Journal: PLoS ONE

Article Title: Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

doi: 10.1371/journal.pone.0019984

Figure Lengend Snippet: Summary of the assembly statistics of the simulated datasets.

Article Snippet: For instance, the 400 bp HC dataset produced 11.0 and 17.4 Mb of correctly annotated contigs assembled with Newbler and Celera respectively, while the 110 bp HChc dataset produced 171 Mbs and 275 Mbs (with SSAKE and VELVET respectively).

Techniques:

Journal: PLoS ONE

Article Title: Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

doi: 10.1371/journal.pone.0019984

Figure Lengend Snippet: (A) 400 bp and (B) 110 bp datasets respectively. N stands for Newbler, C for Celera Assembler, S for SSAKE and V for Velvet.

Article Snippet: For instance, the 400 bp HC dataset produced 11.0 and 17.4 Mb of correctly annotated contigs assembled with Newbler and Celera respectively, while the 110 bp HChc dataset produced 171 Mbs and 275 Mbs (with SSAKE and VELVET respectively).

Techniques:

Journal: PLoS ONE

Article Title: Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

doi: 10.1371/journal.pone.0019984

Figure Lengend Snippet: (A) Newbler (400 bp datasets) and (B) Velvet (110 bp datasets) assemblies.

Article Snippet: For instance, the 400 bp HC dataset produced 11.0 and 17.4 Mb of correctly annotated contigs assembled with Newbler and Celera respectively, while the 110 bp HChc dataset produced 171 Mbs and 275 Mbs (with SSAKE and VELVET respectively).

Techniques:

Journal: The Journal of Cell Biology

Article Title: D-Titin

doi:

Figure Lengend Snippet: D-Titin Gene and Protein Structure

Article Snippet: Our assembly of these contigs has been confirmed by Celera Genomics; D-Titin spans position 293742 through 182959 in Celera contig AE003473.1 ( ).

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Revealing the missing expressed genes beyond the human reference genome by RNA-Seq

doi: 10.1186/1471-2164-12-590

Figure Lengend Snippet: Overview of identification of the missing expressed genes beyond the human reference genome . Human brain and cell transcriptome sequencing reads were used to validate the transcribed regions in Asian and African novel sequences, quantify the expression of unalignable RefSeq genes and identify novel transcript contigs.

Article Snippet: Some of our identified novel transcript contigs could be found more than one match locations on HuRef or Celera genomes, indicating that those contigs might be caused by CNVs or were transcribed from the repetitive or homologous sequences.

Techniques: Sequencing, Expressing

Journal: BMC Genomics

Article Title: Revealing the missing expressed genes beyond the human reference genome by RNA-Seq

doi: 10.1186/1471-2164-12-590

Figure Lengend Snippet: Novel transcript contigs in brain and cell lines.

Article Snippet: Some of our identified novel transcript contigs could be found more than one match locations on HuRef or Celera genomes, indicating that those contigs might be caused by CNVs or were transcribed from the repetitive or homologous sequences.

Techniques:

Journal: BMC Genomics

Article Title: Revealing the missing expressed genes beyond the human reference genome by RNA-Seq

doi: 10.1186/1471-2164-12-590

Figure Lengend Snippet: The locations of seven conserved brain novel transcript contigs on GRCh37.

Article Snippet: Some of our identified novel transcript contigs could be found more than one match locations on HuRef or Celera genomes, indicating that those contigs might be caused by CNVs or were transcribed from the repetitive or homologous sequences.

Techniques:

Journal: BMC Genomics

Article Title: Revealing the missing expressed genes beyond the human reference genome by RNA-Seq

doi: 10.1186/1471-2164-12-590

Figure Lengend Snippet: RT-PCR validating of conserved novel transcript contigs . Six conserved novel transcript contigs were validated expressed in three different types of human normal cells. Because gene expression usually exhibit temporal and spatial specificity, not all those novel transcript contigs were validated in every type of normal human cells. MCF10A: normal human breast cell; hFOB: human fetal osteoblast; 293T: human embryonic kidney cell; β-ACTIN: positive control; Luciferase: negative control; Marker: sm0331 DNA Ladder Mix.

Article Snippet: Some of our identified novel transcript contigs could be found more than one match locations on HuRef or Celera genomes, indicating that those contigs might be caused by CNVs or were transcribed from the repetitive or homologous sequences.

Techniques: Reverse Transcription Polymerase Chain Reaction, Gene Expression, Positive Control, Luciferase, Negative Control, Marker