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  • Integrating All Biomedical Knowledge to Systematically Find the Best Opportunities: From Hetionet to Related Sciences

    Presented on 2023-10-03 to the Data-Driven Drug Repurposing Workshop at CZI headquarters in Redwood City, CA. Hosted by EveryCure and the Chan Zuckerberg Initiative.

    Oct 03, 2023 442 0

  • Metapath-based approaches for therapeutic crosspurposing and the challenge of degree/study bias

    Presentation as part of the CZI / Every Cure Data-Driven Drug Repurposing Virtual Workshop Series on 2024-02-12 with a session title: "deep dive into the challenges and potential applications of knowledge graphs." This presentation is released under a CC BY 4.0 License.

    Dec 05, 2022 333 0

  • Classifying EFO/MONDO diseases as low, medium, or high precision using nxontology-ml

    https://github.com/related-sciences/nxontology-ml/issues/13

    Dec 05, 2022 564 0

  • VinUni: How to Become a Modern Open Scientist

    Presentation by Daniel Himmelstein at VinUniversity in Hanoi, Vietnam. This presentation is released under a CC BY 4.0 License.

    Dec 05, 2022 758 0

  • CZI Workshop Lightning Talk on Manubot: Empowering scholars with a personal preprint server & platform for open scholarly writing.

    Presentation by Daniel Himmelstein at the Chan Zuckerberg Biohub on 2019-12-04 for the CZI event titled "Preprints I/O: Strengthening the open science ecosystem by extending preprints". This presentation is released under a CC BY 4.0 License.

    Nov 21, 2019 2,633 0

  • Rocky 2019: Hetnet connectivity search provides rapid insights into how two biomedical entities are related

    Presentation by Daniel Himmelstein at Rocky Bioinformatics Conference on 2019-11-13. This presentation is released under a CC BY 4.0 License.

    Nov 13, 2019 2,872 0

  • Next generation scholarly communication: advancing the conversation

    Presentation by Daniel Himmelstein at Penn Libraries' panel on Open Science on 2019-10-23 for the event titled "#OPENSCIENCE: The Impact of Scientific Research through Open Resources". This presentation is released under a CC BY 4.0 License.

    Oct 20, 2019 4,670 1

  • Frankfurt Book Fair HighWire Panel: Science as conversation

    Presentation by Daniel Himmelstein at HighWire's panel on preprints at the Frankfurt Book Faire on 2019-10-16. This presentation is released under a CC BY 4.0 License.

    Oct 11, 2019 2,539 0

  • Philly DevFest: Using a graph database to Integrate biomedical knowledge and predict drug efficacy

    Presentation by Daniel Himmelstein at GDG Cloud DevFest Philly on 2019-09-28. This presentation is released under a CC BY 4.0 License.

    Sep 28, 2019 2,273 0

  • BGS Orientation: Electronic Lab Notebooks: special considerations for computational research

    Presentation by Daniel Himmelstein on 2019-08-22 as part of the electronic lab notebook orientation module for the Biomedical Graduate Studies program at University of Pennsylvania. This presentation is released under a CC BY 4.0 License.

    Aug 22, 2019 2,234 0

  • Encoding 50 years of biomedical knowledge into a network to predict when a drug treats a disease

    Presentation by Daniel Himmelstein at the Huntsman Cancer Institute of University of Utah on 2019-07-16. This presentation is released under a CC BY 4.0 License. Recording available at https://medicine.utah.edu/dbmi/academics-education/decart/video.php?video=0_bs9x2fww

    Jul 15, 2019 2,931 0

  • Highwire Event: The future of scholarly publication: automated, transparent, and open

    Presentation by Daniel Himmelstein at HighWire's London Lunch & Learn session on 2019-06-14. This presentation is released under a CC BY 4.0 License. A recording is available at https://vimeo.com/344994584.

    May 21, 2019 3,666 2

  • Oxford: Heterogeneous networks to integrate biomedical knowledge and predicting new uses for existing drugs

    Presentation on 2019-02-27 at Oxford University. This presentation is released under a CC BY 4.0 License.

    Feb 27, 2019 2,214 0

  • R2R 2019 workshop: Citation by persistent identifiers

    Introduction slides for the citation-by-identifier workshop at the 2019 Researcher to Reader conference in London. These slides are released under a CC BY 4.0 License.

    Feb 21, 2019 2,203 0

  • PSB 2019: Writing bio-computational manuscripts with Manubot

    Special Working Group in Hawaii at the Pacific Symposium on Biocomputing on 2019-01-04. This presentation is released under a CC BY 4.0 License.

    Jan 03, 2019 4,578 0

  • AI Therapeutics: hetnets for drug repurposing

    Presentation on 2018-12-20 at AI Therapeutics in Guilford Connecticut. This presentation is released under a CC BY 4.0 License.

    Dec 21, 2018 2,281 0

  • FORCE2018: Revolutionizing scholarly writing with Manubot

    Presentation at FORCE2018 in Montreal on 2018-10-12. This presentation is released under a CC BY 4.0 License. An archive of the slides is available at https://doi.org/10.5281/zenodo.1460985. The recording is available at https://youtu.be/sGL0osdby0U and https://busy.org/@dhimmel/opdk4gax.

    Oct 11, 2018 3,611 1

  • Sci-Hub and the future of publishing: Library Science Talk in Switzerland

    Slides for two presentations in Switzerland: 2018-06-25 in Geneva & 2018-06-26 in Zurich. Released under a CC-BY 4.0 License. The recording of the Zurich presentation is online at https://youtu.be/ph04SNZkT4Q and https://d.tube/#!/v/dhimmel/68uly2sj. The Geneva recording is at https://youtu.be/A-unQh2t7rI.

    Jun 15, 2018 6,355 4

  • The hetnet awakens in Mississippi for MCBIOS 2018

    Presentation on 2018-03-30 at MCBIOS 2018. This presentation is released under a CC BY 4.0 License.

    Mar 28, 2018 3,490 1

  • The hetnet awakens in Dedham for Artificial Intelligence: Transforming Pharma Congress

    Presentation on 2018-02-21 at Artificial Intelligence: Transforming Pharma Congress (https://artificialintelligence-pharma.com/events/artificial-intelligence-transforming-pharma). This presentation is released under a CC BY 4.0 License.

    Feb 12, 2018 2,927 0

  • The hetnet awakens in Key West for EDGE 2018

    Presentation on 2018-02-08 at EDGE 2018 (http://edge2018.cloudaccess.host). This presentation is released under a CC BY 4.0 License.

    Feb 06, 2018 2,774 0

  • Science on the Hill: Pirate Website Unlocks Access to Scholarly Literature

    Slides for Science on the Hill, hosted by Saint Joseph's University on 2018-01-18. Released under a CC-BY 4.0 License.

    Jan 18, 2018 3,580 0

  • Greene Lab Journal Club on 2018-01-09

    This presentation is released under a CC BY 4.0 License.

    Jan 08, 2018 2,551 0

  • Sci-Hub's remarkable coverage of scholarly literature & the future of publishing

    Presentation at the Centre for Genomic Regulation in Barcelona on 2017-11-17. Hosted by Guillaume Filion. Released under a CC-BY 4.0 License.

    Nov 14, 2017 5,277 1

  • Sci-Hub the Disruptor: Piracy & Publishing in Academia

    Sci-Hub, the infamous repository of scholarly journal articles, has alternately been hailed as a paragon of open scientific communication and a criminal threat to beleaguered academic publishers. The Friends of the Lehigh University Libraries will host a panel discussion on how Sci-Hub has disrupted the age of open access, featuring Daniel Himmelstein, UPenn, whose researched revealed the enormity of the Sci-Hub database. Commentary and discussion with Lehigh faculty members Sera Cremonini, Jeremy Littau, Kathy Olson and Frank Pazzaglia on the continuing need for open access and Sci-Hub's rogue legal status. International Open Access Week program.

    Oct 26, 2017 3,387 1

  • Cognoma Launch Party

    Slides for the Cognoma Launch Party on October 11, 2017 at MilkBoy Philadelphia. Meetup info at https://meetu.ps/3dzlvc. Pictures from this event at https://photos.app.goo.gl/PdyIPjzYBfx91vty1.

    Oct 11, 2017 2,823 0

  • Penn Libraries Research Tea: Sci-Hub & the Future of Publishing

    Research Tea with Dr. Daniel Himmelstein, Sci-Hub & the Future of Publishing on 2017-10-18. This presentation is released under a CC BY 4.0 license.

    Oct 09, 2017 3,847 0

  • Rising Stars in Data Science: The hetnet awakens in Chicago

    Presentation on 2017-09-13 at the Rising Stars Symposium in Data Science, University of Chicago. This presentation is released under a CC BY 4.0 License.

    Sep 10, 2017 3,242 0

  • Manubot: the manuscript bot

    Powering the next generation of scholarly manuscript. See https://github.com/greenelab/manubot-rootstock. Released under CC BY 4.0.

    Sep 06, 2017 3,965 0

  • The hetnet awakens in Princeton. biology ⭃ network

    Presentation on 2017-06-08 at CSIG (Computational Systems for Integrative Genomics). Details at http://www.greenelab.com/csig-2017. This presentation is released under a CC BY 4.0 License.

    Jun 08, 2017 2,907 0

  • The hetnet awakens in Philadelphia. biology ⭃ network

    Presentation at the 2017-06-06 DataPhilly meetup. Details at https://meetu.ps/39DxjV. This presentation is released under a CC BY 4.0 License.

    Jun 05, 2017 3,393 0

  • Greene Lab Journal Club on 2017-05-30: Sci-Hub / LibGen

    See https://github.com/greenelab/scihub for our Sci-Hub research. This presentation is released under a CC BY 4.0 License.

    May 22, 2017 2,804 0

  • Licensing for the biodata scientist: Presentation to the Moore Lab

    Presentation to the Moore Lab at Penn (epistasis.org) on April 10, 2017 at 12:00 pm in Richards room 309. This presentation is released under a CC BY 4.0 License.

    Apr 09, 2017 3,257 0

  • Integrating data towards a systematic understanding of drug efficacy

    Presentation to Pfizer in Cambridge, MA. These slides are released under a CC BY 4.0 License.

    Feb 21, 2017 3,063 0

  • Integrating biomedical knowledge to predict new uses for existing drugs

    Presentation for the Models, Inference & Algorithms Group on the Broad Institute (https://www.broadinstitute.org/scientific-community/science/mia/models-inference-algorithms) on February 22, 2017. These slides are released under a CC BY 4.0 License. The recording of this presentation in on YouTube at https://goo.gl/Vtd0Gs.

    Feb 20, 2017 4,384 0

  • Big Data Seminar at Penn: Hetionet in Neo4j

    Presentation for the Seminar/Reading Group on Big and Scientific Data at Penn (http://www.cis.upenn.edu/~zives/datascience/) on February 10, 2017.

    Feb 10, 2017 3,150 0

  • To Blackfynn: predicting antiepileptic drugs in Project Rephetio

    Presentation to Blackfynn in Philadelphia on Monday, January 30, 2017.

    Jan 30, 2017 2,743 0

  • Greene Lab Journal Club on January 13, 2017

    Greene Lab Journal Club at the University of Pennsylvania on January 13, 2017.

    Jan 12, 2017 2,698 0

  • OpenCon 2016 Presentation on Project Cognoma

    Project Cognoma is an open source project to create a webapp for analyzing cancer data. We're a community-driven philanthropic project that began as a collaboration between the Greene Lab, DataPhilly, and Code for Philly. This presentation covers mobilizing community contributors for full stack data science. It's licensed as CC BY 4.0.

    Nov 10, 2016 2,713 0

  • The Cognoma Collaborative creates a webapp to predict cancer mutations from gene expression

    Presentation at Rocky Bioinformatics 2016 on Friday December 9, 10:05–10:15 am (OP 18). Titled: The Cognoma Collaborative creates a webapp to predict cancer mutations from gene expression.

    Nov 09, 2016 4,585 0

  • Lecture for CIS 550 at Penn: the emerging role of graph databases in information systems

    Lecture on graph databases for Database & Information Systems (CIS 450/550) at the University of Pennsylvania. This course is instructed by Susan Davidson. This presentation is released under a CC BY 4.0 License.

    Oct 30, 2016 3,620 0

  • Open Data Science

    Guest lecture for the course Data Science for Biomedical Informatics (EPID 600) at the University of Pennsylvania. This course was instructed by Assistant Professor Blanca Himes. This presentation is released under a CC BY 4.0 License.

    Oct 18, 2016 3,865 1

  • Hetionet Awakens: Integrating all of Biology into a Public Neo4j Database

    Lightning talk at GraphConnect 2016. See abstract at http://graphconnect.com/speaker/daniel-himmelstein/. This presentation is released under a CC BY 4.0 License.

    Oct 07, 2016 3,391 0

  • Greene Lab Journal Club on September 9, 2016

    Greene Lab Journal Club on September 9, 2016.

    Sep 08, 2016 2,852 0

  • Greene Lab Journal Club on July 15, 2016

    Greene Lab Journal Club on July 15, 2016. Since this is my first time giving journal club in the Greene Lab, I am entitled to discuss any articles of my choosing, not just recent articles.

    Jul 15, 2016 2,645 0

  • Cognoma Datathon Meetup on July 12, 2016

    Outline and tasks for the Cognoma Datathon Meetup on July 12, 2016 located at Industrious in Philadelphia. This presentation is released under CC0 unless otherwise noted.

    Jul 12, 2016 3,376 1

  • DataPhilly Datathon Workshop · Hetnets + Biomedicine + Neo4j = Hetionet

    This presentation introduces Hetionet and Neo4j for the datathon workshop organized by the DataPhilly and Code for Philly meetups on July 5, 2016. At the end, we introduce Project Cognoma, which will be the focus of future hack nights.

    Jul 05, 2016 4,138 1

  • Thesis Seminar · Daniel Himmelstein · Biological & Medical Informatics · UCSF

    Daniel Himmelstein's Thesis Seminar covering his PhD studies. See the accompanying recording on YouTube (https://youtu.be/H8DfXop8K7g). This presentation is released under a CC BY 4.0 license.

    Mar 16, 2016 6,721 2

  • Drug repurposing by hetnet relationship prediction: a new hope

    The Rebels have searched the galaxy and obtained neo4j technology. They now plan to use the force on hetnets to predict new uses for existing drugs. Learn to use the dark side of the force and stop the Rebels before they destroy the Empire. (My presentation for iPQB Journal Club on February 29, 2016.)

    Feb 27, 2016 2,806 0

  • 2015 QBC Retreat: hetnets in human disease

    My talk for the 2015 UCSF QBC retreat at the Asilomar Conference Grounds. All original content is CC0.

    Nov 18, 2015 2,901 0