Dongxiao Zhu
Tin Nguyen

Guorong Xu
Nan Deng
Kristen Johnson
Zhiyu Zhao

Getting help

If you have questions and comments, please joint  SAMMate Group or email to

News and updates

5/11/2013 assemblySAM 1.1 is released.

11/10/2012 SAMMate 2.7.4 is released.

10/10/2012 SAMMate 2.7.3 is released.

8/9/2012 SAMMate 2.7.2 is released.

Selected SAMMate User Publications

Piazza, Rocco, et al. "Recurrent SETBP1 mutations in atypical chronic myeloid leukemia." Nature genetics 45.1 (2012): 18-24.

Ferrari, Roberto, et al. "Reorganization of the host epigenome by a viral oncogene." Genome Research 22.7 (2012): 1212-1221.

Routh, Andrew, Tatiana Domitrovic, and John E. Johnson. "Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus." Proceedings of the National Academy of Sciences 109.6 (2012): 1907-1912.

SAMMate Publications:

Nguyen T, Deng N and Zhu D: SASeq: A Selective and Adaptive Shrinkage Approach to Detect and Quantify Active Transcripts using RNA-Seq. Submitted.

Zhao Z, Nguyen T, Deng N, Johnson K, Zhu D: SPATA: A Seeding and Patching Algorithm for de novo Transcriptome Assembly.
Bioinformatics & Biomedicine Workshops, 2011 IEEE International Conference.

Xu G, Deng N, Zhao Z, Flemington E, Zhu D. (2011) SAMMate: A GUI tool for processing short read alignment information in SAM/BAM format. Source Code for Biology and Medicine.

Deng N, Puetter A, Zhang K, Johnson K, Zhao Z, Taylor C, Flemington E and Zhu D (2011) Isoform-level microRNA-155 Target Prediction using RNA-seq. Nucleic Acid Research.