Pawel P.
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Campbell, Matthe ...
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Wos, Frank
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Raine, Amanda
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Liljedahl, Ulrik ...
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Axelsson, Tomas
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Wang, Charles
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Chen, Zhong
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Yang, Zhaowei
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Li, Jing
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Yang, Xiaopeng
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Wang, Hongwei
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Melnick, Ari
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Guo, Shang
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Blume, Alexander
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Franke, Vedran
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Ibanez de Cacere ...
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Rodriguez-Antoli ...
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Rosas, Rocio
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Davis, Justin Wa ...
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Ishii, Jennifer
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Megherbi, Dalila ...
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Xiao, Wenming
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Liao, Will
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Xu, Joshua
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Hong, Huixiao
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Ning, Baitang
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Tong, Weida
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Akalin, Altuna
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Wang, Yunliang
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Deng, Youping
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Mason, Christoph ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Genetik
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Genome Biology
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Uppsala universitet