Hoffman Lab: news archive

A record of previous activities at the Hoffman Lab.

2017

• 2017-05-08: Chang Cao joins the lab as a summer student.
• 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 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 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 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.
• 2015-03-24: 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 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 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.