הפקולטה להנדסה ע"ש איבי ואלדר פליישמן

הנדסה ביו רפואית - סמינר 04.01.15

Understanding and modeling mRNA translation based on ribosome profiling data

04 בינואר 2014, 14:15

חדר 315 , הבניין הרב תחומי

תלמידת המחלקה להנדסה ביו רפואית לתואר שלישי תרצה בנושא:

Understanding and modeling mRNA translation based on ribosome profiling data

Gene expression is the process in which information encoded in the DNA is used to synthesize new proteins. Naturally, understanding, modeling and engineering this fundamental process has important contribution to every biomedical discipline, including human health and biotechnology. Gene expression has two major steps: transcription of the DNA to mRNA molecules and the translation of the mRNA molecules to proteins by molecular machines called ribosomes.

During mRNA translation ribosomes attach to the messenger RNA (mRNA) and then scan it in a sequential manner; each such scanning produces a new protein. Recently, a new experimental method - ribosome profiling was suggested for large scale study of ribosomal movement on the transcript. This method is based on next-generation sequencing and enables simultaneous estimation of the relative time ribosomes spend on the messenger RNAs of all translated transcripts in a genome, at a resolution of single nucleotides.

This work presents various new aspects of translation that were studied by analyzing ribosome profiles of thousands of genes in various organisms and their relation to translation efficiency. Among others, I decipher the way biophysical properties of the mRNA molecules affect translation; I develop novel computational simulation of this experiment; and I suggest novel filters for analyzing these data. The reported results should improve the understanding of the translation process and also contribute towards developing new methods for gene expression engineering.

The talk is mainly based on four papers published in the recent years: Dana and Tuller, PLoS Comput Biol. 2012; Dana and Tuller, Nucleic Acids Res. 2014; Dana and Tuller, BMC Genomics. 2014; Dana and Tuller, G3. 2014.

העבודה נעשתה בהנחיית דר' תמיר טולר, המחלקה להנדסה ביו-רפואית, אוניברסיטת תל-אביב

ההרצאה תתקיים ביום ראשון 04.01.15, בשעה 14:15,

בחדר 315, הבניין הרב תחומי, אוניברסיטת תל אביב

EE Seminar: Dr. Raviv Raich

~~(The talk will be given in English)

Speaker: Dr. Raviv Raich,
Associate Professor, School of Electrical Engineering and Computer Science,
Oregon State University, Corvallis, OR 97331-5501

Thursday, January 1st, 2015
13:45 - 14:45
Room 011, Kitot Bldg., Faculty of Engineering

Efficient instance annotation in multiple-instance multiple-label learning
Abstract
Recent work in machine learning focuses on the framework of multiple instance multiple label learning. In this setting, objects consist of multiple components termed instances. For example, an image may consist of multiple segments.
Moreover, objects are labeled by a set of labels. For examples, images can be labels with a list of objects present in the image (e.g., 'sky' and 'building'). The multiple instance multiple label framework is considered for a variety of
application areas including computer vision, acoustic scene analysis, and activity recognition. Bag level prediction, i.e., the prediction of the label set of a multi-instance object has been a focus of research for over a decade. Our interest
is in the somewhat less studied problem of instance annotation, the problem of associating each instance with a label. A novel model and computationally efficient inference, are introduced. The model can be used for both bag level
prediction and instance annotation. Empirical evaluations show that the approach outperforms state-of-the-art methods for instance annotation on a collection of both synthetic and real datasets.

01 בינואר 2015, 13:45

חדר 011, בניין כיתות-חשמל

Seminar 8.1.15

Yoav Livneh

M.Sc. student under supervision of Prof. Yossi Rosenwaks, Dr. Philip Klipstein

School of Electrical Engineering, Tel-Aviv University, Tel-Aviv 69978, Israel

On the subject:

Band Structure Calculation and Analysis

of Antimonide Based Type-II Superlattices

08 בינואר 2015, 9:30

Room 101, Software Eng. Build.

Physical Electronics Dept.

You are invited to attend a lecture

Yoav Livneh

(M.Sc. student under supervision of Prof. Yossi Rosenwaks, Dr. Philip Klipstein,

School of Electrical Engineering, Tel-Aviv University, Tel-Aviv 69978, Israel)

On the subject:

Band Structure Calculation and Analysis

of Antimonide Based Type-II Superlattices

Superlattices are a kind of quantum structure, made up of alternating thin layers of two materials. By changing the layer widths of the individual materials in the superlattice, we can control the optical and electrical properties of the material (bandgap engineering). In recent years, InAs/GaSb type-II superlattices (T2SLs) have become a very attractive potential sensing material in photonic devices used for infrared sensing and imaging.

This work presents a new and effective model for the prediction of T2SL band structure and absorption spectra, based on the k.p method, including a novel approach to the effect of the interfaces between the two individual materials. The main difference between this method and other k.p based methods is in the operator ordering, and in the use of delta-function like interface potentials. The model has reduced the number of fitting parameters to only six, all of which can be deduced empirically.

Calculation results show very good agreement with measurements on over 30 samples grown by Molecular Beam Epitaxy, both in the band gaps and the absorption spectra.

Thursday, 8 January 2015 at 09:30

Room 101, Software Eng. Build.

Special Seminar

Collagen-based nano-biocomposite materials and their potential
applications as tissue scaffolds

Prof. Rina Tannenbaum

Stony Brook University

31 בדצמבר 2014, 16:00

בניין כיתות, חדר 101

Collagen-based nano-biocomposite materials

7.1.15

07 בינואר 2015, 11:00

Wolfson 206

יועצים אקדמיים

שם	מגמה/שנת לימוד	תחום התמחות	דוא"ל
פרופ' אבישי אייל	חשמל / א' ו-ב'	אלקטרואופטיקה, ביו-אלקטרוניקה	avishay@eng.tau.ac.il
פרופ' עופר עמרני	חשמל / ג' ו-ד' וכן חשמל-אביב / ג' ו-ד'	תקשורת, עיבוד אותות	ofera@eng.tau.ac.il
פרופ' דורון שמילוביץ	חשמל-אביב / א' ו-ב'	אנרגיה והספק	shmilo@post.tau.ac.il
ד"ר אמיר נתן	חשמל-פיזיקה / א'-ד'	התקנים, חומרים	amirnatan@post.tau.ac.il
פרופ' אריה רוזין	חשמל-פיזיקה / א'-ד'	התקנים	ruzin@tauex.tau.ac.il
פרופ' יצחק תמו	חשמל-מדמ"ח / א'-ד'	מחשבים	tamo@post.tau.ac.il
ד"ר יקיר חדד		אלקטרומגנטיות	hadady@eng.tau.ac.il
פרופ' ג'ורג וייס		בקרה	gweiss@eng.tau.ac.il

28 דצמבר 2014

ידיעות נוספות בנושא

Seminar 31.12.14

31 בדצמבר 2014, 16:00

וולפסון 206

Physical Electronics Dept.

***** Seminar *****

Gideon Segev

(PhD. student under the supervision of Prof. Yossi Rosenwaks and Prof. Abraham Kribus)

School of Electrical Engineering, Tel-Aviv University, Tel-Aviv 69978, Israel

Photon Enhanced Thermionic Emission for Solar Energy Conversion

To date, the vast majority of solar energy conversion research focused on two parallel paths: photovoltaics and solar thermal energy conversion. Attempts were made to combine photovoltaic and thermal conversion such as cogeneration and thermo-photonics. However, these attempts did not yield very high efficiencies, and these concepts were not widely implemented. As a result, researchers are still looking for a conversion path that exploits both the photonic nature of sunlight and the high temperatures that can be achieved by focusing it.

Photon Enhanced Thermionic Emission (PETE) was recently proposed as a novel concept in solar energy conversion. Similar to traditional thermionic emission devices, a PETE device consists of a high-temperature cathode emitting energetic electrons and a lower temperature anode absorbing the electrons. By using a semiconductor cathode, optically generated electrons increase the cathode’s conduction band charge population allowing high electron emission at temperatures lower than the common range for thermionic emitters. In this seminar, we will discuss the efficiency limits of PETE devices. The theoretical efficiency limits of PETE converters can theoretically rise above 40% at concentration of 1000 suns, exceeding the Shockley Queisser limit for an ideal single junction PV cell. When coupled to secondary thermal cycle the limits were shown to be exceptionally high reaching close to 70% for a flux concentration 1000. Furthermore, unlike traditional thermionic converters, PETE conversion is possible even under isothermal conditions. Next, the loss mechanisms of more realistic PETE devices will be surveyed through elaborated models. Negative space charge between the two electrodes and surface recombination at the cathode contact are shown to heavily restrict the conversion efficiency. Implementation of back surface field layers in the form of homo-junction or hetero-junction cathodes can reduce surface recombination and bring the efficiency closer to the ideal limits.

Wednesday, December 31, 2014, at 16:00

Room 206, Wolfson Mechanical Engineering Building

סמינר מחלקתי

30 בדצמבר 2014, 14:00

חדר 206 בניין וולפסון

ConSent: Context-Based Sentiment Analysis

Dr. Gilad Katz

Abstract:

Sentiment analysis refers to the inference of people's views, positions and attitudes in their written or spoken texts. The applications of this field are numerous, ranging from the classification of hotel reviews to the analysis of public opinion on Twitter.

In this talk I will present ConSent, a context-based approach for the task of sentiment analysis. Our approach builds on techniques from the field of information retrieval to identify key terms indicative of the existence of sentiment. We model these terms and the contexts in which they appear and use them to generate features for supervised learning. The two major strengths of the proposed model are its robustness against noise and the easy addition of features from multiple sources to the feature set. In addition, I will present a set of domain-specific features, designed specifically for sentiment analysis in automatically transcribed text.

Bio:

Gilad Katz is a fourth-year PhD student in the Department of Information Systems Engineering, Ben Gurion University. His advisers are Prof. Yuval Elovici and Prof. Bracha Shapira. His research interest include text mining, machine learning and recommender systems.

ההרצאה תתקיים ביום חמישי,30.12.14, בשעה 14:00 בחדר 206, בנין וולפסון הנדסה, הפקולטה להנדסה, אוניברסיטת תל-אביב.

30.12.14

30 בדצמבר 2014, 15:00

KITOT 011

You are invited to attend a lecture

Atef Shalabney

Institut de Science et d'Ingènierie Supramolèculaires, University of Strasbourg, Strasbourg, France

On the subject:

Light-matter strong coupling and potential for chemistry and biology

When matter is placed in the confined field of electromagnetic radiation, it can lead to modified and even new properties. This is of great interest from both the fundamental point of view as well as for many radiation engineering applications. For instance, the field confinement can lead to effects such as extraordinary optical transmission, enhanced absorption and emission of light, high-resolution spectroscopy and imaging. Under certain conditions, the light-matter interaction can become so strong that it enters the so-called strong coupling regime where new hybrid light-matter states are formed, offering a vast potential for chemistry and biology that has hardly been explored.

In this talk, I'll present the nature of enhanced optical phenomena using nanophotonics and plasmonic structures, emphasizing the applications of harnessing radiation fields into confined regions for bio-sensing and molecular detection. Then, a basic introduction to strong coupling of optically-active substances will be presented. Strong coupling of molecular vibrational transitions in the infra-red region will be particularly elaborated with new prospects to modify molecular and structural processes. New directions for exploiting strong light-matter interactions for bio-sensing and biomedical applications will be discussed.

Short biography:

Dr. Shalabney graduated from the Electrical Engineering Department of the Technion in 1997. He received his M.Sc. and Ph.D. degrees from the Electro-Optics Engineering Department at the Ben-Gurion University in the years 2010 and 2013 respectively. During his Ph.D., he worked within the group of Prof. Ibrahim Abdulhalim on developing plasmonic nanostructures to enhance the sensitivity of optical bio-sensors. In 2013, Dr. Shalabney joined the group of Prof. Thomas Ebbesen at the University of Strasbourg, where his work has been focused on light-matter strong coupling with applications in biology and chemistry.

30 December 2014, at 15:00,

Room 011, Engineering Kitot Building

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