Teaching Materials

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62 Comments

  1. Posted February 16, 2014 at 3:36 pm | Permalink

    Ben – Thanks for the great illustrations in your BWT/FM and assembly slides. We are using them in my graduate subject at MIT. Job well done! David Gifford

  2. Rob Patro
    Posted August 25, 2014 at 2:15 pm | Permalink

    Hi Ben, I’m using some of these slides in the Comp. Bio. course here at Stony Brook. Thanks for providing this resource; it’s really useful!

  3. Jian Ma
    Posted September 4, 2014 at 11:21 pm | Permalink

    Hi Ben – I am using some of your slides in my computational genomics class at the University of Illinois at Urbana-Champaign. Thank you very much for the great resource! — Jian Ma

  4. Outi Sasvolainen
    Posted September 25, 2014 at 2:18 am | Permalink

    I have used some slides for an avolutionary genomics and genomics method class – thanks a lot!

  5. Posted October 8, 2014 at 3:11 pm | Permalink

    Thanks so much for making this material available. I made use of the De Bruijn Graph code to have students interactively explore small De Bruijn Graphs, see https://github.com/lexnederbragt/INF-BIOx121_fall2014_de_novo_assembly under ‘practicals’

  6. Posted October 21, 2014 at 10:15 am | Permalink

    Great slides, thanks for making them available. I am using some of the assembly slides in a genome assembly workshop organized by the informatics group in Research Computing at Harvard.

  7. Posted November 3, 2014 at 9:36 pm | Permalink

    Hi Ben — thanks for the slides (and for TopHat). I’m using the de Bruijn graph slides for an Intro to Comp Bio course for CS undergraduates.

  8. Jonathan Flowers
    Posted November 8, 2014 at 1:24 pm | Permalink

    Thanks for posting teaching materials Ben. I am using some of your slides in an applied genomics course at New York University

  9. Posted November 10, 2014 at 3:47 am | Permalink

    Hi Ben, I’m using some of your slides in a a viral biodiversity course here at University of Brasilia- Brazil. Thanks for sharing your teaching material. Fernando

  10. Posted November 18, 2014 at 12:44 am | Permalink

    Thanks so much for making this material public! I have adapted much of the material on the BW transform and the FM index (which you present in an incredibly lucid way!) for a lecture in my Genomics course at the Free University Berlin.

  11. Posted November 20, 2014 at 10:54 am | Permalink

    Thank you for your material!! I plan to use some of your slides for a part of the course Programming for Bioinformatics at University of Bologna.

  12. Will
    Posted January 18, 2015 at 9:29 pm | Permalink

    Thank you for making your slides available Professor Langmead. Best concise description of de Bruijn graph assembly I have found. I am using them to develop an understanding of genome assemblers for a rotation project at Stanford.

  13. Dr. Qaiser
    Posted January 31, 2015 at 3:28 pm | Permalink

    I have found your lecture slides on the topic Edit Distance useful and decided to use it, partially or fully. I hope that the rest of the material on this page is also useful. Thank you so much for such a nice platform for the subject of algorithms. I am going to use this lecture during a course “Advance Analysis of Algorithms” at graduate level at University of Sargodha, Pakistan.

  14. Carl Vangestel
    Posted February 27, 2015 at 6:11 am | Permalink

    Hi Ben,
    just downloaded them for personal use. Brilliant talk on FM and BWT!!

  15. Jeanne W
    Posted March 23, 2015 at 11:46 am | Permalink

    Hi, I used the De Bruin Graph Assembly presentation to help me understand the algorithm in my research. Thank you!

  16. Susan Van Riper
    Posted March 29, 2015 at 4:07 pm | Permalink

    Thank you for providing such a wonderful resource! I am using your some of your lecture slides on de Bruijn Graph assembly in an Intro to Computational Biology graduate course at the University of Minnesota.

  17. Kevin Kanda
    Posted April 14, 2015 at 8:02 am | Permalink

    Thank you for making your slides available. They are very well informed and goes into immense detail. We are planning on using these slides, at reference De Brujin modeling for sequencing, for our bioinformatics presentation.

  18. Sanzhen Liu
    Posted April 17, 2015 at 1:02 pm | Permalink

    Thanks Ben for these nice slides. I will use some slides from the assembly slide deck for a bioinformatics course at Kansas State University.

  19. Tom Bair
    Posted June 16, 2015 at 5:55 pm | Permalink

    Using figure as part of a informatics summer course at the University of Iowa — Thanks!

  20. Richard Walker
    Posted June 18, 2015 at 2:50 pm | Permalink

    Taking online courses (edX MOOCs) in BioInformatics by professors at UC San Diego. This looks like a wealth of great supporting material

  21. Posted July 24, 2015 at 11:58 am | Permalink

    Hi Ben,

    I use these to learn about bioinformatics myself, and also to teach others at Public Health England.

    Thanks!

    Phil

  22. Sheida
    Posted August 20, 2015 at 2:44 pm | Permalink

    Thanks for the materials. I will use some of the slides for a computational genomics course at Uconn.

  23. Posted August 28, 2015 at 5:36 am | Permalink

    Hi Ben – Thanks so much for making this wonderful material public! I have used or adapted some slides for my computational genomics introductory class at the Universidad Autonoma de Madrid.

  24. Arjan Hada
    Posted August 30, 2015 at 7:15 pm | Permalink

    Awesome lectures with super-awesome analogies. Please more advanced courses on Coursera or even a specialization on Computational Biology.

  25. Karthi Sivaraman
    Posted September 9, 2015 at 6:26 am | Permalink

    Thanks for making your slides / material public. I am training graduates in NGS specifically, and your material makes for wonderful references – along with the published work. Much appreciated.

    Regards,

  26. Abigail
    Posted September 12, 2015 at 2:43 pm | Permalink

    Thanks so much for making these slides available. I’m adapting some of the assembly slides for an intro bioinformatics class.

  27. Prashanth
    Posted September 21, 2015 at 2:11 am | Permalink

    Introductory Bioinformatics elective @ CS Engineering, Amrita University

  28. Krista Dubin
    Posted September 26, 2015 at 12:30 pm | Permalink

    I adapted your notes on strings and matching to give a brief tutorial to members of my lab (MSK) – thanks.

  29. Rebecca Kratsch
    Posted September 30, 2015 at 11:37 am | Permalink

    Ben, thank you so much for making your slides public. I am studying the ones about BWT and FM-Index in addition to your video-lectures in preparation for a presentation on Bowtie/Bowtie2 at a ‘NGS methods” seminar at Ludwig-Maximillian University, Munich.

  30. Lars Barquist
    Posted October 6, 2015 at 9:01 am | Permalink

    Thanks for these – I’m using some bits and pieces in a seminar on high-throughput sequencing in microbiology at the Mahidol-Oxford Research Unit in Bangkok, Thailand.

  31. Ewa
    Posted October 12, 2015 at 3:57 am | Permalink

    Dear Ben, thank you for great teaching material. I am using your slides in an NGS course at the University of Warsaw,
    with best wishes,
    Ewa Szczurek

  32. Zilu Zhou
    Posted October 25, 2015 at 4:18 pm | Permalink

    Dear Ben, Thank you for sharing such a great teaching material with us. I am contenting several slides in a Computational Biology course at Upenn.

    Best,
    Zerry

  33. Posted October 28, 2015 at 7:39 am | Permalink

    Thanks! I’m using part of the materials in an Algorithms in Bioinformatics course at the University of Turku, Finland. –Filip

  34. Posted November 2, 2015 at 12:30 pm | Permalink

    I am using your materials on de Bruijn graph algorithms for genome assembly in my undergraduate class (CS 173)

  35. Posted November 4, 2015 at 9:31 am | Permalink

    Hi Ben,

    Thank you so much for sharing this nice teaching resource. I am using several slides in a Bioinformatics course at the Universitat Autònoma de Barcelona (degree in Genetics).

    Best,
    Sònia

  36. Posted November 12, 2015 at 11:40 am | Permalink

    Nice work, particularly when education becomes so important in this area.
    I am using some slides for an “introduction to bioinformatics” course in the University of Texas GSBS program. Some problem definitions are easy enough for biology students to understand.
    Thanks for the contribution, Ben!

  37. Georgina Jiménez
    Posted November 15, 2015 at 9:09 pm | Permalink

    Thank you for sharing. I’m using your material about hash tables for an exposition in a Bioinformatics class that I’m taking in The Université de Montreal .

  38. Posted November 26, 2015 at 4:13 pm | Permalink

    Hi! I used some parts of your slides for a presentation that covered DNA sequencing/assembly/alignment, here at a local tech meetup in Uppsala, Sweden. Thanks!

  39. Briana Gross
    Posted December 2, 2015 at 5:05 pm | Permalink

    Thank you for making these slides available! I am using some on de Bruijn graph approaches in my Evolution in Agriculture class at the University of Minnesota Duluth.

  40. Posted January 18, 2016 at 1:45 pm | Permalink

    Hoping to use in a graduate course on Pattern Matching Algorithms.

  41. Ted Ahn
    Posted January 26, 2016 at 5:22 am | Permalink

    Dear Ben,

    Thank you very much for sharing your great teaching material. I am using some of your materials in Intro to Bioinformatics course at Saint Louis University.

    Best wishes,

    Ted

  42. Marc Noguera
    Posted January 31, 2016 at 7:18 am | Permalink

    Thanks for sharing! I will be using some slides from the assembly part for a metagenomics course in Barcelona

  43. Adam Rivers
    Posted February 2, 2016 at 4:22 pm | Permalink

    Nice slides. I’m using some of the slides on assembly for a guest lecture at UC Berkeley.

  44. Posted February 9, 2016 at 2:46 pm | Permalink

    Ben – Thanks so much for sharing. I’m adapting some of your slides for my computational biology class at Carleton College. -Layla Oesper

  45. Posted February 16, 2016 at 1:16 am | Permalink

    Hi Ben, thanks for sharing your slides. I am using parts of your lectures and teaching materials for my Introduction to Genomics class at Princeton University. Mohamed

  46. Miguel Loera
    Posted February 21, 2016 at 1:48 pm | Permalink

    Hi Ben, awesome job. I’m using some of your slides about de Bruijn graphs and BWT for a genome assembly course at the UANL (Mexico). Many thanks.

  47. Deb
    Posted March 1, 2016 at 1:36 am | Permalink

    Hey there, using your slides as a reference while I do my homework for Bioinformatics Algorithms at Harvard Extension School. Thanks much – DF

  48. R. Chikhi
    Posted March 4, 2016 at 12:01 pm | Permalink

    Hi Ben, I have taken some of your figures for teaching a BWT class. Thanks much for making this material available. Rayan

  49. Anton Nekrutenko
    Posted March 10, 2016 at 10:27 am | Permalink

    Fantastic materials. Using them to teach BMMB554 at Penn State

  50. Asli Uyar
    Posted March 13, 2016 at 7:01 am | Permalink

    Hi, thanks for sharing your teaching materials. I am adapting some of the slides for Intro to Bioinformatics course at Okan University.

  51. Posted March 23, 2016 at 8:36 pm | Permalink

    Hi Ben,
    These slides are really great. I am giving a talk to the BIG (Bioinformatics Group) at MIT about Sailfish, kallisto and Salmon and would like to use a couple of these slides to get across the idea of a De Bruijn graph which are essential to kallisto. Thank you for making them available. De Bruijn graphs are not what a lot of biologists are very familiar with and these slides explain them very well.

  52. Posted March 27, 2016 at 11:43 pm | Permalink

    Ben, thanks for posting these. I am using/adapting some of these for my GENE245 course on Compbio at Stanford.

  53. Nathaniel Jue
    Posted April 5, 2016 at 12:12 pm | Permalink

    Ben, thanks for sharing this. I used some of your stuff on indexes for teaching mapping in my Bioinformatics and Systems Biology course. Nice examples.

    • Nathaniel Jue
      Posted April 5, 2016 at 12:13 pm | Permalink

      Ah, forgot to say, I’m at Cal State University, Monterey Bay

  54. Alexis Battle
    Posted April 7, 2016 at 1:20 pm | Permalink

    Thanks Ben, I grabbed a few slides on alignment and sequencing for background in my class – and directed students to your course next Fall if they wanted more.

  55. Tyler Dae Devlin
    Posted April 22, 2016 at 1:09 am | Permalink

    Thank you for sharing your slides, Ben. I’ll be borrowing from them for a presentation at Brown University’s ASA DataFest this weekend.

  56. Posted April 28, 2016 at 11:17 am | Permalink

    Dear Ben, thanks for sharing the materials. We’re referencing them for our Data Science for Sequencing course at Univ of Washington. They’re really helpful! Best wishes.

  57. Israel Dilan
    Posted May 14, 2016 at 5:08 pm | Permalink

    Many thanks for the access to the materials, they helped me explain to my friends, classmates and peers about RNA-Sequencing during a group presentation in the University of Puerto Rico Rio Piedras Campus.

  58. Posted June 22, 2016 at 4:20 am | Permalink

    Ben, thanks so much for making and publishing these materials! I grabbed some images from the sequence alignment section for a lecture I will be giving in Leiden University.

  59. Jared Simpson
    Posted July 26, 2016 at 1:53 pm | Permalink

    Thanks for these excellent slides Ben – I’m going to use some for CSC2417 at the University of Toronto this fall.

  60. Maheshi Dassanayake
    Posted September 6, 2016 at 10:38 am | Permalink

    Thanks so much for sharing your slides and allowing us to use it. I’m using some of your slides on sequence assembly and alignments in my comparative genomics class taught at Louisiana State University, Baton Rouge.

  61. Giri Athrey
    Posted September 12, 2016 at 3:11 pm | Permalink

    I came across slides from your lectures while preparing for my own course. I teach an introductory genomics/bioinformatics course for graduate students in the college of Agriculture. I find the graphics in your slides extremely useful. Really great work and thank you for sharing.

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