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Articles by Schäffer AA

Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models

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By Li XC, Schäffer AA, Rashidi Mehrabadi F, Crawford DR
| ncbi.nlm.nih.gov
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PSI-BLAST pseudocounts and the minimum description length principle

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By Altschul SF, Schäffer AA, Gertz EM, Yu YK
| ncbi.nlm.nih.gov
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Optimizing cancer immunotherapy response prediction by tumor aneuploidy score and fraction of copy number alterations

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By Schäffer AA, Chang TG, Shulman ED, Ben-David U
| ncbi.nlm.nih.gov
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Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers

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By Schäffer AA, Bhosale PG, Mahimkar MB
| ncbi.nlm.nih.gov
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Beyond Synthetic Lethality: Charting the Landscape of Pairwise Gene Expression States Associated with Survival in Cancer

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By Lee JS, Schäffer AA, Das Sahu A, Gutkind JS, Assaf Magen
| ncbi.nlm.nih.gov
doi: 10.1016/j.celrep.2019.06.067. Affiliations Affiliations 1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees

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By Altschul SF, Ahn TH, Madden TL, Schäffer AA
| PeerJ
Pathogenic bacteria represent a considerable danger for human health worldwide. For effective outbreak detection and epidemiological surveillance, bacterial pathogens must be rapidly identified. For this, the pathogen is usually isolated and various molecular typing methods used, most are based on polymerase chain reaction, or, in the last few years, whole-genome sequencing (WGS) (Inouye et al., 2014; Hasman et al., 2014).
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