ISCB Accomplishments by a Senior Scientist Award: Bonnie Berger
2019 ISCB Accomplishments by a Senior Scientist Award: Bonnie Berger
Bonnie Berger, Simons Professor of Mathematics and Professor of Electrical Engineering & Computer, Massachusetts Institute of Technology, United States
The ISCB Accomplishments by a Senior Scientist Award recognizes leaders in the fields of computational biology and bioinformatics for their significant research, education, and service contributions. Bonnie Berger is being honored as the 2019 winner of the ISCB Accomplishments by a Senior Scientist Award.
Professor Bonnie Berger is the Simons Professor of Mathematics with a joint appointment in Computer Science, and Associate Member of the Broad Institute at Massachusetts Institute of Technology (MIT), Cambridge, MA, United States. She is also Faculty of Harvard and MIT Health, Science and Technology. She received her Ph.D from MIT in 1990 in computer science and completed a postdoctoral fellowship in applied mathematics in 1992.
After beginning her career working in algorithms at MIT, she was one of the pioneer researchers in computational biology and, together with the many students she has mentored, has been instrumental in defining the field. She continues to lead efforts to design algorithms to gain biological insights from recent advances in automated data collection and the subsequent large data sets drawn from them. Dr. Berger works on diverse areas, including Compressive Genomics, Network Inference, Structural Bioinformatics, Population Genomics, and Genomic Privacy.
She has co-authored over 185 scholarly research articles and has been invited to present at conferences in fields ranging from randomized algorithms and graph theory to computational Molecular Biology. Dr. Berger was recently elected to serve as a Member-at-Large of the Section on Mathematics at American Association for the Advancement of Science (AAAS). Over the years, she has received numerous honors including: election to the American Academy of Arts and Sciences, the NIH Margaret Pittman Director’s Award for Outstanding Scientific Achievement & Lectureship, Biophysical Society's Dayhoff Award, Technology Review Magazine's inaugural TR100 as a top young innovator, ACM Fellow, ISCB Fellow, American Institute for Medical and Biological Engineering Fellow, American Mathematical Society Fellow, NSF Career Award and Honorary Doctorate from EPFL.
ISCB will present award winners Bonnie Berger (Accomplishments by a Senior Scientist Award), Christophe Dessimoz (Overton Prize), William Stafford Noble (Innovator Award) and Barbara Bryant (Outstanding Contributions to ISCB Award), at ISMB/ECCB 2019 (www.iscb.org/ismbeccb2019), which is being held in Basel, Switzerland, July 21-25. Berger, Dessimoz, and Noble will present keynote addresses during the conference.
Full bibliographical articles profiling the award recipients will be available in the ISMB/ECCB 2019 focus issue of the ISCB newsletter later this year, as well as the ISCB Society Pages in OUP Bioinformatics, and F1000 Research ISCB Community Journal.
Outstanding Contributions to ISCB Award Barbara Bryant
2019 Outstanding Contributions Award: Barbara Bryant
Barbara Bryant, Senior Director, Constellation Pharmaceuticals
The Outstanding Contributions to ISCB Award recognizes an ISCB member for her or his outstanding service contributions toward the betterment of ISCB through exemplary leadership, education, and service. The 2019 recipient of the Outstanding Contributions to ISCB Award is Barbara Bryant.
Barbara Bryant is the Senior Director for Bioinformatics at Constellation Pharmaceuticals. A computational biologist with over 20 years of industry experience, Barbara designs and builds data analysis systems, and provides bioinformatics services.
Barbara is being recognized for her significant contributions to ISCB. During the early years of ISCB, she held the officer positions of Secretary and Vice President and remained as a member of the Board of Directors until 2008. She helped to shape the Society in the early years, including crafting the advocacy section of the first ISCB strategic plan in 2003. That led to the development of a Public Affairs and Policy committee, which she later chaired. She served as the ISCB representative on the FASEB Board of Directors from 2003 to 2007, and continued as alternate Board Member until 2011. At FASEB, she served on the Science Policy Committee, and advocated on Capitol Hill for funding for basic scientific research. Becoming aware of anecdotal evidence of problems scientists were facing to obtain visas to come to the USA for conferences and research collaborations, she conducted a survey of ISCB members. The results were shared with the National Academy of Sciences in preparation for a 2008 Senate hearing on the topic of barriers to scientific exchange. Barbara then authored an article about the importance of open scholarly travel for collaboration, with recommendations for scientific societies. She along with others wrote the ISCB software sharing policy, which was approved by the Board of Directors in 2008 and remains an important policy statement of the Society today. In 2005 Barbara joined the editorial board of the Public Library of Science Computational Biology journal, rising to Deputy Editor in Chief. She served on the ISMB committees in 2010 and 2012. Barbara organized the orienteering ice-breaker at ISMB conferences for many years, including in San Diego, Copenhagen, Edmonton, Brisbane, Glasgow, Detroit, Toronto, Vienna, Stockholm, and Boston. _______________________________________________________
ISCB will present award winners Bonnie Berger (Accomplishments by a Senior Scientist Award), Christophe Dessimoz (Overton Prize), William Stafford Noble (Innovator Award) and Barbara Bryant (Outstanding Contributions to ISCB Award), at ISMB/ECCB 2019 (www.iscb.org/ismbeccb2019), which is being held in Basel, Switzerland, July 21-25. Berger, Dessimoz, and Noble will present keynote addresses during the conference.
Full bibliographical articles profiling the award recipients will be available in the ISMB/ECCB 2019 focus issue of the ISCB newsletter later this year, as well as the ISCB Society Pages in OUP Bioinformatics, and F1000 Research ISCB Community Journal.
William Stafford Noble, Professor, Department of Genome Sciences, Department of Computer Science and Engineering, Director, Computational Molecular Biology Program, University of Washington, United States
The year 2016 marked the launch of the ISCB Innovator Award, which is given to a leading scientist who is within two decades of receiving the PhD degree, has consistently made outstanding contributions to the field, and continues to forge new directions. William Stafford Noble is the 2019 winner of the ISCB Innovator Award.
Dr. Noble is a Professor in the Department of Genome Sciences and in the Paul G. Allen School of Computer Science and Engineering at the University of Washington, United States. He received the Ph.D. in computer science and cognitive science from University of California, San Diego in 1998. After a one-year postdoc with David Haussler at University of California, Santa Cruz, he became an Assistant Professor in the Department of Computer Science at Columbia University. In 2002, he joined the faculty of the Department of Genome Sciences at the University of Washington where he now is a Professor and the Director of the Computational Molecular Biology Program.
Noble's research applies statistical and machine learning methods to the analysis of complex biological data sets. He has extensive experience developing novel analytical methods, creating user-friendly software implementing those methods, and collaborating with experimentalists. The most notable areas of research for Noble and his group are sequence analysis methods for DNA and proteins, kernel methods for learning from heterogeneous data, semi-automated genome annotation, the 3D structure of the genome and machine learning and statistical methods for analyzing shotgun proteomics data.
He is the author of >230 peer reviewed publications and has advised 27 postdoctoral fellows and 24 graduate students. William is the recipient of an NSF CAREER award, is a Sloan Research Fellow, is on the Clarivate Analytics list of “Highly cited researchers,” and is a Fellow and former member of the Board of Directors of the International Society for Computational Biology. _______________________________________________________
ISCB will present award winners Bonnie Berger (Accomplishments by a Senior Scientist Award), Christophe Dessimoz (Overton Prize), William Stafford Noble (Innovator Award) and Barbara Bryant (Outstanding Contributions to ISCB Award), at ISMB/ECCB 2019 (www.iscb.org/ismbeccb2019), which is being held in Basel, Switzerland, July 21-25. Berger, Dessimoz, and Noble will present keynote addresses during the conference.
Full bibliographical articles profiling the award recipients will be available in the ISMB/ECCB 2019 focus issue of the ISCB newsletter later this year, as well as the ISCB Society Pages in OUP Bioinformatics, and F1000 Research ISCB Community Journal.
Christophe Dessimoz, SNSF Professor, University of Lausanne; Associate Professor, University College London; Group Leader, Swiss Institute of Bioinformatics
The Overton Prize recognizes the research, education, and service accomplishments of early to mid-career scientists who are emerging leaders in computational biology and bioinformatics. The Overton Prize was instituted in 2001 to honor the untimely loss of G. Christian Overton, a leading bioinformatics researcher and a founding member of the ISCB Board of Directors. Christophe Dessimoz is being recognized as the 2019 winner of the Overton Prize.
Christophe Dessimoz is a SNSF Professor at the University of Lausanne; an Associate Professor at the University College London; a Group Leader at the Swiss Institute for Bioinformatics. Christophe obtained his Master in Biology (2003) and PhD in Computer Science (2009) from ETH Zurich, Switzerland. After a postdoc at the European Bioinformatics Institute near Cambridge (UK), he joined University College London as Lecturer (2013) and was promoted to a Reader in 2015. He joined the University of Lausanne as a SNSF Professor in 2015. With 70 papers published, Christophe has made varied and sustained contributions to bioinformatics.
He is renowned for his contributions to and subsequently management of the OMA resource providing high quality information on orthologous proteins. OMA is a very highly regarded resource with important applications in protein function prediction.
Another important thread across Christophe’s work has been his pursuit of benchmarking. Christophe’s rigorous approach to benchmarking had a major impact on three key subfields of computational biology: orthology inference, sequence alignment, and gene ontology.
ISCB will present award winners Bonnie Berger (Accomplishments by a Senior Scientist Award), Christophe Dessimoz (Overton Prize), William Stafford Noble (Innovator Award) and Barbara Bryant (Outstanding Contributions to ISCB Award), at ISMB/ECCB 2019 (www.iscb.org/ismbeccb2019), which is being held in Basel, Switzerland, July 21-25. Berger, Dessimoz, and Noble will present keynote addresses during the conference.
Full bibliographical articles profiling the award recipients will be available in the ISMB/ECCB 2019 focus issue of the ISCB newsletter later this year, as well as the ISCB Society Pages in OUP Bioinformatics, and F1000 Research ISCB Community Journal.
Complete List of Winners - ISCB Art in Science Competition
2014 FIRST PLACE
Hai Fang Julian Gough University of Bristol, United Kingdom
supraHex
This artwork called ‘supraHex’ is inspired by the prevalence of natural objects such as a honeycomb or at Giant’s Causeway. supraHex has architectural design of a supra-hexagonal map: symmetric beauty around the center, from which smaller hexagons radiate circularly outwards. In addition to this architectural layout, supraHex also captures mechanistic nature of these objects: formation in a self-organising manner. For this, supraHex is able to self-organise the input data (eg transcriptome data). In doing so, genes with similar data patterns are clustered to the same or nearby nodes (hexagons). The map distance (the hexagon size) tells how far each node is away from its neighbors, thus characterising relationships between clustered genes. Based on this map distance, supraHex is also able to partition the map to obtain gene meta-clusters covering continuous regions, as colour-coded by the ‘potato-peach-tomato’ colormap. This artwork is generated by an open-source R/Bioconductor package ‘supraHex’ (http://bioconductor.org/packages/release/bioc/html/supraHex.html).
2015 FIRST PLACE
Luke Wilson Jim Procter Geoff Barton University of Dundee, United Kingdom
Analogue Alignment
“Multiple sequence alignments were once performed manually, and even today, we still examine automatically computed alignments to check that we can't do better.” –Jim Procter This is an image of the Jalview Abacus, a sculptural attempt to visually represent the function of the Jalview protein alignment program. The program can be used to find alignments of amino acids in similar proteins. These alignments are then used to find similarities and differences between these proteins.
This object expresses the core process of Jalview in a physical space, and plays on the relationship between high tech and low tech solutions. It is a functioning abacus built by hand from wood and steel. Each row is an extract from different similar proteins (cysteine proteases) and an alignment can be found by lining up the beads of like amino acids in the columns. If it was long enough it could be used to align the entire sequence manually.
Photography: Luke Wilson Design and Construction: Luke Wilson in collaboration w. Jim Procter and Geoff Barton
2016 FIRST PLACE
Sean O'Donoghue, CSIRO & Garvan Institute, Australia Christopher Hammang, Garvan Institute, Australia Julian Heinrich, CSIRO, Australia
The Dark Proteome
Here, we use light and darkness to represent the known and unknown proteome of structural biology. Currently, only 12% of the human proteome has been observed with experimental structure determination methods such as crystallography or NMR spectroscopy. For a further 36%, structural information can be inferred by homology modelling. The remaining 52% of the proteome is 'dark', i.e., has completely unknown molecular conformation.
2017 FIRST PLACE
Nick Schurch Chris Cole University of Dundee, United Kingdom
ImpactFactor
impactFactor is a perspective on the use of the Journal Impact Factor scores in science. In taking a literal interpretation of this score we, as scientists, are questioning its use as a measure of scientific quality or importance.
Journal Impact Factor aims to reflect the importance of a journal, however it is now used to assess the quality of the scientists who publish within it. Employers and funding bodies conflate this artificial metric as a simplistic judge of a scientist’s quality with their choice of publisher. With this perspective for modern scientists, it could be argued that where they publish has become more important than the science itself! We feel it would be much better to judge both the scientist and their publications on merit alone.
The use of artificial quality metrics is an issue for all scientists and this piece is part of the discussion of moving scientific publishing away from its 17th Century roots. Publication remains a cornerstone of scientific research but impactFactor highlights the need for a better way to judge, and, perhaps publish, impactful science.
The original acrylic on canvas artwork was exhibited at Symbiosis, a local collaborative Science/Art exhibition in Dundee. The piece measures 2m x 2m and is too big to bring to the conference, instead, we present here a 70cm x70cm photographic interpretation of the piece.
2018 FIRST PLACE
Ruth Callaway Swansea University, Biosciences, UK
Mondrian’s Sum of Squares
Science inspired many artist, but here it was the other way around. The visualisation of marine biodiversity data was modelled on paintings by the early 20th century Dutch artist Piet Mondrian. It is an ongoing challenge for ecologists to compress and simplify complex data and to illustrate patterns in marine ecosystems. Differently coloured and sized rectangles and squares were assembled in this Mondrian’s Sum of Squares and simultaneously shows numerical and taxonomic information of a benthic invertebrate seafloor community (Swansea Bay, Wales, UK). Each field, large or small, represents a different species. The size of the square or rectangle indicates how numerically common a species was, and colours indicate taxonomic or functional groups (blue: polychaete worms, yellow: bivalves, red: crustaceans, white: other mobile species, grey: other sessile species). The few large squares highlight that the seafloor community consists of just a handful of common species, while most occur in low densities. The overwhelming number of blue fields shows the importance of worm species for biodiversity. Like many of Mondrian’s paintings, this artwork is an abstract representation of the natural world. It differs in that Piet Mondrian deliberately stepped away from reality, while this work translates scientific data into art.
2018 SECOND PLACE
Alaa Abi Haidar University of Pierre and Marie Curie
dEYEversity
The two contrasted eyes are composed of the same ingredients and diversity of eyes, ad infinitum. The artist owns all images’ rights.
Featured at La Nuit de la Photographie Contemporaine and soon in a gallery.
As for the technique, I developed image processing algorithms to crop the eyes from the 1001faces.org project to have them automatically reassembled in this mosaic using another algorithm that optimizes the images' position according to the best matching pixel intensities.
2018 THIRD PLACE
Marwan Abdellah École polytechnique fédérale de Lausanne (EPFL)
In Silico Brainbow
In silico brainbow optical section of a neocortical slice (920 × 640 × 1740 μm3) created with a virtual light-sheet fluorescence microscope (LSFM).
The simulation of the LSFM is performed on a physically-plausible basis using Monte Carlo ray tracing and geometric optics. The tissue model is reconstructed in a three-step process: 1) converting the morphological skeletons of the neurons into piecewise surface meshes that represent their membranes, 2) reconstructing a volumetric model of the tissue using solid voxelization and finally 3) tagging the neurons with the optical properties of the neocortical tissue and also the spectroscopic properties of different fluorescent dyes.
The slice is virtually-tagged with six different fluorescent proteins (GFP, CFP, eCFP, mBanana, mCherry and mPlum) and illuminated at the maximum excitation wavelength of each respective dye
2019 FIRST PLACE
Dr. Kliment Olechnovic Department of Bioinformatics, Life Sciences Center Vilnius University Lithuania
Nick Schurch Chris Cole University of Dundee, United Kingdom
ImpactFactor
impactFactor is a perspective on the use of the Journal Impact Factor scores in science. In taking a literal interpretation of this score we, as scientists, are questioning its use as a measure of scientific quality or importance.
Journal Impact Factor aims to reflect the importance of a journal, however it is now used to assess the quality of the scientists who publish within it. Employers and funding bodies conflate this artificial metric as a simplistic judge of a scientist’s quality with their choice of publisher. With this perspective for modern scientists, it could be argued that where they publish has become more important than the science itself! We feel it would be much better to judge both the scientist and their publications on merit alone.
The use of artificial quality metrics is an issue for all scientists and this piece is part of the discussion of moving scientific publishing away from its 17th Century roots. Publication remains a cornerstone of scientific research but impactFactor highlights the need for a better way to judge, and, perhaps publish, impactful science.
The original acrylic on canvas artwork was exhibited at Symbiosis, a local collaborative Science/Art exhibition in Dundee. The piece measures 2m x 2m and is too big to bring to the conference, instead, we present here a 70cm x70cm photographic interpretation of the piece.
2018 ISCB Art in Science Competition
Alaa Abi Haidar University of Pierre and Marie Curie
dEYEversity
The two contrasted eyes are composed of the same ingredients and diversity of eyes, ad infinitum. The artist owns all images’ rights.
Featured at La Nuit de la Photographie Contemporaine and soon in a gallery.
As for the technique, I developed image processing algorithms to crop the eyes from the 1001faces.org project to have them automatically reassembled in this mosaic using another algorithm that optimizes the images' position according to the best matching pixel intensities.
2018 ISCB Art in Science Competition
Marwan Abdellah École polytechnique fédérale de Lausanne (EPFL)
In Silico Brainbow
In silico brainbow optical section of a neocortical slice (920 × 640 × 1740 μm3) created with a virtual light-sheet fluorescence microscope (LSFM).
The simulation of the LSFM is performed on a physically-plausible basis using Monte Carlo ray tracing and geometric optics. The tissue model is reconstructed in a three-step process: 1) converting the morphological skeletons of the neurons into piecewise surface meshes that represent their membranes, 2) reconstructing a volumetric model of the tissue using solid voxelization and finally 3) tagging the neurons with the optical properties of the neocortical tissue and also the spectroscopic properties of different fluorescent dyes.
The slice is virtually-tagged with six different fluorescent proteins (GFP, CFP, eCFP, mBanana, mCherry and mPlum) and illuminated at the maximum excitation wavelength of each respective dye.
2018 ISCB Art in Science Competition
FIRST PLACE
Ruth Callaway Swansea University, Biosciences, UK
Mondrian’s Sum of Squares
Science inspired many artist, but here it was the other way around. The visualisation of marine biodiversity data was modelled on paintings by the early 20th century Dutch artist Piet Mondrian. It is an ongoing challenge for ecologists to compress and simplify complex data and to illustrate patterns in marine ecosystems. Differently coloured and sized rectangles and squares were assembled in this Mondrian’s Sum of Squares and simultaneously shows numerical and taxonomic information of a benthic invertebrate seafloor community (Swansea Bay, Wales, UK). Each field, large or small, represents a different species. The size of the square or rectangle indicates how numerically common a species was, and colours indicate taxonomic or functional groups (blue: polychaete worms, yellow: bivalves, red: crustaceans, white: other mobile species, grey: other sessile species). The few large squares highlight that the seafloor community consists of just a handful of common species, while most occur in low densities. The overwhelming number of blue fields shows the importance of worm species for biodiversity. Like many of Mondrian’s paintings, this artwork is an abstract representation of the natural world. It differs in that Piet Mondrian deliberately stepped away from reality, while this work translates scientific data into art.
The ISCB Student Software Prize
Congratulations to TEPIC, ISCB's 2019 studentSoftware Award winner!
The ISCB Student Software Prize was created to recognize the development of excellent bioinformatics software by students and postdocs that are members of the International Society for Computational Biology.
The winner(s) of the ISCB Student Software Prize will receive the prize of their choice:
Complimentary ISCB membership
Free registration to any official ISCB conference, at membership rate.
Prize Winner (s) will be announced in ISCB’s Spring Newsletter!
If you are an ISCB Member and a Student or Postdoc who has created bioinformatics software you would like to share, submit your work for a chance to win the ISCB Student Software Prize!
How to Submit Your Software Use the link provided below to submit a brief cover letter stating the purpose of the software, the scope of the nominees contribution, the distribution license and URL to the software along with a manuscript or a reprint.
Student Requirements:
Must be a major contributing author of the software being developed
An ISCB member in good standing at both the time of submission and acceptance
Students or postdoc at an accredited degree-granting institution at the time of the nomination
Software Requirements:
The software must be usable on at least one of the major operating systems (Un*x, MacOS, Windows)
The software must be distributed under an open source license that allows for reuse and is recognized by the Open Source Initiative. https://opensource.org/licenses/category
Self-nominations are accepted
Softwaremay be nominated more than once, as long as it has not been awarded the prize yet.
Each nomination is limited to a single piece of software and three (3) student/postdoc-developers.
