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Search: genetic - Matches: 215


Event sections:


 event sectionComputational Biology
Machine Learning in Computational Biology The field of computational biology has seen dramatic growth over the past few years, both in terms of new available data, new scientific questions, and new challenges for learning and inference. In particular, biological data ...
 event sectionFrom Statistical Genetics to Predictive Models in Personalized Medicine
The purpose of this cross-discipline workshop is to bring together machine learning and healthcare researchers interested in problems and applications of predictive models in the field of personalized medicine. The goal of the workshop will be to bridge the gap ...
 event sectionMachine Learning in Computational Biology
The field of computational biology has seen dramatic growth over the past few years, both in terms of new available data, new scientific questions, and new challenges for learning and inference. In particular, biological data is often relationally structured and ...
 event sectionOptimization for Machine Learning
Optimization lies at the heart of ML algorithms. Sometimes, classical textbook algorithms suffice, but the majority problems require tailored methods that are based on a deeper understanding of the ML requirements. ML applications and researchers are driving some of the ...

Events:


 eventInternational Workshop on Advances in Machine Learning for Computational Finance (AMLCF), London 2009
During recent years, the use of intelligent systems in the financial and economic industries have increased substantially, providing a new perspective to the agenda of finance and economics by their ability to handle large amounts of financial data and simulate ...
 eventLecture Series by Howard Cedar: Epigenetics and Methylation
Professor Chaim Cedar is a pioneer in the field of DNA methylation and epigenetics. His earliest work established the pattern of DNA methylation, after which he demonstrated its regulatory mechanisms and its role in development and cancer. Over the last ...
 eventMednarodni posvet Biološka znanost in družba: GENIalna prihodnost - genetika, determinizem in svoboda / International Conference Bioscience and Society: GENIal future – genetics, determinism and freedom
Na mednarodnem posvetu GENIalna prihodnost - genetika, determinizem in svoboda (Biološka znanost in družba) so sodelovali priznani tuji in domači predavatelji s področja biološke znanosti in medicine ter družboslovnih znanosti. V panelnih diskusijah je tekla razprava o vplivih raziskovanja in ...
 eventMIT 7.012 Introduction to Biology - Fall 2004
The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers ...
 eventMIT 7.014 Introductory Biology - Spring 2005
The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers ...
 event John Shawe-Taylor, Manfred Opper, Cedric Archambeau: NIPS Workshop on Dynamical Systems, Stochastic Processes and Bayesian Inference, Whistler 2006
The modelling of continuous-time dynamical systems from uncertain observations is an important task that comes up in a wide range of applications ranging from numerical weather prediction over finance to genetic networks and motion capture in video. Often, we may ...
 eventNIPS Workshop on Machine Learning in Computational Biology, Whistler 2008
The field of computational biology has seen dramatic growth over the past few years, both in terms of new available data, new scientific questions, and new challenges for learning and inference. In particular, biological data is often relationally structured and ...
 event Kelly D. Brownell: YALE PSYC 123 The Psychology, Biology and Politics of Food with Professor Kelly D. Brownell
This course encompasses the study of eating as it affects the health and well-being of every human. Topics include taste preferences, food aversions, the regulation of hunger and satiety, food as comfort and friendship, eating as social ritual, and social ...

Project:


 projectNIB - Nacionalni inštitut za biologijo
Nacionalni inštitut za biologijo (NIB) je tretji največji javni raziskovalni zavod na področju naravoslovnih ved v Sloveniji in predstavlja najprodornejše in najsodobnejše raziskovalne potenciale v osnovnih in uporabnih bioloških raziskavah. Osrednjo dejavnost Nacionalnega inštituta za biologijo predstavljajo temeljne in aplikativne ...

Debate:


 debate Kari Stefansson, Edward Jung, Craig Venter, Steve Wozniak, Spencer Reiss: Invention and Innovation: Emerging Technologies that Will Change the World The Inventor View
When Steve Wozniak was young, he found his first transistor radio inspiring. He has channeled his passion for useful, convenient machines into a new company that makes global positioning satellite (GPS) locators for everyday purposes. He imagines tagging a child ...

Demonstration videos:


 demonstration video Seong-Hwan Jun: Entangled Monte Carlo
We propose a novel method for scalable parallelization of SMC algorithms, Entangled Monte Carlo simulation (EMC). EMC avoids the transmission of particles between nodes, and instead reconstructs them from the particle genealogy. In particular, we show that we can reduce ...
 demonstration video Travis Brown, Sekou Remy: Machine Learning for Bipedal Walking
Bipedal robotic locomotion presents a significant challenge to the controls designer. The equations of motion governing these systems are generally hybrid or switched due to intermittent ground contact and consist of numerous coupled non-linear differential equations even in the simplest ...

Invited talks:


 invited talk James M. Rehg: Behavior Imaging and the Study of Autism
Beginning in infancy, individuals acquire the social and communication skills that are vital for a healthy and productive life. Children with developmental delays face great challenges in acquiring these skills, resulting in substantial lifetime risks. Children with an Autism Spectrum ...
 invited talk Holger H. Hoos: Computer-Aided Algorithm Design: Automated Tuning, Configuration, Selection and Beyond
High-performance algorithms can be found at the heart of many software systems; they often provide the key to effectively solving the computationally difficult problems encountered in the application areas in which these systems are deployed. Examples of such problems include ...
 invited talk Hans Lehrach: Deep sequencing and systems biology: steps on the way to an individualised treatment of cancer patients
Biological processes are driven by complex networks of interactions between molecular and cellular components. Predicting the outcome of potential disturbances is of prime importance to be able to prevent disease, as well as to identify possible therapies for diseases, which ...
 invited talk Grace Wahba: Examining the Relative Influence of Familial, Genetic, and Environmental Covariate Information in Flexible Risk Models
We present a novel method for examining the relative influence of familial, genetic and environmental covariate information in flexible nonparametric risk models. Our goal is investigating the relative importance of these three sources of information as they are associated with ...
 invited talk Nir Friedman: Exploring transcription regulation through cell-to-cell variability
The regulation of cellular protein levels is a complex process involving many regulatory mechanisms. These regulatory mechanisms introduce a cascade of stochastic events leading to variability of protein levels between cells. Previous studies have shown that perturbing genes involved in ...
 invited talk Kristin P. Bennett: Fighting the Tuberculosis Pandemic Using Machine Learning
Tuberculosis (TB) infects one third of the world's population and is the second leading cause of death from a single infectious agent worldwide. The emergence of drug resistant TB remains a constant threat. We examine how machine learning methods can ...
 invited talk Sayan Mukherjee: Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets
 invited talk Xavier Gidrol: Integration of genome-wide data to infer genetic networks
To comprehend biology as a system, one needs to analyze the structure and dynamics of cell components as modules rather than isolated part. Progress in technological devices, analytical methods and biological models are required to decipher molecular networks and eventually ...
 invited talk Jason Bond: Integrative approaches to delimiting species and taxonomy: lesson learned form highly structured arthropod taxa
Advances in molecular techniques over the past decades have significantly shaped the field of systematics and taxonomy. Approaches to species delimitation that employ methods like DNA barcoding and generalized mixed Yule coalescent models are seemingly attractive because they present a ...
 invited talk Eileen Hebets: Interacting traits and secret senses – arachnids as models for studies of behavioral evolution
Arachnids are extremely well equipped to both extract salient information from their environment and to transmit salient information through their environment utilizing a diverse array of sensory structures. Many of these sensory structures are highly specialized and are unique to ...
 invited talk Yves Moreau: Kernel methods for genomic data fusion
Despite significant advances in omics techniques, the identification of genes causing rare genetic diseases and the understanding of the molecular networks underlying those disorders remains difficult. Gene prioritization attempts to integrate multiple, heterogeneous data sources to identify candidate genes most ...
 invited talk Jukka Jernvall: Lost in Translation from Genes to Organisms
Data mining genomes and developmental genetics provides information for building mathematical gene-network models on development. These models can be used to provide insilico predictions about processes such as developmental expression and regulation of genes.
 invited talk Nataša Pržulj: Network Topology Uncovers Function, Disease, and Phylogeny
We present our new tools that are advancing network analysis towards a theoretical understanding of the structure of biological networks. Analogous to tools for analyzing and comparing genetic sequences, we are developing new tools that decipher large network data sets ...
 invited talk Florence d'Alche-Buc: Protein-protein network inference with regularized output and input kernel methods
Prediction of a physical interaction between two proteins has been addressed in the context of supervised learning, unsupervised learning and more recently, semi-supervised learning using various sources of information (genomic, phylogenetic, protein localization and function). The problem can be seen ...
 invited talk Pascal Falter-Braun: Signatures of evolution and systems organization from an Arabidopsis interactome network map
Elucidating mechanisms of life requires analysis of whole systems and understanding the complex interplay of the individual components. Proteins control and mediate the majority of biological activities and interactions among proteins play a decisive role in the dynamic modulation of ...
 invited talk Michael I. Jordan: Statistical Inference of Protein Structure and Function
The study of the structure and function of proteins serves up many problems that offer challenges and opportunities for computational and statistical research. I will overview my experiences in several such problem domains, ranging from domains where off-the-shelf ideas can ...
 invited talk Roman Jerala: Synthetic Biology Achievements And Future Prospects
Synthetic biology, which combines engineering approach in biological systems is getting a strong momentum due to the recent technological advances, which allow us to manipulate the genetic information at an unprecedented scale. Currently synthetic biology is exploiting its potentials and ...
 invited talk Ben Lehner: The genetics of individuals: why would a mutation kill me, but not you?
To what extent is it possible to predict the phenotypic differences among individuals from their completely sequenced genomes? We use model organisms (yeast, worms) to understand when you can, and why you cannot, predict the biology of an individual from ...
 invited talk Munir Pirmohamed: Using human genomic variation for individualisation of drug treatment
There is inherent variation in the responses to drugs used in medicine. This can affect both efficacy and toxicity, which in some individuals leads to a poor benefit-risk ratio of drugs. Strategies to improve the benefit-risk ratio of drugs by ...

Keynotes:


 keynote Nikola Kasabov: Computational Neurogenetic Modelling: Methods, Systems, Applications
We would like to notify you that the first ten minutes of the lecture were not recorded due to the technical problems. For additional content please check the presentation under section "See Also".
 keynote Florence Demenais: New advances in the genetics of melanoma: how can it contribute to personalized medicine?
 keynote Florian Markowetz: Reconstructing networks from experimental and natural genetic perturbations
Functional genomics has demonstrated considerable success in inferring the inner working of a cell through analysis of its response to various perturbations. Perturbations can take the form of experimental interventions, like gene deletions or RNA interference, or natural perturbations, like ...

Lectures:


 lecture H. Robert Horvitz: 2002 Nobel Prize in Physiology or Medicine Nobel Lecture
In October 2002, The Nobel Prize in Physiology or Medicine was awarded to H. Robert Horvitz, Sydney Brenner and John El Sulston "for their discoveries concerning genetic regulation of organ development and programmed cell death."
 lecture Adriana Pietramala, Veronica L. Policicchio, Pasquale Rullo, Inderbir Sidhu: A Genetic Algorithm for Text Classification Rule Induction
This paper presents a Genetic Algorithm, called Olex-GA, for the induction of rule-based text classifiers of the form ``classify document $d$ under category $c$ if $t_1 in d$ or ... or $t_n in d$ and not ($t_{n+1} in d$ or ...
 lecture Li-Huei Tsai: Alzheimer’s Disease: Current State and Hope for the Future
Measured in human suffering, and by statistics, Alzheimer’s Disease (AD) presents a formidable specter: with incidence approaching 30 million worldwide and growing rapidly, it is now the sixth leading cause of death in the US. As life expectancy lengthens, AD ...
 lecture Suyash Shringarpure: A New Admixture Model for Inference of Population Structure in Light of Both Genetic Admixing and Allele Mutations
Traditional methods for analyzing population structure, such as the Structure program, ignore the influence of mutational effects. We propose mStruct, an admixture of population-specific mixtures of inheritance models, that addresses the task of structure inference and mutation estimation jointly through ...
 lecture Jacqueline A. Lees: Animal Models of Cancer
Jacqueline Lees holds the lowly mouse in high regard. It is “beautifully developed” as a model system for cancer. Lees says that while researchers can learn much from cells in a Petri dish, they require living organisms to observe, for ...
 lecture David Botstein: An Introductory Science Curriculum for 21st Century Biologists
How will biology move beyond the Human Genome Project and the task of reducing living things to their genetic sequences? According to David Botstein, the answer lies in “educating the biologist of the 21st century”—someone who will be conversant not ...
 lecture Salomon Israel: Association between genetic polymorphisms for vasopressin and oxytocin receptors and pro-social behavior in economic decision tasks
Human altruism is a widespread phenomenon that has puzzled evolutionary biologists since Darwin. Economic games illustrate human altruism by demonstrating that behavior deviates from economic predictions of selfish utility maximization. A game that most plainly demonstrates this altruistic tendency is ...
 lecture Simon Rogers: Bayesian Inference of transcription factor activity - an application to the fission yeast cell cycle
When modeling genetic regulatory interactions, it is often assumed that the mRNA expression of a transcription factor is a reliable proxy for the regulatory activity of that transcription factor. There are many examples where this assumption does not hold due ...
 lecture Jože Trontelj: Bioetika, raziskovanje in nevarnost zlorabe / Bioethics, Research on Human Beings, and Risks of Misuse
Nedavni napredek biologije in medicine napoveduje nastop nove dobe v zgodovini človeštva. Posebno spoznanja in novi posegi na področju genetike utegnejo imeti težko predvidljive posledice za posameznika in za družbo. Koristi tega napredka pa ne bodo zastonj. V ceni, ki ...
 lectureCan a New Theory of the Neocortex Lead to Truly Intelligent Machines?
Talk about intelligent designs: Jeff Hawkins says he’s mapped out the way the human brain works, and has begun to fashion thinking machines to emulate the process. It comes down to Hierarchical Temporal Memory (HTM). Basically, he says, our brains ...
 lecture Eric S. Lander: Cancer Research in the Genomic Era
Eric Lander likens the current age of biological discovery to the days of great ocean-going exploration. After the world was mapped, no one could imagine what it was like to live “before you knew what would happen if you sailed ...
 lecture Raúl Alberto Laumann: Chemical Ecology applied to pest management: a Brazilian experience
In this talk the chemical ecology studies developed at Brazilian Agriculture Research Corporation, EMBRAPA will be presented. The team of the Laboratory of Semiochemicals of Embrapa Genetic Resources and Biotechnology (Brasília, central Brazil) is developing chemical ecology researches including pheromone ...
 lecture Francis Lévi: Circadian control of xenobiotic carcinogenesis and cancer pharmacology
Xenobiotic metabolism and detoxification, as well as cell cycle events, DNA repair, apoptosis and angiogenesis are rhythmically controlled by the Circadian Timing System (CTS), a hierarchical and coordinated network of cellular clocks. Interwoven transcription/translation feedback loops involving 15 clock genes ...
 lecture Rok Košir: Circadian gene expression patterns on the periphery depend on the genotype
Questions Biological clock is an important component in body homeostasis. However, it is not clear how the genetic background of each individual influences circadian expression and regulation. We addressed this question by investigating gene expression in liver and adrenal glands ...
 lecture Radovan Komel: Človeške dedne bolezni, njihovo izražanje in napovedovanje prihodnosti / Human Hereditary Diseases, their Expression and Prediction
Genetske nepravilnosti nastanejo zaradi nepravilnosti v genih ali kromosomih. Nekatere med njimi, kot je npr. rak, so posledica poškodb dednine, ki se v življenju zgodijo v določenih celicah našega organizma, sam izraz “genetske bolezni” pa v splošnem raje uporabljamo v ...
 lecture Tandy Warnow: Computational and mathematical challenges involved in estimating
Phylogenetic inference presents enormous computational and mathematical challenges, but these are particularly exacerbated when dealing with very large datasets (containing thousands of sequences) or when sequences evolve under complex evolutionary processes (ranging from simple "indel" models, to horizontal gene transfer, ...
 lecture Stanislaw Cebrat: Computer Modeling of Genome Evolution during Sympatric Speciation
In the natural, even large and panmictic populations, the inbreeding coefficient could be relatively high, because individuals are looking for sexual partners in the relatively short distances. We have simulated the evolution of such population on the square lattice. Results ...
 lecture Kunihiko Kaneko: Consistency Principle in Biological Dynamical Systems
We propose consistency principle between different levels, to understand a biological system. Three topics are discussed. First, as a result of consistency between molecule replication and cell reproduction, universal statistical laws on chemical abundances over cells are derived as also ...
 lecture Niels Landwehr: Constrained Hidden Markov Models for Population-based Haplotyping
Analysis of genetic variation in human populations is critical to the understanding of the genetic basis for complex diseases. Although genomes of several species have been sequenced, it is still too expensive to sequence genomes of several individuals to analyze ...
 lecture Hitoshi Iba: Controlling Humanoid Robots by Means of Genetic Programming
We show the real-world applications of EC (evolutionary computation) to robotics, which is called "evolutionary robotics". Machine Learning techniques can be applied to a robot in order to achieve a task for it if the appropriate actions are not predetermined. ...
 lecture Karsten Michael Borgwardt: Data Mining in the Life Sciences: The Path to Personalized Medicine
In this course, we will describe common data mining problems in the life sciences and state-of-the-art approaches for solving them. These problems include questions that arise traditionally in bioinformatics, such as sequence analysis and structural comparisons, and those which have ...
 lecture Elisa Loza Reyes: Detecting Evolutionary Inter-Gene Heterogeneity in Borrelia burgdorferi
Borrelia burgdorferi is one of the bacterial species responsible for the most prevalent vector-borne disease in the temperate zone of the northern hemisphere, Lyme borreliosis [1]. Phylogenetic analyses of B. burgdorferi are now based on a concatenation of several housekeeping ...
 lecture Thiemo Krink: Differential Evolution and Particle Swarm Optimization in Partitional Clustering
In recent years, many partitional clustering algorithms based on genetic algorithms (GA) have been proposed to tackle the problem of finding the optimal partition of a data set. Surprisingly, very few studies considered alternative stochastic search heuristics other than GAs ...
 lecture Hans-Hilger Ropers: Disease gene discovery through genome sequencing and data exchange: perspectives for genetic diagnosis and drug development
During the early 1990ies, genome research has shifted to common diseases, driven by the intuitive but unproven hypothesis that for common disorders, common genetic risk factors must exist. Today, after almost two decades of genome-wide association studies (GWAS), there is ...
 lecture Bert Kappen: DNA matching as an example of Bayesian inference
In this talk, I show how Bayesian networks can be used for missing person identification in forensics. In large scale disasters, it is tremendously important that victims of tragedies are quickly and accurately identified. But when there may be limited ...
 lecture Natalie Kuldell, Reshma Shetty: Do-It-Yourself Biology
Inspired by the vast potential of bioengineering, ordinary people are seeking their inner Frankenstein -- doctor, not monster. Two speakers who know their way around Petri dish and beaker discuss the possibilities and pitfalls of do-it-yourself biology with an MIT ...
 lecture Brian McWilliams: Dynamic Asset Allocation for Bivariate Enhanced Index Tracking using Sparse PLS
Index tracking is a popular portfolio management strategy which involves creating a portfolio whose returns track very closely those achieved by a benchmark index. There are two interconnected problems associated with index tracking: asset selection and asset allocation. Asset selection ...
 lecture Gedi Lukšys: Effects of Stress and Genotype on Exploration-Exploitation Dynamics in Reinforcement Learning
Stress and genetic background regulate different aspects of behavioral learning through the action of stress hormones and neuromodulators. Similarly, in reinforcement learning (RL) models, exploitation-exploration factor and other meta-parameters control learning dynamics and performance. We found that many different measures ...
 lecture Kristine A. Pattin: Employing Publicly Available Biological Expert Knowledge from Protein-Protein Interaction Information
Genome wide association studies (GWAS) are now allowing researchers to probe the depths of common complex human diseases, yet few have identified single sequence variants that confer disease susceptibility. As hypothesized, this is due the fact that multiple interacting factors ...
 lecture Richard A. Young: Engineering a New Attack on Disease
Out of a world population of 6 billion, 57 million people die each year. And while we have gained 20 years in life expectancy since World War 2, diseases like HIV have taken a toll on morbidity in many developing ...
 lecture François Képès: Epigenomics and Morphodynamics
The substrate for heredity, DNA, is chemically rather inert. However, it bears one of the elements of information that specify the form of the organism. How can a form be specified, starting from DNA ? Recent observations indicate that the ...
 lecture Nicolò Fusi: Estimating the contribution of non-genetic factors to gene expression using Gaussian process latent variable models
Thanks to the recent increase in the amount of genetic profiling data available and to the ability to characterize disease activity through gene expression, it is possible to understand more in detail the multitude of causal factors linked with each ...
 lecture Barbara Vilhar: Evolucija kot osrednji koncept pri pouku biologije / Evolution as the Central Concept in Biology Education
Evolucija ima osrednje mesto v sodobni biološki znanosti, saj predstavlja ključ za razumevanje delovanja živih sistemov. Evolucija pridobiva osrednje mesto tudi pri pouku biologije kot koncept, ki razumevanje različnih tem biologije povezuje v celoto. Pri pouku lahko uporabimo galapaške želve ...
 lecture Antonio Carlos Marques, Amanda Ferreira Cunha: Evolution in Cnidaria
Integrative studies merging life cycle, morphological and molecular data unravel phylogenetic patterns of Cnidaria Medusozoa, including time of origin, major evolutionary trends and patterns of diversification. Major taxonomical consequences of this updated view of cnidarian evolution have demonstrated a concerted ...
 lecture Eva Jablonka: Evolution in Four Dimensions
Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, ...
 lecture Eörs Szathmáry: Evolution of language / Evolucija jezika
It is difficult to gain an understanding of language since we do not know how it is processed in the brain. Many areas of the human brain are involved in language- related activities, including syntactic operations. Aspects of the language ...
 lecture Oliver Stegle: Factor models for QTL studies
The recent availability of large scale data sets profiling single nucleotide polymorphisms (SNPs) and gene expression across different human populations, has directed much attention towards discovering patterns of genetic variation and their association with gene regulation. Two aspects of the ...
 lecture Susan Hockfield, Robert J. Silbey, Tyler Jacks: Fundamentals of Cancer Research: Introduction and Overview
This inaugural address lays the groundwork for an 11-part series on MIT’s efforts in cancer research. Susan Hockfield views MIT’s Center for Cancer Research as a central example of how “life sciences are coming into conversation with engineering in a ...
 lecture Garrett Mitchener: Game Dynamics with Learning and Evolution of Universal Grammar
I will present a model of language evolution, based on population game dynamics with learning. Specifically, we consider the case of two genetic vari- ants of universal grammar (UG), the heart of the human language faculty, assuming each admits two ...
 lecture Pierre Geurts: Gene regulatory network inference using tree-based ensemble methods
One of the pressing open problems of computational systems biology is the elucidation of the topology of genetic regulatory networks. In this talk, we first present a method, called GENIE3, for the unsupervised inference of gene regulatory networks from expression ...
 lecture Thomas Baerecke: Genetic Approximate Matching of Attributed Relational Graphs
 lecture Goran Klemenčič: Genetika, zasebnost in diskriminacija – raba in zloraba informacij / Genetics, Privacy and Discrimination – Use and Abuse of Information
Človeštvo se danes sooča z vsaj dvema tehnološkima revolucijama: revolucijo informacijskih in komunikacijskih tehnologij ter revolucijo na področju genetike. Obe izzivata tradicionalne poglede na bistvo posameznika, njegovo vlogo v družbi, njegovo dostojanstvo, avtonomijo in svobodo. Poleg (očitne) uporabe v medicini ...
 lecture Jana Žel: Gensko spremenjene rastline / Genetically Modified Plants
Razumevanje in poznavanje gensko spremenjenih organizmov ni enostavno, saj je že izraz »gensko spremenjen« težko predstavljiv in različno pojmovan. Poleg tega zajema različne organizme od mikroorganizmov, živali do rastlin. Tudi lastnosti, ki so vnesene v te organizme so lahko zelo ...
 lecture Yosef Maruvka: Global Features Of Species Network
A simple model for competition induced speciation is presented and analyzed. Logistic growth with nonlocal interaction is studied on regular and random networks, and the large scale structure of the emerging genomic frequencies is examined. The neutrality assumption is violated ...
 lecture Hidde Ploegh: Global Pandemics
About the Lecture In his role as a biochemist, Hidde Ploegh explains the "essential features of the lifestyle of the flu virus" discussing not only how viruses work to invade our systems and cause the flu, but also adding insights ...
 lecture Robert A. Weinberg: How Cancer Begins
If you’re worried about getting cancer, do yourself a favor: steer clear of red meat and rich foods, and avoid cigarettes. In this lecture, Robert Weinberg provides the scientific basis for this commonplace advice, as well as a layman’s look ...
 lecture Benjamin Podbilewicz: How cells form organs / Kako nastajajo organi
Fundamental basic biological questions include: how cells interact with one another and rearrange themselves to produce organs, how complex organisms develop from a single cell, and how organisms evolve. We are using the nematode Caenorhabditis elegans to investigate cell fusion, ...
 lecture Robert A. Weinberg: How Did We Get Here?
Robert Weinberg plots the 200-year course of cancer research, finding neglected byways, wrong turns, and astonishing advances. He starts with Percival Pott, a London surgeon who noticed that chimney sweeps often developed a rare kind of cancer. In Europe, where ...
 lecture Rudolf Jaenisch, Stephen P. Marks: Human Cloning and Human Rights: Promises and Perils
Ignore the noisy debate around cloning, Rudolf Jaenisch quietly insists, and instead look closely at the biology involved. First, note that there are two different kinds of cloning: reproductive cloning, the attempt to create an exact replica of a human ...
 lecture David Altshuler: Human Genetics: Our Past and Our Future
Will genomics vanquish our most common diseases, or create a society based on vile eugenics – or both? David Altshuler outlines these possibilities in his informal talk and conversation at the MIT Museum. Altshuler is a self-described optimist, and sees ...
 lecture Jennifer Listgarten: Improving Large-Scale Genetic Association Studies by Accounting For Hidden Confounders
 lecture Catherine Higham: Inference in a probabilistic model of dynamic DNA
Microsatellites are simple sequence repeats present in both coding and non-coding regions of the genome. DNA instability at some microsatellites is the underlying genetic defect in a number of human diseases including myotonic dystrophy type 1 (DM1). New quantitative data, ...
 lecture John Pinney: Inferring ancestral states of the bZIP transcription factor interaction network
As whole-genome protein interaction network datasets become available for a wide range of species, evolutionary biologists have the opportunity to address some of the unanswered questions surrounding the evolution of these complex systems. Protein interaction networks from divergent organisms may ...
 lecture Van Anh Huynh-Thu: Inferring regulatory networks from expression data using tree-based methods
One of the pressing open problems of computational systems biology is the elucidation of the topology of genetic regulatory networks (GRNs) using high throughput genomic data, in particular microarray gene expression data. The Dialogue for Reverse Engineering Assessments and Methods ...
 lecture Ray Kurzweil: Innovation Everywhere - How the Acceleration of “GNR” (genetics, nanotechnology, robotics) Will Create a Flat and Equitable World
Ray Kurzweil may be the closest thing we have to a crystal ball. And if anyone has the right to some credibility in the prognostication arena, this overachieving inventor can. With crackling speed, Kurzweil powerpoints through charts illustrating the growth ...
 lecture Chiara Damiani: Interacting Random Boolean Networks
Random Boolean networks (RBN) have been extensively studied asmodels of genetic regulatory networks. While many studies have been devoted tothe dynamics of isolated random Boolean networks, which may considered asmodels of isolated cells, in this paper we consider a set ...
 lecture Susan Hockfield, Mriganka Sur: Introduction/Overview of Brain Disorders
In their symposium introduction, Susan Hockfield and Mriganka Sur place MIT at the forefront of a revolution in neuroscience. Hockfield, a neuroscientist by training, recaps the evolution of the discipline at MIT, from its 1964 start in the Department of ...
 lecture Robert A. Weinberg: Introduction to Cancer Genetics
During the human lifetime, there are 10 million billion cell divisions and each division represents, as Robert Weinberg puts it, “an opportunity for disaster, for chaos to occur.” The longer-lived the organism, the more likely it is that one cell ...
 lecture Al Vrezec: Invazijski proces tujerodnih vrst / Invasive process of non-native species with examples from Slovenia
Tujerodne vrste so danes eden glavnih dejavnikov, ki prispevajo k upadanju globalne biodiverzitete. Z vnosi tujerodnih vrst prihaja do izumiranja domorodnih vrst, vplivi pa se odražajo tako na genetskem, individualnem kot populacijskem nivoju, pri čemer lahko prihaja do sprememb združb ...
 lecture Gregor Serša: Kaj kontrolira dolžino življenja celic in človeškega življenja / What Controls the Length of the Life in Cells and Organism
Življenje celice je odvisno od genetskih dejavnikov in okolja, v katerem živi. Oboji vplivajo na DNA celice, jo neposredno poškodujejo ali pa povzročajo epigenetske spremembe, ki vodijo v celično senescenco. Taka celica doživi biokemične spremembe, ki povzročijo, da se preneha ...
 lecture Jean-Philippe Vert: Kernel Methods in Computational Biology
Many problems in computational biology and chemistry can be formalized as classical statistical problems, e.g., pattern recognition, regression or dimension reduction, with the caveat that the data are often not vectors. Indeed objects such as gene sequences, small molecules, protein ...
 lecture Kelly D. Brownell: Lecture 11 - Sustainability II: The Impact of Modern Agriculture on Biodiversity, Genetic Modification and Animal Welfare
In this lecture, Professor Brownell asks whether modern agriculture is environmentally, culturally, and morally sustainable. First, he explores how genetically modified foods both benefit and hinder world sustainability, such as with the case study of BT corn, and contamination to ...
 lecture John Gabrieli: Lecture 14: Intelligence
How much is intelligence determined by our childhood environment vs. our genetics? Are there things we can do later in life to become more intelligent? What exactly is intelligence, anyway? This session explores the strengths and weaknesses of IQ testing, ...
 lecture Stephen C. Stearns: Lecture 14 - Species and Speciation
Speciation is the process through which species diverge from each other and/or from a common ancestor. There are several definitions of species, most of which focus on reproductive isolation and/or phylogenetic similarities. This can cause some controversy. Speciation can result ...
 lecture Graham Walker: Lecture 15: Bacterial Genetics
 lecture Douglas W. Rae: Lecture 15 - Mass Affluence Comes to the Western World
Professor Rae discusses the rise of mass affluence, the joint stock corporation, and advertising/consumer culture in America. Gregory Clark's theory of the causes of the Industrial Revolution, including England's "downward social mobility" in the medieval and early modern periods, are ...
 lecture Stephen C. Stearns: Lecture 15 - Phylogeny and Systematics
The Tree of Life must be discovered through rigorous analysis. Genetic information is crucial because appearances can be deceiving, and species that look similar can prove to be genetically very dissimilar and not share recent common ancestors. Two criteria, used ...
 lecture Stephen C. Stearns: Lecture 16 - Comparative Methods: Trees, Maps, and Traits
We can use methods of genetic analysis to connect phylogenic information to geographical histories. Human migration has left genetic traces on every continent, and allows us to trace our roots back to Africa. Molecular genetic methods allow us to determine ...
 lecture Frank Snowden: Lecture 16 - Malaria (I): The Case of Italy
Of all the diseases studied in this course, malaria has been responsible for the most human suffering. It has evolved alongside humans, and impacted human biology as well as civilization. In the former case, this impact is evident in genetic ...
 lecture John Gabrieli: Lecture 16: Personality
What type of personality do you have? What factors can influence our personality? In this session, we will study different types of personalities, the ways in which we measure personality, and how cognition and learning can contribute to make us ...
 lecture James Paradis: Lecture 17: Evolution and Cybernetics
Topics: Evolution and Cybernetics Norbert Wiener, the golem, and the problem of control The key issue of cybernetics Evolution as Phylogenetic Learning Biological versus machine reproduction, Sorcery versus science An increasingly automated world
 lecture Stephen C. Stearns: Lecture 17 - Key Events in Evolution
The history of life and evolution has been characterized by several key events. These events can be grouped as new hierarchal levels of selection coming into play, as biological units coming together in symbiosis and specialization, or in a number ...
 lecture John Gabrieli: Lecture 20: Psychopathology I
What is psychopathology? Why is psychopathology important? During this lesson, we will examine the history of psychopathology and various experiments that demonstrate the importance of accurate diagnoses of mental disorders. We will also look in detail at the symptoms, causes, ...
 lecture Robert Wyman: Lecture 21 - Global Demography of Abortion
Abortion is very common both worldwide and in the US. There is one abortion for every 3.2 live births. In places where contraception is not used, abortion is used as birth control. Neither legal nor religious proscriptions have a strong ...
 lecture Graham Walker: Lecture 21: Mendelian Genetics
 lecture Graham Walker: Lecture 23: Diploid Genetics
 lecture Stephen C. Stearns: Lecture 2 - Basic Transmission Genetics
Genetic transmission is the mechanism that drives evolution. DNA encodes all the information necessary to make an organism. Every organism's DNA is made of the same basic parts, arranged in different orders. DNA is divided into chromosomes, or groups of ...
 lecture Howard Cedar: Lecture 2: Replication Timing
Professor Cedar explains how the DNA methylation pattern is established in development. Starting with the embryo, he shows how initially DNA lacks methylation, and how during development, the methylation pattern is established. This pattern is then preserved throughout organismal growth, ...
 lecture Martin Polz: Lecture 31: Population Genetics and Evolution
 lecture W. Mark Saltzman: Lecture 3 - Genetic Engineering
Professor Saltzman introduces the elements of molecular structure of DNA such as backbone, base composition, base pairing, and directionality of nucleic acids. He describes the processes of DNA synthesis, transcription, RNA splicing, translation, and post-translational processing required to make a ...
 lecture Howard Cedar: Lecture 3: How the methylation patterns are formed in development
Professor Cedar gives a “whole genome” perspective on DNA methylation. He explains the different methylation patters that are found in each tissue and shows what controls this disparity in gene expression. Additionally, there is an in depth explanation of CpG ...
 lecture Howard Cedar: Lecture 4: Cancer and Stem Cells
Professor Cedar explains the role of DNA methylation in cancer and stem cells. While initially many people thought that in cancer there was less DNA methylation, it turns out not to be so simple. Presenting a serious of experiments and ...
 lecture W. Mark Saltzman: Lecture 4 - Genetic Engineering (cont.)
Professor Saltzman continues his presentation on DNA technology by discussing control of gene expression using two methods of RNA silencing: anti-sense therapy and RNA interference. Molecular cloning techniques to mass-produce proteins using plasmid, restriction enzymes, ligase, and antibiotic selection in ...
 lecture Stephen C. Stearns: Lecture 4 - Neutral Evolution: Genetic Drift
Neutral evolution occurs when genes do not experience natural selection because they have no effect on reproductive success. Neutrality arises when mutations in an organism's genotype cause no change in its phenotype, or when changes in the genotype bring about ...
 lecture Kelly D. Brownell: Lecture 5 - Biology, Nutrition and Health III: The Psychology of Taste and Addiction
This lecture addresses the complicated relationship between biology and eating. Professor Brownell explores the physiology of taste and eating. Many parts of the body are affected when people eat food, and many biological factors affect what people choose to eat, ...
 lecture Stephen C. Stearns: Lecture 5 - How Selection Changes the Genetic Composition of Population
Genetics controls evolution. There are four major genetic systems, which are combinations of sexual/asexual and haploid/diploid. In all genetic systems, adaptive genetic change tends to start out slow, accelerate in the middle, and occur slowly at the end. Asexual haploids ...
 lecture Eric S. Lander: Lecture 6: Genetics 1
 lecture Stephen C. Stearns: Lecture 6 - The Origin and Maintenance of Genetic Variation
Mutations are the origin of genetic diversity. Mutations introduce new traits, while selection eliminates most of the reproductively unsuccessful traits. Sexual recombination of alleles can also account for much of the genetic diversity in sexual species. In some instances, population ...
 lecture Eric S. Lander: Lecture 7: Genetics 2
 lecture Stephen C. Stearns: Lecture 7 - The Importance of Development in Evolution
Development is responsible for the complexity of multicellular organisms. It helps to map the genotype into the phenotype expressed by the organism. Development is responsible for ancient patterns among related organisms, and many structures important to development shared by many ...
 lecture Graham Walker: Lecture 8: Biochemistry VI (cont.) DNA as Genetic Material
 lecture Eric S. Lander: Lecture 8: Genetics 3
 lecture Stephen C. Stearns: Lecture 8 - The Expression of Variation: Reaction Norms
Reaction norms depict the range of phenotypes a single genotype can produce, depending on the environment. Reaction norms must fit within an organism's phylogenetic constraints. They can differ for different individuals within a population, but some traits differ very little ...
 lecture Eric S. Lander: Lecture 9: Human Genetics
 lecture Barry Horowitz, F. Stan Settles, Daniel Hastings, William B. Rouse, Thomas L. Magnanti: Looking Ahead
At the start of this panel, Thomas Magnanti wonders whether engineering feats of the 21st century will rival 20th century systems built to provide electricity, water, and communications throughout the nation. Subsequent speakers focus mainly on the practice and teaching ...
 lecture Douglas Saddy: Measuring Language in the Brain / Merjenje jezika v možganih
Attempts to understand the relationship between language and the brain have a long history. Recent theoretical, technological, methodological and analytic developments have provided us with the opportunity to look a little closer at the workings of the intact and damaged ...
 lecture Nicholas Barton: Modeling the evolution of flower colour in snapdragons
Species are often subdivided into distinct populations, which are separated by narrow zones of hybridisation. These can be modelled using reaction-diffusion equations, yielding estimates of quantities such as the strength of selection and the rate of diffusion of genes. I ...
 lecture Yee Whye Teh: Modelling Genetic Variations with Fragmentation-Coagulation Processes
We propose a novel class of Bayesian nonparametric models for sequential data called fragmentation-coagulation processes (FCPs). FCPs model a set of sequences using a partition-valued Markov process which evolves by splitting and merging clusters. An FCP is exchangeable, projective, stationary ...
 lecture Peter Schönswetter: Molecular markers and their application in biogeography / Molekulski markerji in njihova uporaba v biogeografiji
The application of molecular tools (DNA sequences, DNA fingerprinting) has revolutionized biogeographic research over the last two decades. Molecular biogeography can be summarized under “phylogeography”, a term coined by John Avise twenty years ago. It is describing the branch of ...
 lecture Maja Bresjanac: Možgani in vpliv genov na njihov razvoj in delovanje / Nature and Nurture in Brain Development and Function
Klasična razprava o vplivu “prirojenega” in “pridobljenega” na posameznikove sposobnosti in njihovo izražanje je z genetskimi raziskavami v zadnjih desetletjih 20. stoletja dobila nov okvir in poudarke. Razmah zanimanja za genetske študije in finančna ter politična podpora tem raziskavam sta ...
 lecture Steffen Bickel: Multi-Task Learning for HIV Therapy Screening
We address the problem of learning classifiers for a large number of tasks. We derive a solution that produces resampling weights which match the pool of all examples to the target distribution of any given task. Our work is motivated ...
 lecture Subra Suresh: Nanotechnology and the Study of Human Diseases
Subra Suresh fleshes out the promise of nanotechnology, at least in regard to our understanding of disease. His talk, which focuses on malaria and its impact on red blood cells, demonstrates how the fields of engineering, biology and medicine are ...
 lecture Barbara Vilhar: Napačne in nepopolne predstave o živih sistemih / Misconceptions about living systems
Posodobitev biološkega izobraževanja temelji na premiku od opisovanja pojavov in učenja pretežno nepovezanih podatkov na pamet proti celostnemu razumevanju delovanja narave, ki ga je treba pri učencih začeti razvijati že zgodaj v procesu izobraževanja in nato postopno nadgrajevati. Ta premik ...
 lecture Edward Scolnick: New Frontiers in Schizophrenia and Bipolar Disorder Research
In contrast to cardiovascular disease, few breakthrough remedies for psychiatric illness have emerged in the past half century. Edward Scolnick lays blame for this dismal situation on barriers to understanding the genetic basis behind such illnesses. But the research drought ...
 lecture Jacqueline A. Lees: New Lessons in Cancer Research
Cancer is a conniving enemy. Try to kill it off through surgery or chemotherapy, and it finds a way to sneak back in. Jacqueline Lees tells an engaged Soap Box audience what insights and tools research now offers in the ...
 lecture Nathalie Questembert-Balaban: Non-Genetic Individuality in a Predator-Prey system
Isogenic bacteria can exhibit a range of phenotypes, even in homogeneous environmental conditions. Such non-genetic individuality has been observed in a wide range of biological processes, including differentiation and stress response(1). A striking example is the heterogeneous response of bacteria ...
 lecture Elizabeth Halloran: Novel Applications of Computational Biology in Infectious Disease Interventions
Interventions in infectious diseases are increasingly relying on computational biology and genomic methods. Estimating changes in viral genetic diversity in a population could be a new potential method to evaluate vaccination strategies in populations. Transgenic mosquitoes immune to a pathogen ...
 lecture Rudolf Jaenisch: Nuclear Cloning and Cell Therapy: Fact and Fiction
The subject of cloning can instantly spark passionate debate: Will it enable us to resurrect beloved family members, or create Frankensteins? Rudolf Jaenisch wants to remove “hot air” from the discussion. His talk provides a clear picture of what is ...
 lecture Jože Trontelj: O dvojni rabi biologije in medicine: žlahtnjenje človeka / Dual use of biology and medicine: "human enhancement"
Med vsemi znanostmi največkrat napovedujejo biologiji in medicini, da bosta zaznamovali sedanje stoletje. Zagon jima je dala vrsta velikih dosežkov ob koncu prejšnjega in začetku tega stoletja. Naj omenim samo razvozlanje človeškega genoma, odkritje matičnih celic, prve korake sintetične biologije. ...
 lecture Andrew Somogyi: Opioid Pharmacogenomics: More Than Metabolism
Several opioids such as codeine are considered pro-drugs as they are metabolized by the highly polymorphic CYP2D6 to more potent opioids with clinical efficacy and toxicological sequelae. Many opioids are also metabolised by CYP3A4/5. In over 600 cancer patients using ...
 lecture Margaret Atwood: Oryx and Crake Revealed
Here are two facts Margaret Atwood wants you to know: She is the daughter of an entomologist -- the kind of scientist, Atwood says, who is “noteworthy for producing weird writer offspring”; and she hates books where “everybody’s happy all ...
 lecture Jože Trontelj: O umetni biotski pestrosti človeške vrste – etični pomisleki / On Man-Made Biodiversity of the Human Species – Ethical Objections
Znanost je dala ljudem v roke nove možnosti. Genska tehnologija omogoča spreminjanje genoma. Posebno v rastlinskem svetu je prišla že precej daleč. Gensko spremenjeni organizmi paradoksno niso povečali biotske pestrosti, ampak so jo zmanjšali. Tehnologijo so zlorabile multinacionale družbe; pred ...
 lecture Viktor Prasanna: Parallel Exact Inference on Multi-Core Processors
Exact inference in Bayesian networks is a fundamental AI technique that has numerous applications including medical diagnosis, consumer help desk, pattern recognition, credit assessment, data mining, genetics, and others. Inference is NP-hard and in many applications real time performance is ...
 lecture Renata Salecl: Perfektna prihodnost - nove in stare mitologije nadzora nad telesom, smrtjo in reprodukcijo / Future perfect - new and old mythologies of control of the body, death and reproduction
Negotovost in nepredvidljivost sta vedno bila del medsebojnih človeških odnosov. Trudimo se uganiti namere drugih, predvideti, kaj bodo storili v prihodnosti, in celo najti načine, da bi drugi svoje vedenje spremenili. V preteklosti so razlage za to, kaj se dogaja ...
 lecture Darlene Solomon, Jose B. Cibelli, Benjamin Cravatt, David Sabatini, Rebecca Henderson: Personalized Medicine
We've deciphered the human genome and moved into proteomics-the study of the individual proteins that the genes code for. Such advances anticipate the day when drugs are not only targeted at molecular workings or specific diseases but tailor-made for each ...
 lecture Hiltrud Brauch: Pitfalls and shortcomings of pharmacogenomic association studies: The tamoxifen controversy
The Cytochrome P450 2D6 enzyme has been linked with tamoxifen outcome based on its role to convert the parent drug into active metabolites 4-hydroxytamoxifen and endoxifen and in particular because of its high inter-individual variability of enzyme activity. Impaired CYP2D6 ...
 lecture Barbara Vilhar: Pomen biološkega znanja za splošno izobrazbo / The Importance of Biology in General Education
Ob velikem napredku biološke znanosti v zadnjih desetletjih postaja biološko znanje vse pomembnejše pri sprejemanju osebnih in družbenih odločitev (npr. v zvezi z genetskim inženiringom, varstvom narave in okolja ter trajnostnim razvojem). V Sloveniji svetovnim premikom na področju biologije ne ...
 lecturePoster Spotlights 2
A Space of Feature Selection Criteria based on Multivariate Mutual Information Gavin Brown Alternatives to modelling sparsity in gene expression networks N.J. Burroughs, M.A. Juarez, E.R.Morrissey Average-case theory for sparse Bayesian PCA in p > n regime Magnus Rattray Inferring ...
 lecture Scooter Willis: Predicting co-evolving pairs in Pfam using information theory where entropy is determined by phylogenetic mutation events
The accurate prediction of co-evolving pairs in protein sequences plays an important role in tertiary protein structure prediction and protein engineering. Using information theory to detect co-evolving pairs is impacted by the phylogenetic effect on entropy measurements. Mutual Information (MI) ...
 lecture David Wolpert: Predicting the Outcome of a Game
Optimization of many complex systems is often viewed as a black-box optimization problem. Such problems are often difficult to solve using conventional techniques, for a variety of reasons, such as the absence of derivatives, mixed data types, and so on. ...
 lecture Špela Schrader: Primer genske ekspresije v ontogenetskem razvoju / Examples of Gene Expression During Ontogenesis
Živali so zgrajene iz diferenciranih celic najrazličnejših oblik, ki opravljajo različne funkcije, pa vendar vse izvirajo iz ene same oplojene jajčne celice in imajo vse enak genski material. Raznolikost je posledica diferencialne aktivnosti genov, ki se vzpostavi med embrionalnim in ...
 lecture Gyan Bhanot: Principal Component Analysis and Clustering Reveal Human Maternal Ancestry from Complete Mitochondrial Sequences
We develop a simple, direct method to infer the phylogenetic tree for the maternal lineage of all humans using principal component analysis and consensus ensemble clustering. Unlike standard methods such as parsimony and maximum likelihood, our method is fast, gives ...
 lecture Joel L. Vanneste: Pseudomonas syringae pv. actinidiae, three years after its discovery in New Zealand: what have we learned about the pathogen, the disease and how to control it?
In the last few years the causal agent of bacterial canker of kiwifruit, Pseudomonas syringae pv. actinidiae (Psa), has become a global pathogen of economic importance. Before 2008, this little known pathogen had not been the object of many studies ...
 lecture Jože Vogrinc: Razvoj kulture v naravoslovju in družboslovju – je to eno in isto in kaj, če ni? / The Evolution of Culture in Natural and Social Sciences: Is It the Same Thing, and What if It Isn't?
Spoznanje, da kulturno vedenje ni značilno le za našo vrsto, zahteva sodelovanje med biologijo in družbenimi vedami. Razlogi, zakaj ni bolj razvito, so povezani s tematiko sámo. Evolucijska biologija zahteva perspektivo, v kateri se kulturno vedenje razvije kot specifična prilagoditev. ...
 lecture Eva Jablonka: Responding to the environment: Epigenetic variations in heredity and evolution / Odgovor na razmere v okolju: Epigenetska variabilnost pri dedovanju in evoluciji
In his theory of evolution, Darwin recognized that the conditions of life play a role in the generation of hereditary variations as well as in their selection. However, since the mid 20th century, the Modern Synthesis version of Darwinism expelled ...
 lecture Margaret M. McCarthy: Sex differences in the Brain: Fact or Fiction? / Spolne razlike v možganih: Dejstvo ali izmišljotina?
Everyone knows and agrees that men and women are different, they look different, dress different, behave different and often seem to think different. What is not agreed upon is why this is so. Is it societal expectations, parental guidance, biological ...
 lecture Oren Harman: Shakespeare was wrong: Why biology and culture are more connected than we thought? / Shakespeare se je motil: Zakaj sta biologija in kultura bolj povezani, kot smo mislili
In this paper, I will want to argue that the widening causal window between genotype and phenotype allows us to contemplate a different pattern of interaction between culture and biology in man than has guided the thinking of previous generations. ...
 lecture Shruthi Prabhakara: SIMCOMP: A Hybrid Soft Clustering of Metagenome Reads
A major challenge facing metagenomics is the development of tools for the characterization of functional and taxonomic content of vast amounts of short metagenome reads. In this paper, we present a two pass semi-supervised algorithm, SimComp, for soft clustering of ...
 lecture Peter Trontelj: Sistematski pogled na biodiverziteto / A Systematic Perspective on Biodiversity
Prispevek obravnava biodiverziteto kot zgodovinski pojav in produkt evolucije. Zavzema se za dosledno filogenetsko obravnavo pestrosti življenja na Zemlji. Opozarja, da marsikje še vedno prevladuje pojmovanje življenja v obliki premočrtnega niza od primitivnih do bolj popolnih oblik, in da pravilnejša ...
 lecture Eric P. Xing: Some Challenging Machine Learning Problems in Computational Biology: Time-Varying Networks Inference and Sparse Structured Input-Out Learning
Recent advances in high-throughput technologies such as microarrays and genome-wide sequencing have led to an avalanche of new biological data that are dynamic, noisy, heterogeneous, and high-dimensional. They have raised unprecedented challenges in machine learning and high-dimensional statistical analysis; and ...
 lecture Bogdan Filipič: Stochastic Search Methods
Knowledge discovery can be regarded as exploration of high-dimensional and multi-modal search spaces. However, finding the global optimum of an objective function with many degrees of freedom and numerous local optima is computationally demanding. Systems capable of learning and adaptivity ...
 lecture Ben Calderhead: System Identification of Enzymatic Control Processes Using Population Monte Carlo Methods
We demonstrate the superiority of Population Monte Carlo techniques over standard Metropolis Markov Chain Monte Carlo (MCMC) methods for inferring optimal parameters for a particular mechanistic model of a biological process given noisy experimental data. As our understanding of biological ...
 lecture Mark Bear: The Autistic Neuron
This self-described “basic neuroscientist” confesses he never thought he’d give a talk on autism, but as Mark Bear recounts, decades of research in the basics are now paying off with important insights into the etiology and treatment of brain disorders, ...
 lecture Noam Chomsky: The Biology of the Language Faculty: Its Perfection, Past and Future
Noam Chomsky, around whose work much of the Syntax series revolves, gives listeners a glimpse into the evolution of his own thinking, with an emphasis on areas of linguistics where computational considerations play a major role. Chomsky briefly outlines the ...
 lecture Nancy Kanwisher: The Brain Basis of Human Vision
Nancy Kanwisher’s breakthrough scanning research reveals “a teeny part of an answer to the big question of what kinds of brains we have,” she says. Her work depends on functional MRI, a way of imaging people’s brains that detects areas ...
 lecture Angelika Amon: The Cell Cycle and Cancer
We all start out as a single fertilized cell, and wind up, as fully formed humans, with 10 to the 13th cells. “The name of the game,” says Angelika Amon, is to replicate the genetic information in those cells accurately. ...
 lecture Partha Niyogi: The Computational Nature of Language Learning
Language learning research becomes more robust when it incorporates insights from evolutionary theory, Partha Niyogi demonstrates. The principles of natural selection and variation in a population come into play not only when exploring how children learn language but how languages ...
 lecture Stefan Wieland: The coupling of strain evolution and disease dynamics
Influenza A is characterized by seasonal outbreaks and a gradual genetic, yet discontinuous antigenic evolution (antigenic "cluster jumps" occuring every 4-7 years, with a large seasonal epidemic as a result of lacking immunity among the population).The interplay between viral mutations ...
 lecture Jonathan Sacks: The Dignity of Difference
In a talk that interweaves philosophy, history, religion and some classic rabbinic banter, Sir Jonathan Sacks calls for a “paradigm shift in understanding of religion” in the face of globalization, which threatens to pull the world apart in tribal and ...
 lecture David C. Page: The Evolution of Sex: Rethinking the Rotting Y Chromosome
According to David Page, “the Y chromosome is the Rodney Dangerfield of the human genome.” Regarded for 50 years as a genetic wasteland, the Y chromosome just doesn’t get any respect…until now. Page’s lab has made some startling discoveries that ...
 lecture Jeremy Nathans: The Evolution of Trichromatic Color Vision
Sometime around 100 million years ago, when the continents of Africa and South America were still in touch, a female primate -- one of our ancestors -- was born with the capacity to see in vivid color. Jeremy Nathans describes ...
 lecture Eva Jablonka: The Gene in Context: from Developmental Plasticity to Plastic Heredity / Gen v kontekstu: od razvojne plastičnosti do plastičnega dedovanja
The gene-centered view, according to which genes are the most important determinants of development, the sole stuff of biological heredity, and the guide for the understanding of all aspects of evolution, has dominated biological thinking for the last 50 years. ...
 lecture Eric S. Lander: The Human Genome Project
Dr. Lander is a geneticist, molecular biologist and a mathematician, with research interests in human genetics, mouse genetics, population genetics and computational and mathematical methods in biology. He and his research group have developed many of the tools of modern ...
 lecture Drew Endy: The Implications of Synthetic Biology
There’s no mistaking Drew Endy’s profession: “I like to make things -- that’s what I do.” From his engineer’s perspective, the slow and painful methods of bioengineering demand a solution. Endy hopes to refine the tools necessary to move the ...
 lecture Eörs Szathmáry: The Major Transitions in Evolution / Veliki prehodi v evoluciji
Some major transitions in evolution (such as the origin of multicellular organisms or that of social animals) occurred a number of times, whereas others (the origin of the genetic code, or language) seem to have been unique events. One must ...
 lecture Renée Schroeder: The many roles of RNAs in Life: „The RNA world” / Svet RNA in molekulska evolucija
The central dogma of molecular biology suggests that biological information is stored in DNA then flows via RNA into proteins, which execute the functions dictated by DNA. DNA is thought to be the “molecule of life”. With the discovery that ...
 lecture Edward Scolnick: The Power of Basic Science Applied to Medical Progress: Past Examples and Hope for Schizophrenia and Bipolar Illness
An exemplar of the purpose-driven life in medical science, Ed Scolnick details research milestones from a remarkably varied career, revealing how scientific insight and collaborative effort translate into life-saving solutions for millions. This physician turned biochemist has held distinguished positions ...
 lecture Phillip A. Sharp: The RNAi Revolution
When a Nobel Prize-winning pioneer of molecular biology embraces a new area of research as revolutionary, attention must be paid. Phillip A. Sharp’s own discoveries involving gene expression opened up new territory in the search for the genetic causes of ...
 lecture Angela Belcher, Daniel Nocera: The Role of New Technologies in a Sustainable Energy Economy
No single new technology can deliver limitless and clean energy, but Daniel Nocera and Angela Belcher are optimistic that they can harness the physical and natural worlds to move toward this goal. Belcher looks to ancient ocean organisms for her ...
 lecture Angela Belcher, Daniel Nocera: The Role of New Technologies in a Sustainable Energy Economy
No single new technology can deliver limitless and clean energy, but Daniel Nocera and Angela Belcher are optimistic that they can harness the physical and natural worlds to move toward this goal. Belcher looks to ancient ocean organisms for her ...
 lecture Alberto Del Guerra: The Use of Radiation Detectors in Medicine: Radiation Detectors for Morphological Imaging
The development of radiation detectors in the field of nuclear and particle physics has had a terrific impact in medical imaging since this latter discipline took off in late ’70 with the invention of the CT scanners. The massive use ...
 lecture Joan Susan Antokol: The widespread use of cloud computing in the US and where it is heading
This panel will explore the widespread use of cloud computing by organizations in the US. In particular, the panel will discuss: 1) The evolving cloud computing landscape in the US—where it stands now and where it is heading; 2) The ...
 lecture Sophie Lebre: Time-varying genetic network inference using informative priors
 lecture Christopher Penfold: Towards a Polymer Model of Genetic Recombination
Homologous recombination (HR) refers to the shuffling of genetic material during cellular division e.g., meiosis and mitosis, and in response to environmentally-induced genetic damage. HR occurs preferentially over certain regions, and is notably influenced by physical compartmentalization due to chromosome ...
 lecture Katja Drobnič: Ugotavljanje identitete posameznika z uporabo genetskih informacij, metode verižne reakcije s polimerazo in računalniško podprte tehnologije / Determination of Personal Identity on the Basis of Genetic Data, PCR methodology and Computer Tec
Molekula DNK, tako drobcena, da je prostim očem nevidna, je postala eno najmočnejših orodij v boju proti zločinu. Komaj dvajset let po prvi analizi DNK, imenovani »prstni odtis« DNK, je forenzična tipizacija DNK postala odločilen ključ pri obsodbi ali oprostitvi ...
 lecture Daphne Koller: Understanding Gene Regulatory Networks and Their Variations
A key biological question is to uncover the regulatory networks in a cellular system and to understand how this network varies across individuals, cell types, and environmental conditions. In this talk I will describe work that uses machine learning techniques ...
 lecture Andriy Nikolov: Unsupervised Learning of Data Linking Configuration
As commonly accepted identifiers for data instances in semantic datasets (such as ISBN codes or DOI identifiers) are often not available, discovering links between overlapping datasets on the Web is generally realised through the use of fuzzy similarity measures. Configuring ...
 lecture Joshua C Denny: Using Electronic Medical Records to advance genomic medicine
Personalized medicine offers the promise of improved diagnosis and for more effective, patient-specific therapies. Typically, such studies have been pursued using research cohorts. At Vanderbilt, we have created a DNA biobank, BioVU, which now has nearly 180,000 samples linked to ...
 lecture Tobias Kanacher: Using physiology-based pharmacokinetic modelling for mechanistic analyses of drug action in disease and special populations
Inter-individual variability in clinical endpoints and occurrence of potentially severe adverse effects may hamper drug development at all phases of (pre-)clinical research. A comprehensive understanding of drug pharmacokinetics is hence of utmost importance in drug development. Physiology-based pharmacokinetic (PBPK) models ...
 lecture Eric R. Kandel, James D. Watson: Vision of the Future (Part 2)
If the century just passed was “the province of the gene,” then the next hundred years shall be “the province of the mind,” believes Eric Kandel. Brain science is poised to reveal the biology of conscious and unconscious mental processes ...
 lecture Ivan Kos: Vloga vrst v ekosistemskih procesih / Function of Species in Ecosystem Function
Raziskave delovanja ekosistemov potekajo predvsem iz dveh izhodišč - holističnem in redukcionističnem. Bistvo izhodišča holističnega pristopa je v združevanju žive komponente v trofične nivoje ter s tem zanemari vlogo posamezne vrste. Z izkanjem funkcije biodiverzitete pa prihaja v ospredje redukcionističen ...
 lecture Mark Aronoff: What an emerging language can tell us about language evolution / Kaj nam nastajajoči jezik lahko pove o razvoju jezika
Al-Sayyid Bedouin Sign Language (ABSL) is the sign language of a small, insular, endogamous community in the Negev desert with a high incidence of genetically recessive profound neurosensory deafness. The first deaf individuals were born about 75 years ago and ...
 lecture María Apellániz Ruiz: Whole-exome sequencing reveals defective CYP3A4variants predictive for paclitaxel dose-limiting neuropathy
Questions Paclitaxel, a widely-used chemotherapeutic drug, can cause severe peripheral neuropathy, causing dose reductions and treatment suspensions and, when long-lasting, a decrease in the quality of life of patients. Genetic variants altering paclitaxel pharmacokinetics have been proposed to increase the ...
 lecture H. Robert Horvitz: Worms, Life and Death: Cell Suicide in Development and Disease
A microscopic roundworm has come to play a dominant role in some of the most pivotal medical research of our time. In the labs of Robert Horvitz and his colleagues, C. elegans has helped reveal cell death as a normal ...
 lecture Nancy Hopkins: Zebrafish and Cancer: What's the Connection?
Through her rapport with the zebrafish, Nancy Hopkins has made large contributions to the fields of developmental biology and cancer research. But her model organism, and to some degree her particular slant on molecular biology, were a matter of serendipity, ...
 lecture Jože Trontelj: Znanje kot družbena vrednota. Pogled iz medicine / Knowledge as a societal value. Perspectives from medicine
Pravice iz intelektualne lastnine so pomembna spodbuda za raziskovalno delo, ki naj vodi do tržne dobrine. V medicini pa lahko pripelje tudi do resnih etičnih vprašanj. Patente lahko podelijo tudi raziskovalcem, ki imajo le to zaslugo, da so prvi prihiteli ...

Panel:


 panel Rafael Reif, Tomas Lozano-Perez, Jeffrey H. Shapiro: Transforming the Next Century
This panel serves as a fitting finale to the 100th anniversary celebration of EECS, focusing as it does on a fundamental shift in electrical engineering and computing toward biology, and toward a physics of the nearly unimaginable. Tomas Lozano-Perez describes ...

Promotional videos:


 promotional video Franc Batič: Applied Botany, Genetics and Ecology
The research programme of the research group is interdisciplinary. It comprises investigations of the biological and environmental basis of plant production, plant processing and land use. The core of the research programme deals with soil-plant- atmosphere relations and with structures, ...
 promotional video Maja Ravnikar: Biotechnology and plant systems biology
Research of the program Biotechnology and plant systems biology helps to understand and solve the problems regarding food safety, detection and regulation of genetically modified organisms (GMOs), and new diseases, such as fire blight and the disease caused by Flavescence ...
 promotional video Peter Dovč: Comparative genomics and genomic biodiversity
Genomic revolution characterized significantly development of basic and applied biological sciences during the last decade. Application of modern methods in genetics, molecular and cell biology and immunology combined with high throughput genomic techniques opened a new horizon for acquisition of ...
 promotional video Branka Javornik: Genetics and modern technologies of agricultural plants
The programme »Genetics and modern technologies of agricultural plants« includes basic and applied research in the field of food and agriculture. The aim is to ensure that agricultural plants provide optimal yield quantity and quality. Such modern varieties can only ...
 promotional video Robert Veberič: Horticulture
The implementation of sustainable development in agriculture demands new knowledge on the growth and development of plants as the use of numerous "additives" is limited (fertilizers, pesticides, phyto-regulators ...). In order for us to produce health food, the knowledge on ...
 promotional video Janez Stare: Methodology for data analysis in medical sciences
The topic of our research program is methodology for discovering actual or possible patterns, trends and assotiations in medical data. These are the methods for discovering new knowledge or generating new hypotheses that may lead to knowledge. The data that ...
 promotional video Renata Salecl: Social control, criminal justice system, violence and prevention of victimization in highly technological society
Criminology faces serious questioning of who the subject of criminal activity is, what his responsibility is, what leads the individual to perform criminal acts and how criminal behaviour might be prevented. All these questions are addressed in a new way ...
 promotional video Janez Bonča: Theory of condensed matter and statistical physics
We will investigate microscopic physical mechanisms which are responsible for the giant electrostriction and piezoelectric effects in organic and inorganic relaxor ferroelectrics. A model of perovskite ferrolectrics such as barium titanate will be developed, based on the off-center positions of ...

Poster:


 poster Gad Abraham: Sparse Linear Models Explain Phenotypic Variation and Predict Risk of Complex Disease
A central goal of medical genetics is to create models that accurately predict complex disease given genotype. To maximize predictive value and identify causal single-nucleotide polymorphisms (SNPs), all SNPs should be modeled simultaneously. Lasso penalized models have proven to be ...

Tutorial:


 tutorial Clarisse Dhaenens: Optimization and Applications in Bioinformatics
Most of bioinformatics problems deal with the manipulation of large sets of variables. Hence, looking for a good combinaisons of these variables requires advanced search mechanisms. The aim of this tutorial is to provide hints on how to use combinatorial ...