Publications

My publication list is available through my Google Scholar public profile. Below you'll find a list of my papers, pre-prints, presentations and posters in reverse chronological order.

Papers

  1. Jaffe AE, Shin J, Collado-Torres L, Leek JT, et al. Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nat. Neurosci. (2014). doi:10.1038/nn.3898. PDF (English)
  2. Shank EA, Klepac-Ceraj V, Collado-Torres L, Powers GE, Losick R, Kolter R. Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc. Natl. Acad. Sci. U.S.A. 2011 Nov;108(48):E1236–1243. PDF (English)
  3. Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J. RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res. 2011 Jan;39(Database issue):D98–105. PDF (English)

Pre-prints

  1. Collado-Torres L, Frazee AC, Love MI, Irizarry RA, Jaffe AE, Leek JT. derfinder: Software for annotation-agnostic RNA-seq differential expression analysis. bioRxiv 015370 (2015). doi:10.1101/015370. PDF (English)

Books

  1. Frazee AC, Collado-Torres L, Jaffe AE, Langmead B, Leek JT. Measurement, Summary, and Methodological Variation in RNA-sequencing in Statistical Analysis of Next Generation Sequencing Data, Springer, 2014, 115-128,.

Presentations

  1. Does mapping simulated RNA-seq reads provide information? at Joint Genomics Meeting, February 2015.
  2. derfinder tutorial for Leek group meeting, December 2014, live via GitHub here (English).
  3. Developmental regulation of human cortex transcription at base-pair resolution at the 1st International Summer Symposium on Systems Biology at INMEGEN, Mexico. August 2014.
  4. Introduction to ggbio for the Genomics for students group. View here via RPubs (English).
  5. Fast differential expression analysis annotation-agnostic across groups with biological replicates at Biostatistics Journal Club and Joint Genomics Meeting, October 2013. Also at LCG 10 year anniversary symposium, January 2014.
  6. Differential expression analysis of RNA-seq data at base-pair resolution in multiple biological replicates at useR2013, Albacete, Spain.
  7. Introduction to knitr for the Biostatistics computing club. It's live via GitHub pages here (English).
  8. Introduction to High-Throughput Sequencing and RNA-seq for the Genomics for students working group. PDF (English)
  9. DEXSeq paper discussion for the Genomics for students working group. PDF (English)
  10. Introduction to R and Biostatistics (2012 version). I described this presentation in detail in this post (English).
  11. Introducing Git while making your academic webpage for the Biostatistics computing club. The presentation itself is available via Bitbucket PDF (English). I described it in this post (English).
  12. Introducing Biostatistics to first year LCG students as an invited speaker for the Bioinformatics Seminar series 2011 course for LCG students. I wrote a post about this talk at my blog. PDF R Rnw ()
  13. Bacterial Transcription at Bioconductor Developer Meeting Europe 2010. PDF (English)
  14. Introduction to using Bioconductor for High Throughput Sequencing Analysis at the National Bioinformatics Week 2010 hosted by the Center for Genomic Sciences (UNAM). PDF R code (English)
  15. Bacteriófagos: analizando su diversidad (Bacteriophages: analyzing their diversity) at the LCG third generation symphosium. PPT (Spanish)

Posters

  1. Fast Annotation-Agnostic Differential Expression Analysis at Genomics and Bioinformatics Symposium 2013 (Hopkins) and ENAR 2014.
  2. Updated version of Global Analysis of Transcription Start Sites and Transcription Units in Bacterial Genomes at EMBO Conference Series From Functional Genomics to Systems Biology 2010. PDF (English)
  3. Global Analysis of Transcription Start Sites (TSSs) and Transcription Units (TUs) in Bacterial Genomes at BioC2010. PDF (English)

Spanish = material in Spanish. English = material in English.

Contact

  • Address: 615 N. Wolfe Street, Room E3032, Baltimore MD 21205-2179, United States
  • Office Phone: (410) 614 - 5424. It is best to contact me by email!
  • Email: lcollado ^^ jhu DOT edu
  • Fax: (410) 955 - 0958.
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