Hoffman Lab: news archive

A record of previous activities at the Hoffman Lab.

2020

• 2020-01-29: Eric releases Segway 3.0
• 2020-01-26: The 46 Questions for Scientists features an interview with Michael.

  2019

  • 2019-12-18: Coby was awarded the Alfred B. Lehman Graduate Scholarship from the Department of Computer Science, University of Toronto.
  • 2019-12-16: "Using computers to understand cancer with Dr. Michael Hoffman": Michael is featured in the Behind the Breakthrough, a podcast about the people behind the world-leading research at UHN.
  • 2019-12-04: Michael is an invited speaker at the University of Wisconsin-Madison in the Genomics Seminar Series.
  • 2019-11-29: Michael is an invited speaker at the McGill Human Genetics Student's Society 2020 Annual Conference.
  • 2019-11-14: Michael is a co-author on "A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types"
  • 2019-09-18: Danielle successfully defends her Master's thesis.
  • 2019-09-13: Eric releases Segtools 1.2.4.
  • 2019-09-13: Eric releases Segtools 1.2.3.
  • 2019-08-28: Danielle, Coby, and Michael are the authors of "Motif elucidation in ChIP-seq datasets with a knockout control", a preprint on bioRxiv Bioinformatics.
  • 2019-08-28: Michael is featured in The Know Show, a live science-themed comedy variety show, taking on the role of the "real scientist" in the pre-show interview.
  • 2019-08-13: Michael is invited to become an Editorial Board Member at Genome Biology.
  • 2019-07-24: Eric releases Segtools 1.2.2.
  • 2019-07-16: Michael is a co-applicant on a Canadian Institutes of Health Research (CIHR) Foundation Grant on "Risk prediction and early detection of lung and pancreatic cancer".
  • 2019-07-15: Mickael is a co-author on "Functional annotation of human long non-coding RNAs via molecular phenotyping", a preprint on bioRxiv Genomics.
  • 2019-07-12: Mehran was awarded a 2019-2020 Peterborough K.M. Hunter Charitable Foundation Graduate Award from the Faculty of Medicine.
  • 2019-07-10: Michael is a co-applicant on a Canadian Institutes of Health Research (CIHR) Project Grant on "Lung cancer early detection and classification using methylome analysis of plasma cell free DNA".
  • 2019-07-02: Mehran was awarded an Ontario Graduate Scholarship.
  • 2019-06-26: Michael is an invited program committee member for Machine Learning in Computational Biology (MLCB2019) in Vancouver, British Columbia, Canada.
  • 2019-06-26: Eric releases Segway 2.0.5.
  • 2019-06-14: Sam was awarded a Molly Towell Fellowship from the Molly Towell Perinatal Research Foundation.
  • 2019-06-14: Rachel presents a poster on "Semi-supervised learning in Segway" at the ICML 2019 Workshop on Computational Biology in Long Beach, California, USA.
  • 2019-05-31: Segtools 1.2.1 is now available on Bioconda.
  • 2019-05-30: Rachel was awarded an ICML 2019 travel grant.
  • 2019-05-30: Mehran is an invited speaker at the James Lepock Memorial (JLM) Student Research Symposium.
  • 2019-05-18: Shen et al. paper, of which Michael is a co-author, wins the Till and McCulloch Paper of the Year - Translational category.
  • 2019-05-17: Rachel was awarded a School of Graduate Studies (SGS) Conference Grant for her upcoming trip to ICML 2019.
  • 2019-05-17: Michael is PI and Samantha is co-investigator on a McLaughlin Centre accelerator grant entitled "Genome-wide cell-free DNA methylation enrichment and sequencing for preeclampsia diagnosis".
  • 2019-05-15: Eric releases Segway 2.0.4.
  • 2019-05-13: Michael is an invited speaker at the 14th Guelph Biomathematics and Biostatistics Symposium: Artificial Intelligence and Machine Learning in Biology at the University of Guelph.
  • 2019-05-13: Yushan (Ida) Liu and Michael Wrana join the lab as summer students.
  • 2019-05-06: Yi Nian (Jeffrey) Niu, Siddharth Reed and Matthew McNeil join the lab as summer students.
  • 2019-05-06: Coby presents a poster on "Comparing chromatin accessibility profiles with maximal cliques in temporal graphs" at RECOMB at the George Washington University in Washington, D.C., USA.
  • 2019-05-03: Coby presents a poster on "Methyl-sensitive transcription factor motifs in leukemia cell populations" at RECOMB-Computational Cancer Biology (CCB) at the George Washington University in Washington, D.C., USA.
  • 2019-04-24: Shen et al. paper, of which Michael is a co-author, is named one of the European Association for Cancer Research's Top 10 Cancer Research Publications.
  • 2019-04-24: Coby was awarded a PhD Travel Conference Grant from the Department of Computer Science, University of Toronto for his upcoming travels to RECOMB.
  • 2019-04-23: Jai, Coby and Michael publish a paper on "DNAmod: the DNA modification database" in the Journal of Cheminformatics.
  • 2019-04-11: Coby was awarded a CEEHRC Travel Award from the Canadian Epigenetics, Environment and Health Research Consortium Network for his upcoming travels to RECOMB.
  • 2019-04-11: Danielle attends CRA-W Grad Cohort for Women in Chicago, Illinois, USA.
  • 2019-02-13: Mehran finishes a revision of "Virtual ChIP-seq: Predicting transcription factor binding by learning from the transcriptome", a preprint on bioRxiv Bioinformatics.
  • 2019-01-23: Michael (principal applicant) and Samantha (co-applicant) receive a grant from Canadian Institutes of Health Research (CIHR) for their project on "DNA methylation profiling in cell-free DNA: a non-invasive method to screen for pre-term birth".
  • 2019-01-15: Davide, Sarah, and Michael are co-authors on "BEHST: Genomic set enrichment analysis enhanced through integration of chromatin long-range interactions", a preprint on bioRxiv Bioinformatics.
  • 2019-01-10: Francis successfully defends his Master's thesis.
  • 2019-01-03: Michael is an invited speaker at Pacific Symposium on Biocomputing (PSB) 2019 in Kohala Coast, Hawaii, USA. His talk covers: "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet".

  2018

  • 2018-12-08: Coby was awarded the Alfred B. Lehman Graduate Scholarship from the Department of Computer Science.
  • 2018-12-04: Rachel is a co-author on "The STROBE: a system for closed-looped optogenetic control of freely feeding flies", a preprint on bioRxiv Neuroscience.
  • 2018-11-26: Michael is an invited speaker at a special seminar jointly hosted by the School of Computing and the Department of Biomedical and Molecular Sciences at Queen's University, Kingston, Ontario. His talk covers: "Identifying transcription factor binding using open chromatin, transcriptome, and methylation data".
  • 2018-11-16: The final version of Mehran and Michael's paper on "Umap and Bismap: quantifying genome and methylome mappability" in Nucleic Acids Research is now available online.
  • 2018-11-14: Michael is a co-author on "Sensitive tumour detection and classification using plasma cell-free DNA methylomes" in Nature.
  • 2018-11-07: Michael is an invited speaker and co-chair of the Biological Data Science conference at Cold Spring Harbor Laboratory, New York, USA. His talk covers: "Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome".
  • 2018-11-04: Michael is an invited speaker and co-chair of the Probabilistic Modeling in Genomics conference at Cold Spring Harbor Laboratory, New York, USA. His talk covers: "Segway and the Graphical Models Toolkit: a framework for probabilistic genomic inference".
  • 2018-10-18: The final version of Francis and Michael's review on "Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities" in Information Fusion is now available online.
  • 2018-10-11: Rachel is a co-author on "A complex peripheral code for salt taste in Drosophila" in eLife.
  • 2018-09-26: Eric releases Segway 2.0.3.
  • 2018-09-26: Eric releases Genomedata 1.4.4.
  • 2018-09-24: Mehran was awarded an Arshia Tabrizi Memorial Scholarship from the Parya Trillium Foundation.
  • 2018-09-21: Francis publishes a paper on "Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities" in Information Fusion.
  • 2018-09-21: Eric releases Genomedata 1.4.3.
  • 2018-09-17: Mehran was awarded a School of Graduate Studies (SGS) Conference Grant for his recent trip to Genome Informatics 2018.
  • 2018-09-17: Mehran presents a poster and lightning talk on "Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome" at the Genome Informatics conference at the Wellcome Trust Genome Campus in Hinxton, United Kingdom.
  • 2018-09-10: Jai and Coby finish an update to "DNAmod: the DNA modification database", a preprint on bioRxiv Bioinformatics.
  • 2018-09-08: Davide is an organizer of the special session "Machine learning in health informatics and biological systems" at the 15th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2018).
  • 2018-09-06: Eric releases Genomedata 1.4.2.
  • 2018-09-06: Rachel Chan joins the lab as a MSc student in the Department of Computer Science.
  • 2018-08-30: Mehran publishes a paper on "Umap and Bismap: quantifying genome and methylome mappability" in Nucleic Acids Research.
  • 2018-08-10: Mehran was awarded an Ontario Graduate Scholarship.
  • 2018-07-31: Michael is a session organizer, speaker, and chair at the 2018 Joint Statistical Meetings in Vancouver, British Columbia, Canada. His talk covers: "Inference of transcription factor binding sites in new cell types from open chromatin and gene expression data".
  • 2018-07-25: Michael is an invited speaker at BioC 2018 in Toronto, Ontario.
  • 2018-07-10: Danielle was awarded an Ontario Graduate Scholarship.
  • 2018-07-04: Francis is a co-author on "Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities", a preprint on arXiv Quantitative Biology.
  • 2018-07-03: Davide is a co-author on "Bioconda: sustainable and comprehensive software distribution for the life sciences" in Nature Methods.
  • 2018-06-29: Samantha was awarded a Princess Margaret Postdoctoral Fellowship.
  • 2018-06-28: Mehran was awarded a Frank Fletcher Memorial Fund scholarship from the Faculty of Medicine.
  • 2018-06-08: Eric releases Genomedata 1.4.1.
  • 2018-06-08: Flora was awarded a Summer Undergraduate Studentship from the University of Toronto's Undergraduate Research Opportunities Program.
  • 2018-06-06: Davide publishes a paper on "Novelty indicator for enhanced prioritization of predicted Gene Ontology annotations" in IEEE/ACM Transactions on Computational Biology and Bioinformatics.
  • 2018-06-05: Michael is an invited speaker at the Department of Cellular & Molecular Physiology Seminar Series at the Penn State College of Medicine, Pennsylvania, USA.
  • 2018-06-01: Michael is an invited speaker at the Symposium on Advances in Genomics, Epidemiology, and Statistics at the University of Pennsylvania, Pennsylvania, USA.
  • 2018-05-29: Danielle is an invited speaker at the Toronto Women's Data Group meetup at Princess Margaret Cancer Centre, Toronto.
  • 2018-05-18: Mehran publishes a paper on "Aberration hubs in protein interaction networks highlight actionable targets in cancer" in Oncotarget.
  • 2018-05-18: Danielle was awarded a School of Graduate Studies (SGS) Conference Grant for her recent trip to the Biology of Genomes conference.
  • 2018-05-17: Mehran presents a talk at The Great Lakes Genomics Conference in Toronto, Ontario.
  • 2018-05-14: Davide is a co-author on "Supervised deep learning embeddings for the prediction of cervical cancer diagnosis" in PeerJ Computer Science.
  • 2018-05-12: Mehran finishes an update to "Virtual ChIP-seq: Predicting transcription factor binding by learning from the transcriptome", a preprint on bioRxiv Bioinformatics.
  • 2018-05-08: Mehran is a co-author on "A general framework for interrogation of mRNA stability programs identifies RNA-binding proteins that govern cancer transcriptomes" in Cell Reports.
  • 2018-05-08: Danielle presents a poster on "Motif elucidation in ChIP-seq datasets with a knockout control" at the Biology of Genomes conference at Cold Spring Harbor Laboratory, New York, USA.
  • 2018-05-07: Flora (Yufang) Liu joins the lab as a summer student.
  • 2018-04-30: Matthew McNeil joins the lab as a summer student.
  • 2018-04-23: Winnie Xu joins the lab as a summer student.
  • 2018-04-16: Eric releases Segtools 1.1.14.
  • 2018-04-04: Michael is a co-author on "Opportunities and obstacles for deep learning in biology and medicine" in the Journal of the Royal Society Interface.
  • 2018-03-20: Francis presents a poster on "Predicting genomic annotation from chromatin accessibility" at the Systems Biology: Global Regulation of Gene Expression conference at Cold Spring Harbor Laboratory, New York, USA.
  • 2018-03-12: Nicole Dirks (Toronto French School) joins the lab for the Gene Researcher For A Week Program.
  • 2018-03-02: Samantha is a co-author on "Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia" in Clinical Epigenetics.
  • 2018-02-28: Mehran and Michael are the authors of "Virtual ChIP-seq: Predicting transcription factor binding by learning from the transcriptome", a preprint on bioRxiv Bioinformatics.
  • 2018-02-28: Eric releases Segway 2.0.2.
  • 2018-02-20: Danielle and Michael are the authors of "Classification and interaction in random forests" in the Proceedings of the National Academy of Sciences (PNAS).
  • 2018-02-14: Eric releases Genomedata 1.4.0.
  • 2018-02-14: Marc Asenjo joins the lab an undergraduate intern from "Universitat Politecnica de Catalunya (UPC)".
  • 2018-02-01: Samantha Wilson joins the lab as a postdoctoral fellow.
  • 2018-01-22: Michael presents a talk on "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet" at the DNA and RNA Methylation Keystone Symposium, in Vancouver, British Columbia, Canada.
  • 2018-01-04: Mickael is a co-author on "ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets" in Nucleic Acids Research.
  • 2018-01-03: Danielle Denisko joins the lab as a MSc student in the Department of Medical Biophysics.

  2017

  • 2017-12-08: Davide publishes a paper entitled "Ten quick tips for machine learning in computational biology" in BioData Mining.
  • 2017-12-04: Lee Zamparo joins the lab as a visiting postdoctoral fellow.
  • 2017-10-02: Michael presents a talk on "Identifying transcription factor binding using open chromatin, transcriptome, and methylation data" at the British Columbia Cancer Agency Research Centre in Vancouver, British Columbia, Canada.
  • 2017-09-26: Coby wins the Best Oral Presentation Award at the Molecular Biosystems Conference 2017 in Puerto Varas, Chile.
  • 2017-09-22: Rachel, Eric, and Michael are the authors of "Segway 2.0: Gaussian mixture models and minibatch training" in Bioinformatics.
  • 2017-09-08: Coby was awarded an Alexander Graham Bell Canada Graduate Scholarship-Doctoral Program (CGS-D) by the Natural Sciences and Engineering Research Council of Canada (NSERC).
  • 2017-09-07: Vallijah Subasri joins the lab as a rotation student.
  • 2017-07-14: Eric releases Segway 2.0.1.
  • 2017-06-08: Rachel, Eric, and Michael publish a pre-print titled "Segway 2.0: Gaussian mixture models and minibatch training" in bioRxiv Bioinformatics.
  • 2017-06-08: Eric releases Segway 2.0.
  • 2017-05-26: Eric releases Segway 1.4.4.
  • 2017-05-17: Michael presents a talk entitled "Novel inferences from Hi-C data with protein-coding gene data" at the Great Lakes Bioinformatics Conference (GLBIO) 2017, at University of Illinois at Chicago, Chicago, USA.
  • 2017-05-08: Chang Cao joins the lab as a summer student.
  • 2017-04-24: Mehran presents a talk and a poster entitled "Virtual ChIP-seq: Prediction of Transcription Factor Binding by Learning from the Transcriptome" at the 6th Annual Canadian Human Genetics Meeting (CHSGM 2017) in Quebec City, Canada.
  • 2017-04-01: Danielle was awarded an Alexander Graham Bell Canada Graduate Scholarship-Master's Program (CGS-M) by the Natural Sciences and Engineering Research Council of Canada (NSERC).
  • 2017-03-28: Rachel's application for the Computational Biology Undergraduate Summer Student Health Research Award is funded by the Canadian Institutes of Health Research (CIHR).
  • 2017-03-14: Davide presents a talk at the University Health Network Postdoctoral Seminar Series.
  • 2017-03-13: Cathleen Leone (Malvern Collegiate Institute) joins the lab for the Gene Researcher For A Week Program.
  • 2017-02-07: Eric releases Segway 1.4.3.
  • 2017-02-07: Michael's article on "ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data" is recommended on F1000 Prime.
  • 2017-01-31: Davide is lecturer on "Introduction to machine learning and k-NN" in the Translating Bioinformatics for Everyday Biology workshop organized by the University Health Network Office of Research Trainees.
  • 2017-01-25: Davide presents a talk on "Siamese neural network for prediction of long-range interactions in chromatin" at the Toronto Bioinformatics Users Group (TorBug), in Toronto, Canada.
  • 2017-01-20: Eric releases Segway 1.4.2.
  • 2017-01-16: Davide and Michael publish a conference report about "Genome Informatics 2016", in Genome Biology.
  • 2017-01-14: Mehran and Michael publish a paper entitled "Top considerations for creating bioinformatics software documentation", in Briefings On Bioinformatics.
  • 2017-01-09: Michael is promoted to full graduate faculty member at the University of Toronto Medical Biophysics Graduate Department.

  2016

  • 2016-12-01: Michael is interviewed in Ontario Institute for Cancer Research Online News on Expanding the DNA alphabet to understand cancer.
  • 2016-11-22: Michael presents a talk at the A.I. 2016 Day of the University of Toronto Undergraduate Artificial Intelligence Group.
  • 2016-11-21: Michael is panelist on Big Data at Gemini Connaught International Symposium 2016, University of Toronto.
  • 2016-11-17: Michael published a pre-print titled "A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types" in bioRvix.
  • 2016-11-17: Mehran and Michael publish a pre-print on "Top considerations for creating bioinformatics software documentation" at University of Toronto TSpace Research Repository.
  • 2016-11-16: Michael is guest lecturer in the CSC2417 graduate course, entitled "Algorithms for Genome Analysis course", at the University of Toronto.
  • 2016-11-15: Michael is sessions chair for Informs Nashville 2016 Conference on "TA14 - Data Mining in Genetics and Genomics".
  • 2016-11-15: Michael is session chair of the Data Mining in Genetics and Genomics session at the INFORMS Annual Meeting 2016 in Nashville, Tennessee, USA.
  • 2016-11-15: Michael is program committee member for the Synapse Idea Dream Challenge.
  • 2016-11-15: Michael is presents a talk on "Modeling Methyl-sensitive Transcription Factor Motifs With An Expanded Epigenetic Alphabet" at the Informs Nashville 2016 Conference.
  • 2016-11-08: Michael is guest lecturer on Cold Spring Harbor Laboratory Course "Advanced Sequencing Technologies and Applications".
  • 2016-10-26: Michael presents a talk entitled "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet" at the Biological Data Science meeting of Cold Spring Harbor Laboratory, in Cold Spring Harbor, New York, USA.
  • 2016-10-17: Maya Schonbach and Kathleen Houlahan join the lab as rotation students.
  • 2016-10-17: Eric, Mickael, Coby, Mehran, Rachel, Davide, and Michael are co-authors on "Semi-automated genome annotation using epigenomic data and Segway", a preprint in bioRxiv.
  • 2016-10-11: Davide presents a talk on "Deep siamese neural networks for prediction of long-range interactions in chromatin" at the Machine Intelligence Toronto MeetUp group, in Toronto, Canada.
  • 2016-10-03: Coby presents a talk on "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet", Davide presents a poster on "Deep siamese neural networks for prediction of long-range interactions in chromatin", Mickael presents a poster on "Semi-automated transcriptome annotation with segRNA", and Mehran presents a poster on "Transcription factor expression and its effects on binding site occupancy and motif preference" at the Abcam 2016 Toronto Symposium.
  • 2016-09-20: Michael presents a talk on "Transcription factor expression and its effects on binding site occupancy and motif preference" at the Genome Informatics 2016 conference, Cambridge, United Kingdom.
  • 2016-09-20: Eric releases Segway 1.4.1.
  • 2016-09-16: Rachel's application for an Undergraduate Student Research Award is funded by the Natural Sciences and Engineering Research Council of Canada.
  • 2016-08-22: Michael presents a talk on "The expanded epigenetic alphabet" at the Princess Margaret Cancer Centre Funding Announcement by the Ontario Minister of Research, Innovation and Science, Dr. Reza Moridi.
  • 2016-08-10: Michael is judge of University of Toronto's Medical Biophysics Summer Students poster day.
  • 2016-08-06: Davide presents a talk on "Deep siamese neural network for prediction of long-range interactions in chromatin" at the Deep Learning Summer School 2016 at the Universite de Montreal, Canada.
  • 2016-08-05: Michael received two team project award grants from University of Toronto Medicine by Design on "Deciphering and manipulating cell-specific regulatory networks to produce therapeutic designer cells " and "Regulatory network control of neural stem cells for endogenous repair".
  • 2016-07-12: Michael is invited speaker and presents a talk on "Semi-automated human genome annotation using chromatin data" at the Special session on Genomic Big Data Management, Modeling and Computing of the Intelligent Systems for Molecular Biology conference (ISMB 2016), in Orlando (Florida, USA).
  • 2016-07-11: The Ontario Ministry of Training, Colleges and Universities has awarded Coby Viner an Ontario Graduate Scholarship.
  • 2016-06-30: Michael published a paper entitled "Statistical Inference, Learning and Models in Big Data" in International Statistical Review.
  • 2016-06-29: Davide presents a talk on "Distal chromatin loop prediction with deep siamese neural networks" at the University Health Network (UHN) postdoctoral seminar series.
  • 2016-06-17: Michael is invited speaker and presents a talk on "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet" and "Genomic Computing challenges and perspectives" at the Bioinformatics Italian Society Annual National Conference (BITS 2016) at the University of Salerno (Fisciano, Italy).
  • 2016-06-16: Davide is a reviewer for the Conference on Neural Information Processing Systems (NIPS 2016).
  • 2016-06-09: Davide is a program committee member on the IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2016).
  • 2016-06-07: Michael is judge on The James Lepock Memorial Student Symposium (JLM) poster and oral M.Sc. and Ph.D presentations at University of Toronto.
  • 2016-05-30: Michael presents a talk on "Epigenomics" at the University of Toronto 2016 Summer Student Seminar Series.
  • 2016-05-18: Davide presented a talk on "Distal chromatin loop prediction with deep siamese neural networks", and Mehran presented a poster on "Transcription factor expression and its effects on binding site occupancy and motif preference" at GLBIO/CCBC 2016 at the University of Toronto.
  • 2016-05-17: Coby presented a flash talk and poster on "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet", and Mickael presented a poster on "Semi-automated transcriptome annotation with SegRNA" at GLBIO/CCBC 2016 at the University of Toronto.
  • 2016-05-16: Michael is a program committee member on the Great Lakes Bioinformatics and Canadian Computational Biology Conference (GLBIO/CCBC), being hosted at the University of Toronto.
  • 2016-05-09: Sarah Bi and Danielle Denisko joined the lab as summer students.
  • 2016-05-04: Michael is a co-PI working on "Deciphering and manipulating cell-specific regulatory networks to produce therapeutic designer cells" which was funded by Ontario Institute of Regenerative Medicine (OIRM).
  • 2016-05-02: Rachel Chan joined the lab as a co-op student.
  • 2016-05-02: Michael published a paper entitled "Learning the human chromatin network from all ENCODE ChIP-seq data" in Genome Biology.
  • 2016-04-27: Michael is interviewed in ASH Clinical News on "Attack of the data suckers".
  • 2016-04-16: Sarah Bi's and Danielle Denisko's applications for the Computational Biology Undergraduate Summer Student Health Research Award were funded by the Canadian Institutes of Health Research (CIHR).
  • 2016-04-06: Michael is approved as a faculty member of the Collaborative Graduate Program in Genome Biology and Bioinformatics at the University of Toronto.
  • 2016-04-06: Davide is an author of the paper entitled "Ontology-based prediction and prioritization of gene functional annotations" published in IEEE/ACM Transactions on Computational Biology and Bioinformatics.
  • 2016-04-05: Eric releases Segway 1.4.0.
  • 2016-03-18: Michael is panelist for Ministry of Research and Innovation's Ontario Open Access: Accelerating Science Symposium.
  • 2016-03-15: Michael and Coby are co-authors on "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet", a preprint in bioRxiv Bioinformatics.
  • 2016-03-14: Michael's application for an Early Researcher Award on "The expanded epigenetic alphabet: transcription factor binding in methylated DNA and beyond" was funded by the Ontario Ministry of Research and Innovation, Ontario Research Fund.
  • 2016-03-13: Davide is member of the judge board of the University of Toronto BioHacks 2016 competition.
  • 2016-03-04: Eric releases Segway 1.3.4.
  • 2016-03-01: Michael is judge of iGEM for University of Toronto Biohacks at Bahen Centre for Information Technology.
  • 2016-02-11: Michael presents a talk on "Semi-automated genome annotation and an expanded epigenetic alphabet" for the IEEE Signals and Computational Intelligence Joint Chapter, Toronto Section at Ryerson University.
  • 2016-01-31: Michael interviewed in Politico magazine on "Biden's cancer bid exposes rift among researchers".
  • 2016-01-29: Michael is author on "Statistical Inference, Learning and Models in Big Data", now revised at arXiv.
  • 2016-01-27: Coby has transitioned from the MSc to the PhD program in the Department of Computer Science.
  • 2016-01-26: Michael interviewed in Medscape Medical News on "NEJM Editor Backtracks on Data-Sharing 'Parasites'" Editorial.
  • 2016-01-10: Michael is an organizer of the Early Career Investigators Meeting on Quantitative Problems in Human Genetics and Health at the Banff International Research Station in Banff, Alberta, Canada.
  • 2016-01-08: Coby won a CIHR travel award for the upcoming Keystone Symposia on Chromatin and Epigenetics for his abstract entitled "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet".
  • 2016-01-07: Mickael Mendez joins the lab as a PhD student in the Department of Computer Science.

  2015

  • 2015-12-12: Davide presents a poster entitled "Deep Siamese Neural Networks for Prediction of Long-Range Interactions in Chromatin" at the 2015 Machine Learning in Computational Biology (MLCB) workshop of Neural Information Processing Systems (NIPS) conference in Montreal, Quebec, Canada.
  • 2015-12-11: Mehran is accepted as PhD student to the MBP Program at the University of Toronto.
  • 2015-12-07: Eric releases Segway 1.3.2.
  • 2015-11-20: Coby is awarded a Fall 2015 University of Toronto School of Graduate Studies Conference Grant to the ISCB/RECOMB RSG conference for his presentation "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet".
  • 2015-11-18: The Research in Computational Molecular Biology (RECOMB)/International Society for Computational Biology Conference on Regulatory and Systems Genomics 2015 has selected "Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression" as one of top 11 papers of 2014–2015.
  • 2015-11-17: Coby presents a talk on "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet" at the 2015 RECOMB/ISCB Conference on Regulatory & Systems Genomics.
  • 2015-11-09: Michael presents a poster on "Segway: semi-automated genome annotation with chromatin data" at the 2015 Canadian Cancer Research Conference.
  • 2015-11-02: Michael is session chair in "Big Data Analytics in Genomics" at the INFORMS 2015 Annual Meeting.
  • 2015-11-02: Michael presented a talk on "Semi-automated Human Genome Annotation Using Chromatin Data" at the INFORMS 2015 Annual Meeting.
  • 2015-10-28: Michael presented a talk on "Semi-automated genome annotation and an expanded epigenetic alphabet" at the Department of Biology, New York University.
  • 2015-10-20: Michael presented a talk on "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet"at the Geneva Park Retreat 2015, Department of Medical Biophysics, University of Toronto.
  • 2015-10-19: Michael is invited panelist for student session on "Geneva election day" at the Geneva Park Retreat 2015, Department of Medical Biophysics, University of Toronto.
  • 2015-10-09: Segway 1.3.1 Released.
  • 2015-09-28: Davide is a co-author of a chapter entitled "Extended Spearman and Kendall Coefficients for Gene Annotation List Correlation" of the Springer Lecture Notes in Bioinformatics (LNBI) book of the Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) 2014 conference selected papers.
  • 2015-09-22: Xing presented a poster on "Semi-supervised Genomic Pattern Discovery using Segway" at the University of Toronto Department of Computer Science's Annual Undergraduate Research Showcase.
  • 2015-09-11: Segway 1.3.0 released.
  • 2015-09-10: Seyed Ali Madani Tonekaboni joins the lab as a rotation student.
  • 2015-09-09: Michael is author on a meeting report on "Statistical Inference, Learning and Models in Big Data" for the Fields Institute's Big Data program now available on arXiv.
  • 2015-08-14: Jai presented a poster on "DNAmod — The DNA Modification Database" at the University of Toronto Medical Biophysics Summer Student Poster Day.
  • 2015-08-06: Davide's paper entitled "Software Suite for Gene and Protein Annotation Prediction and Similarity Search" was published on IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • 2015-08-04: Michael is a co-author on "Learning the human chromatin network from all ENCODE ChIP-seq data", a preprint in bioRxiv Genomics.
  • 2015-06-19: Eric released Segway 1.2.2.
  • 2015-05-19: Xing Zeng has joined the lab as a summer student.
  • 2015-05-14: The University of Toronto Undergraduate Research Opportunities Program has awarded Jai Sood a Summer Undergraduate Studentship.
  • 2015-05-14: Jai Sood has joined the lab as a summer student.
  • 2015-05-08: Michael presented a poster on "Transcription factor binding in an expanded epigenetic alphabet" at the EMBO conference on Chromatin and Epigenetics.
  • 2015-05-05: Michael presented a talk on "Semi-automated genome annotation and an expanded epigenetic alphabet" at a seminar at the New York Genome Center
  • 2015-05-03: Michael conducted a workshop on "Regulatory Network Analysis" at a Bioinfomatics.ca course on High-throughput Biology: From Sequence to Networks 2015.
  • 2015-05-01: Michael's application for a Accelerator Grant Competition on "Interpreting epigenetic DNA modifications in glioblastoma stem cells" was funded by the University of Toronto McLaughlin Centre.
  • 2015-04-25: Michael is a co-author on a paper on "Entropic Graph-based Posterior Regularization", accepted for oral and poster presentation at the International Conference on Machine Learning.
  • 2015-04-21: Michael presents a talk on "Transcription factor binding motifs in an expanded epigenetic alphabet" at the Canadian Human and Statistical Genetics Meeting Taiwan-Canada Joint Workshop in Epigenetics.
  • 2015-04-19: Michael co-chairs the session on "Genomics and Big Data-Data Integration" at the 4th Annual Canadian Human and Statistical Genetics Meeting.
  • 2015-04-17: Davide's paper on "Computational algorithms to predict Gene Ontology annotations" was published in BMC Bioinformatics.
  • 2015-04-15: Coby presents a poster on "Expanding the Epigenetic Alphabet: A New Dimension in Transcription Factor Binding Prediction" at the University of Toronto Department of Computer Science Research in Action Showcase.
  • 2015-04-03: Michael presents a talk on Semi-automated genome annotation and an expanded epigenetic alphabet at the University of Colorado School of Medicine Department of Biochemistry and Molecular Genetics.
  • 2015-04-02: Michael's application for Discovery Grant Competition on "Transcription factor recognition models with modified nucleobases" was funded by Natural Sciences and Engineering Research Council of Canada (NSERC).
  • 2015-04-01: Michael presents a talk on "Transcription Factor Binding in an Expanded Epigenetic Alphabet" at the Keystone Symposium on Molecular and Cellular Biology.
  • 2015-04-01: The Natural Sciences and Engineering Research Council of Canada (NSERC) has awarded Coby an Alexander Graham Bell Canada Graduate Scholarship-Master's Program (CGS-M).
  • 2015-03-24: Michael presents a talk on "Semi-automated genome annotation and an expanded epigenetic alphabet" at the University of Waterloo Bioinformatics Club.
  • 2015-03-09: Michael presents on "Semi-automated human genome annotation" and Davide presents on "Deep Autoencoder Neural Networks for Gene Ontology Annotation Predictions" to the Institute of Electrical and Electronics Engineers (IEEE) Toronto Signals and Computational Intelligence Chapter, Signal Processing Chapter, and Engineering in Medicine and Biology Chapter.
  • 2015-03-01: Michael and Coby are co-authors on "Determining the epigenome using DNA alone" in Nature Methods.
  • 2015-03-01: Davide wrote a conference report about Neural Information Processing Systems (NIPS) 2014 for the ORT Times published by the University Health Network Office of Research Trainees.
  • 2015-02-12: Michael is a co-author of "Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression" in Genome Research.
  • 2015-01-23: Eric released Segway 1.2.1.
  • 2015-01-22: Michael is a co-author on "Extending reference assembly models" in Genome Biology.
  • 2015-01-22: Michael presents a talk on "Transcription factor binding prediction" at the University of Toronto iGEM Biohackathon
  • 2015-01-15: Michael is co-presenter on "Bioinformatics" at the Third Annual Cancer Genomics Program Retreat at the Princess Margaret Cancer Centre.
  • 2015-01-05: Michael presents a talk on "Semi-automated genome annotation and an expanded epigenetic alphabet" at the McGill Bellairs Research Institute Conference on "Understanding non-coding DNA through intra and inter-species epigenomic variation".

  2014

  • 2014-12-23: Mehran Karimzadeh has joined the lab as a research assistant.
  • 2014-12-15: The University Health Network Office of Research Trainees has granted Davide a Conference Travel Award.
  • 2014-11-24: Coby presents a poster on "Transcription factor motif discovery and prediction in an expanded epigenetic alphabet" at Genomics: the Power & the Promise organized by Genome Canada and the Gairdner Foundation.
  • 2014-11-22: Michael presents a poster on "Transcription factor binding in an expanded epigenetic alphabet" at the Canadian Institutes of Health Research New Investigators meeting.
  • 2014-11-21: Michael presents a talk on "Semi-automated genome annotation and an expanded epigenetic alphabet" as part of the McGill University Seminars for the Systems Biology Training Program.
  • 2014-11-08: Michael presents a talk on "Epigenetics" at the Princess Margaret Cancer Foundation Board Retreat.
  • 2014-10-21: Coby presents a poster on "Transcription factor motif discovery and prediction in an expanded epigenetic alphabet" at the symposium on Complex Data and Analytics in Medical Research organized by the High Performance Computing Virtual Laboratory.
  • 2014-10-13: Michael interviewed in "Strength In Numbers: Finding And Developing Bioinformaticians" by Front Line Genomics.
  • 2014-10-04: Michael is a panelist on "Informatics, Annotation, and Computing" at the Applied Cancer Genomics Symposium organized by the University Health Network Cancer Genomics Program.
  • 2014-09-22: Michael presents a selected talk on "Transcription factor motif discovery and prediction in an expanded epigenetic alphabet" at Genome Informatics 2014 organized by the Wellcome Trust Scientific Conference Programme.
  • 2014-09-16: Michael is a co-author on "Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression", a preprint in bioRxiv Genomics.
  • 2014-09-08: Davide Chicco has joined the lab as a postdoctoral fellow.
  • 2014-09-01: Michael appointed Assistant Professor in the Department of Computer Science, University of Toronto.
  • 2014-08-28: Michael is a co-author on "Comparative analysis of metazoan chromatin organization" in Nature.
  • 2014-08-28: Eric releases Segway 1.2.0.
  • 2014-08-11: Eric releases Genomedata 1.3.5
  • 2014-07-27: Michael appointed to the Program Committee of the International Conference on Research in Computational Biology (RECOMB).
  • 2014-07-26: Michael interviewed in "Kelso: For barbecue, this Texan-turned-Canadian goes to great lengths" by the Austin American-Statesman.
  • 2014-07-04: Michael presents on "One genome, many epigenomes, machine learning" at the Summer Workshop on Big Data for Health organized by the University of Toronto Strategic Training for Advanced Epidemiology Program.
  • 2014-06-26: The Ontario Ministry of Training, Colleges and Universities has awarded Coby Viner an Ontario Graduate Scholarship.
  • 2014-06-05: Michael interviewed in "As Biomedical Researchers Face Tough Job Market, Experts Offer Advice and Propose Changes" by GenomeWeb Daily News.
  • 2014-06-04: Michael gives an invited talk, "Transcription Factor Regulatory Analysis," at "Pathway and Network Analysis of -omics Data", a Canadian Bioinformatics Workshop.
  • 2014-06-04: Michael chairs a session on "Genomic and epigenomic signatures in cancer" at the symposium on Epigenetic Mechanisms in Cancer organized by the Structural Genomics Consortium.
  • 2014-06-02: Coby Viner has joined the lab as a MSc student in the Department of Computer Science.
  • 2014-04-24: The Canadian Cancer Society Research Institute has granted Michael a Junior Investigator Grant Panel Travel Award.
  • 2014-04-22: Eric Roberts has joined the lab as a Bioinformatics Programmer.
  • 2014-04-22: The 101 Questions with a Bioinformatician series on acgt.me features an interview with Michael.
  • 2014-04-21: Adam Shaw will be working with us on "Hierarchical Models in Segway," a Google Summer of Code project organized by the National Resource for Network Biology.
  • 2014-04-01: Michael appointed Assistant Professor in the Department of Medical Biophysics and Associate Member, Graduate Faculty in the University of Toronto.
  • 2014-03-05: The National Resource for Network Biology names Michael a mentor for their Google Summer of Code project.
  • 2014-03-05: Michael delivers an invited presentation for the Major Discoveries of Biology seminar series, Undergraduate Program in Genomic Sciences, National Autonomous University of Mexico.
  • 2014-02-25: Michael named core faculty of the Canadian Bioinformatics Workshops and added to the list of Bioinformatics Experts in Canada by Bioinformatics.ca.
  • 2014-01-16: The Faces of the Princess Margaret series of the Princess Margaret Cancer Foundation Blog features an interview with Michael.

  2013

  • 2013-11-27: Michael delivers an invited talk, "Semi-automated annotation of the human genome using chromatin and RNA-seq data" at the Toronto Bioinformatics Users Group.
  • 2013-11-17: Michael delivers an invited tutorial, "Semi-automated Genome Annotation with Segway" at the Genomic Signal Processing and Statistics of the Institute of Electrical and Electronics Engineers.
  • 2013-11-04: The Cancer Genomics Program, University Health Network has named Michael co-chair of its bioinformatics subcommittee.
  • 2013-11-04: The Princess Margaret Genomics Centre has named Michael to its advisory board.