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  1. Article ; Online: Motif elucidation in ChIP-seq datasets with a knockout control.

    Denisko, Danielle / Viner, Coby / Hoffman, Michael M

    Bioinformatics advances

    2023  Volume 3, Issue 1, Page(s) vbad031

    Abstract: Summary: Chromatin immunoprecipitation-sequencing is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and ... ...

    Abstract Summary: Chromatin immunoprecipitation-sequencing is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout (KO) experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO-a computational method to automatically optimize motif analyses with KO controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of KO controls, which far outperform input controls.
    Availability and implementation: PeaKO is freely available at https://peako.hoffmanlab.org.
    Contact: michael.hoffman@utoronto.ca.
    Language English
    Publishing date 2023-03-16
    Publishing country England
    Document type Journal Article
    ISSN 2635-0041
    ISSN (online) 2635-0041
    DOI 10.1093/bioadv/vbad031
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Assessing and assuring interoperability of a genomics file format.

    Niu, Yi Nian / Roberts, Eric G / Denisko, Danielle / Hoffman, Michael M

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 13, Page(s) 3327–3336

    Abstract: Motivation: Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, making it difficult or impossible for the creators of these tools to robustly test them for ... ...

    Abstract Motivation: Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, making it difficult or impossible for the creators of these tools to robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results.
    Results: We developed a new verification system, Acidbio, which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases-potentially unexpected inputs that exemplify the limits of the format. To analyze the performance of existing software, we tested the input validation of 80 Bioconda packages that parsed the Browser Extensible Data (BED) format. We also used a fuzzing approach to automatically perform additional testing. Of 80 software packages examined, 75 achieved less than 70% correctness on our test suite. We categorized multiple root causes for the poor performance of different types of software. Fuzzing detected other errors that the manually designed test suite could not. We also created a badge system that developers can use to indicate more precisely which BED variants their software accepts and to advertise the software's performance on the test suite.
    Availability and implementation: Acidbio is available at https://github.com/hoffmangroup/acidbio.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Genomics/methods ; Software
    Language English
    Publishing date 2022-05-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac327
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Classification and interaction in random forests.

    Denisko, Danielle / Hoffman, Michael M

    Proceedings of the National Academy of Sciences of the United States of America

    2018  Volume 115, Issue 8, Page(s) 1690–1692

    MeSH term(s) Algorithms ; Catheter Ablation ; Humans ; Varicose Veins/therapy
    Language English
    Publishing date 2018-02-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1800256115
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: GA4GH: International policies and standards for data sharing across genomic research and healthcare.

    Rehm, Heidi L / Page, Angela J H / Smith, Lindsay / Adams, Jeremy B / Alterovitz, Gil / Babb, Lawrence J / Barkley, Maxmillian P / Baudis, Michael / Beauvais, Michael J S / Beck, Tim / Beckmann, Jacques S / Beltran, Sergi / Bernick, David / Bernier, Alexander / Bonfield, James K / Boughtwood, Tiffany F / Bourque, Guillaume / Bowers, Sarion R / Brookes, Anthony J /
    Brudno, Michael / Brush, Matthew H / Bujold, David / Burdett, Tony / Buske, Orion J / Cabili, Moran N / Cameron, Daniel L / Carroll, Robert J / Casas-Silva, Esmeralda / Chakravarty, Debyani / Chaudhari, Bimal P / Chen, Shu Hui / Cherry, J Michael / Chung, Justina / Cline, Melissa / Clissold, Hayley L / Cook-Deegan, Robert M / Courtot, Mélanie / Cunningham, Fiona / Cupak, Miro / Davies, Robert M / Denisko, Danielle / Doerr, Megan J / Dolman, Lena I / Dove, Edward S / Dursi, L Jonathan / Dyke, Stephanie O M / Eddy, James A / Eilbeck, Karen / Ellrott, Kyle P / Fairley, Susan / Fakhro, Khalid A / Firth, Helen V / Fitzsimons, Michael S / Fiume, Marc / Flicek, Paul / Fore, Ian M / Freeberg, Mallory A / Freimuth, Robert R / Fromont, Lauren A / Fuerth, Jonathan / Gaff, Clara L / Gan, Weiniu / Ghanaim, Elena M / Glazer, David / Green, Robert C / Griffith, Malachi / Griffith, Obi L / Grossman, Robert L / Groza, Tudor / Auvil, Jaime M Guidry / Guigó, Roderic / Gupta, Dipayan / Haendel, Melissa A / Hamosh, Ada / Hansen, David P / Hart, Reece K / Hartley, Dean Mitchell / Haussler, David / Hendricks-Sturrup, Rachele M / Ho, Calvin W L / Hobb, Ashley E / Hoffman, Michael M / Hofmann, Oliver M / Holub, Petr / Hsu, Jacob Shujui / Hubaux, Jean-Pierre / Hunt, Sarah E / Husami, Ammar / Jacobsen, Julius O / Jamuar, Saumya S / Janes, Elizabeth L / Jeanson, Francis / Jené, Aina / Johns, Amber L / Joly, Yann / Jones, Steven J M / Kanitz, Alexander / Kato, Kazuto / Keane, Thomas M / Kekesi-Lafrance, Kristina / Kelleher, Jerome / Kerry, Giselle / Khor, Seik-Soon / Knoppers, Bartha M / Konopko, Melissa A / Kosaki, Kenjiro / Kuba, Martin / Lawson, Jonathan / Leinonen, Rasko / Li, Stephanie / Lin, Michael F / Linden, Mikael / Liu, Xianglin / Udara Liyanage, Isuru / Lopez, Javier / Lucassen, Anneke M / Lukowski, Michael / Mann, Alice L / Marshall, John / Mattioni, Michele / Metke-Jimenez, Alejandro / Middleton, Anna / Milne, Richard J / Molnár-Gábor, Fruzsina / Mulder, Nicola / Munoz-Torres, Monica C / Nag, Rishi / Nakagawa, Hidewaki / Nasir, Jamal / Navarro, Arcadi / Nelson, Tristan H / Niewielska, Ania / Nisselle, Amy / Niu, Jeffrey / Nyrönen, Tommi H / O'Connor, Brian D / Oesterle, Sabine / Ogishima, Soichi / Wang, Vivian Ota / Paglione, Laura A D / Palumbo, Emilio / Parkinson, Helen E / Philippakis, Anthony A / Pizarro, Angel D / Prlic, Andreas / Rambla, Jordi / Rendon, Augusto / Rider, Renee A / Robinson, Peter N / Rodarmer, Kurt W / Rodriguez, Laura Lyman / Rubin, Alan F / Rueda, Manuel / Rushton, Gregory A / Ryan, Rosalyn S / Saunders, Gary I / Schuilenburg, Helen / Schwede, Torsten / Scollen, Serena / Senf, Alexander / Sheffield, Nathan C / Skantharajah, Neerjah / Smith, Albert V / Sofia, Heidi J / Spalding, Dylan / Spurdle, Amanda B / Stark, Zornitza / Stein, Lincoln D / Suematsu, Makoto / Tan, Patrick / Tedds, Jonathan A / Thomson, Alastair A / Thorogood, Adrian / Tickle, Timothy L / Tokunaga, Katsushi / Törnroos, Juha / Torrents, David / Upchurch, Sean / Valencia, Alfonso / Guimera, Roman Valls / Vamathevan, Jessica / Varma, Susheel / Vears, Danya F / Viner, Coby / Voisin, Craig / Wagner, Alex H / Wallace, Susan E / Walsh, Brian P / Williams, Marc S / Winkler, Eva C / Wold, Barbara J / Wood, Grant M / Woolley, J Patrick / Yamasaki, Chisato / Yates, Andrew D / Yung, Christina K / Zass, Lyndon J / Zaytseva, Ksenia / Zhang, Junjun / Goodhand, Peter / North, Kathryn / Birney, Ewan

    Cell genomics

    2022  Volume 1, Issue 2

    Abstract: The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic ... ...

    Abstract The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
    Language English
    Publishing date 2022-02-24
    Publishing country United States
    Document type Journal Article
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2021.100029
    Database MEDical Literature Analysis and Retrieval System OnLINE

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