Research after I received my Bachelors in 2005.

I began working in the labora-tory of Dr. David Sabatini, MD, PhD on a project to increase the

speed and reliability of ana-lyzing high content biologi-cal images. The name of the project was CellProfiler (www.cellprofi ler.com) which is now available for free to the research commu-nity. This unique software reduced the variability and human error inherent to analyzing biological images by applying mathematically determined algorithms for segmentation and measure-ment. This powerful soft-ware is used by Dr. Sabatini’s laboratory to (cont’d p 6)

MARCH 2011 VOLUME 3, ISSUE 1

Professors Van C. Mow, X. Edward Guo, Shu Chien, Yingxiao Wang, Ning Wang, Masaaki Sato, and Cheng Dong at the Gala Dinner.

The rise of engineering in the twentieth century led to pro-found change for humankind. The advances in biology were equally amazing. The term “cellular and molecular bio-engineering” (CMBE) became accepted, and it became pos-sible to culture cells outside of the body. Both the Bio-medical Engineering Society (BMES) and the Society for Physical Regulation in Biol-ogy and Medicine (SPRBM) realized the importance of research at this remarkable (cont’d p 4)

GRADUATE STUDENT PROFILE: MICHAEL LAMPRECHT

My undergraduate studies at Boston University laid the groundwork for my future as a Biomedical Engineer. Through extensive course-work and my senior project, I developed an appreciation for the complexity of human physiology. However, I saw an immense opportunity to apply both engineering princi-ples and our vast and rapidly growing technologies to tease apart even the most complex biological systems. It is this drive which led me to con-tinue my work at The White-head Institute for Biomedical

THE FU FOUNDATION SCHOOL OF ENGINEERING AND APPLIED SCIENCE, COLUMBIA UNIVERSITY

BME INSIGHTS

DEPARTMENTAL STATISTICS

AY2010-11

CORE FACULTY: 21

UNDERGRADUATE CLASS, JUNIORS AND SENIORS:

70

M.S. CANDIDATES: 44

M.S.-TO-PH.D. CANDIDATES: 25

PH.D. CANDIDATES: 69

INSIDE THIS ISSUE:

NEW CENTER FOR REGENERATION

2

FACULTY PROFILE 3

BIOENGINEERING CONFERENCE

4

NEWS & STUDENT AWARDS

5

GRADUATE PROFILE

6

FACULTY AWARDS 7

KEY ACADEMIC DATES

8

Inaugural Conference on cellular and molecular bioengineering

The New Craniofacial Regeneration Center (CRC)

Six Columbia University Bio-medical Engineering students received new National Sci-ence Foundation (NSF) fel-lowships for 2010-2011. The new fellows are: Michael Khalil, Zen Liu, Hoang Lu, Genevieve Miller, An Nguyen, and Niccola Perez. Congratulations to the winners!

These students will receive three-year support with $30,000 in annual stipend and $10,500 to support the costs of education, including tui-tion.

To prepare students for the application process, Professor Helen Lu holds annual work-shop sessions to provide an overview of the salient points

Bme National Science Foundation Graduate Student Awards

PAGE 2 BME INSIGHTS

of application procedures and key points that should be in-cluded in fellowship applica-tions. Current fellows also attend to discuss their experi-ences with the application process and their strategies for emphasizing the primary NSF goals of finding projects that have high intellectual merit and significant broader impacts.

Further, Professor Lu reviews some individual applications to provide direct feedback to ap-plicants. These efforts had led to significantly improved suc-cess rates, including capturing 10% of all NSF fellowships awarded in 2008.

Keep your eyes peeled for the next NSF Fellowship Work-shop!

The Center for Craniofacial Regeneration is co-founded by the College of Dental Medicine (CDM) and Department of Bio-medical Engineering (DBME) to foster fundamental research, development of new technologies, interdisciplinary training and interactions with other centers of excellence at Columbia University and worldwide. The Center will be co-directed by Professor Jeremy Mao (CDM) and Professor Gordana Vunjak-Novakovic (DBME), and hosted in their laboratories in the Vanderbilt Clinic, 12th floor, Columbia University Medical Center.

Dr. Ira B. Lamster Dean, College of Dental Medicine

Dr. Feniosky Peña-Mora

Dean, Fu Foundation School of Engineering & Applied Science

Dr. Jeremy Mao & Dr. Gordana Vunjak-NovakovicCo-Directors, Center for Craniofacial Regeneration

will inaugurate the Center for Craniofacial Regeneration

Wednesday, March 2, 20112:30 - 5:30 PM

The agenda for the inauguration follows:

2:00-2:05 PM: Dr. Thomas Cangialoni, Waugh Professor of Dental Medicine and Chair, Section of Growth and Develop-ment, Columbia

2:05-2:10 PM: Dr. Ira Lamster, Dean, College of Dental Medi-cine

2:10-2:15 PM: Dr. Lee Goldman, Dean, Faculty of Health Sci-ences and Medicine, Columbia

2:15-2:20 PM: Dr. Feniosky Peña-Mora, Dean, Columbia Fu Foundation School of Engineering and Applied Science

2:20-3:00 PM: Keynote Speaker, Dr. Robert Langer, Institute Professor, MIT

3:00-3:30 PM: Dr. Jeremy Mao, E.V. Zegarek Professor of Dental Medicine, Co-Director, CRC, Columbia

3:30-4:00 PM: Dr. Gordana Vunjak-Novakovic, Professor of Biomedical Engineering, Co-Director, CRC, Columbia

4:00-5:00 PM: Reception (Faculty Club) & Tour (VC12)

Tell us a bit about yourself.

I received my B.S. in Electri-cal Engineering from MIT and an M.S. and Ph.D. in Bioengi-neering from the University of Pennsylvania. My disserta-tion focused on developing a neuro-inspired computational model of surface and object representations in intermedi-ate-level vision. After receiv-ing my Ph.D. I took a job in industry at the David Sarnoff Research Center in Princeton NJ, where I eventually be-came the Head of a Group in Adaptive Image and Signal Processing. At Sarnoff I did quite a bit of work in machine learning and computer vision, largely applied to neural sig-nals and imaging data, and was also involved in the de-velopment of several spin-out companies. I came to Colum-bia because I wanted to keep studying basic questions on how our visual system works; in particular how we rapidly analyze information in a visual scene.

What is your primary research focus?

In general I work on under-standing how we humans are able to make rapid decisions given visual information. For example, how is it that when we run through the park and, with the briefest of glances of a fellow jogger, we can im-mediately recognize that they are one of our classmates, a famous movie star or some-body we could swear we met on the street? Our ability to make rapid visual judgements

is amazing given how slow individual neurons fire rela-tive to the switching speeds of transistors in state-of-the-art digital electronics--neurons are a billion times slower! So it is likely the basic principles of how we rapidly assess a visual scene and make snap decisions is very different from how a computer might do it. My research uses mul-timodal neuroimaging and large-scale computational modeling to investigate the information processing prin-ciples and representations that lead to our abilities for rapid visual decision making.

Why is this important to study?

Understanding how we make decisions is a fundamental question studied by many groups, including neuroscien-tists, psychologists, econo-mists and philosophers. Thus to understand the principles and processing strategies of decision making is to also u n d e r s t an d , i n s o m e sense, the essence of what makes us human. However I am also a pragmatist and I believe we can use our basic science knowledge to build systems to assist us in our decision making processes, particularly when decisions must be made under stress, information overload or other non-optimal factors. For example, I have built a system called "cortically-coupled computer vision" which inte-grates human visual process-ing and computer vision via a

brain computer interface(BCI). The system enables a new type of image search, where the human operator can convey to the computer information on what they decided is interesting and the computer can take that infor-mation and retrieve visually similar images. What is novel about the system is that the conveying of the information between the human and ma-chine is done using brain sig-

nals derived from the electro-encephalogram (EEG), and that by combining rapid hu-man judgments of images and computer based processing, p e o p l e c a n s u b j e c -tively search much larger image databases than they ever could before. This sys-tem is being activity tested by the U.S. Government for a n u m b e r o f s e c u r i t y /intelligence applications, ranging from analysis of satel-lite imagery to screening air-plane cargo. Finally, there are many neurological dis-eases and deficits that have their basis in abnormal deci-sion making and some of the basic research and applied

FACULTY PROFILE: PAUL SAJDA

PAGE 3 VOLUME 3, ISSUE 1

“Understanding how we make decisions is a fundamental

question”

system designs my labora-tory works on will be used to not only better character-ize these diseases/deficits but to develop new interac-tive methods for their moni-toring and treatment.

What are the unique aspects and strengths of your research field and approach?

I am a neuroengineer and my background and training is highly multidisciplinary and I think that serves as a strength to my approach. In addition to using methods and techniques in neural and decision sciences, I also em-ploy substantial tools in ma-chine learning, statistical inference, and high-per formance comput-ing. Also, since I am an en-gineer, I am a big believer in "you understand it once you can build it" and I think we learn a lot when we have to build or interface with a system in real-world envi-ronments, e.g. as one does with the brain when doing BCI.

(Cont’d page 7)

Professor Sajda with an EEG cap.

cent cutting edge advances in CMBE as well as brainstorm about the future of Cellular and Molecular Bioengineer-ing. Professor Van C. Mow gave an inspiring Keynote talk “The Tipping Point in Cellu-lar and Molecular Bioengi-neering”.

The President of BMES, Pro-fessor Richard Waugh, who was also a Keynote Speaker, wrote in his monthly Presi-dent Column on the BMES website that “Ed Guo of Co-lumbia University and Cheng Dong from Penn State de-serve heartfelt congratulations for their outstanding work in putting this conference to-gether. We hope that it will become an annual event. In addition to the excellent sci-ence, there were also discus-sions at the meeting about the future of the field of Cell and Molecular Bioengineering and the possibility of a merger between SPRBM and BMES that would result in the estab-lishment of the first official

(cont’d from front cover)

nexus of CMBE. In 2008, the BMES formed a new soci-ety journal, Cellular and Mo-lecular Bioengineering, co-edited by Professor X. Ed-ward Guo from the Columbia University Department of Biomedical Engineering and Professor David J. Odde from the University of Min-nesota. Professor Van C. Mow, the Chair of the Co-lumbia University Depart-ment of Biomedical Engi-neering, is the chair of Edito-rial Advisory Board of this new Journal.

Now, the inaugural joint BMES-SPRBM Conference on Cellular and Molecular Bioengineering, co-chaired

by Professor Guo and Profes-sor Cheng Dong from the Pennsylvania State University, is the beginning of a new fo-cus in this promising subfield in biomedical engineering and a much needed forum for this exciting field, and the new CMBE journal.

This new CMBE Conference brought top world leaders in the world to update the re-

CONFERENCE ON CELLULAR AND MOLECULAR BIOENGINEERING

PAGE 4 BME INSIGHTS

subgroup within BMES in this area”.

Indeed, Professor Guo, the President-Elect of SPRBM and Professor Chris Jacobs, the Treasurer of SPRBM (also from the Columbia Univer-sity’s Department of Biomedi-cal Engineering), and Professor Anshu Mathur, President of SPRBM, are working closely with BMES regarding the merger and formation of new Division of Cellular and Mo-lecular Bioengineering.

This Inaugural CMBE Confer-ence was officially endorsed by the US National Committee on Biomechanics, and supported by NIBIB, NIAMS, NSF, and many industrial sponsors as well as our Department of Biomedical Engineering (the program committee raised more than $40,000).

The local committee, mostly consisted of postdoctoral fel-lows and graduate students from the Columbia Univer-sity’s Department of Biomedi-cal Engineering, did a fantastic job and ensured the success of this Conference. They also enjoyed the sunny Miami Beach in between big snow-storms in New York City!

Current members of the Department of Biomedical Engineering served on the Local Committee for the conference. From left to right: Jun Qiu,

Ji Wang, X. Edward Guo, Andrew Baik, and Genevieve Brown.

Professor Van C. Mow was the keynote speaker for the welcome reception.

This Conference

was supported by the US National Committee on Biomechanics, NIBIB, NIAMS

and NSF.

“We hope that it will become an annual event.”

- BMES President Waugh

A group of researchers including Professor X. Edward Guo presented a study at the Orthopaedic Research Society’s 2011 annual meeting in Long Beach, CA, that demonstrated that premenopausal Chinese-American women exhibit significantly increased trabecular bone strength compared to Caucasian counterparts. Collaborating on this project were Columbia University Medical Center’s (CUMC) John P. Bilezikian, Marcella Walker, and X. Sherry Liu.

To study trabecular bone strength, the research team used an analytical technique called Individual Trabecular Segmentation (ITS), which uses high-resolution computed tomography imag-ing to extract three-dimensional information about the struc-ture of bone. Specifically, they showed that in tibial trabecular

The Biotechnology Networking Session, organized by the Co-lumbia University chapter of the Society For Biomaterials,

was held on February 21, 2011 in the historic Low Li-brary. The event featured representatives from LifeCell, Covidien, NuVasive and L’Oreal, who came to net-work with graduate students in the life sciences and pro-vide them with insight on research opportunities in in-dustry. The event was well received and attended by over 60 M.S. and Ph.D. students from a variety of disciplines,

ranging from Earth and Environmental Engineering to the Bio-logical Sciences. The Columbia SFB chapter aims to make the event an annual occurrence and hopes to attract a larger and more diverse group of employers next year.

PAGE 5 VOLUME 3, ISSUE 1

Society of BiomateriaLs EVENT

bone of Chinese-American women, plate-like structures were more domi-nant compared to rod-like structures. Because a higher plate-to-rod ratio is thought to increase bone strength, these findings provide a mechanism by which differences in bone structure may be used to determine the risk of fracture related to osteoporosis.

Amandine Godier-Fournemont received a fellowship from German Science Foundation (DAAD) for one year of research in Dr Zimmermann’s laboratory in Gottingen.

George Eng won the 1st place at the annual poster session of the MD/PhD program at Columbia University Medical School. The College of Physicians and Surgeons ran an article and TV interview with George.

Julia Chen received the best podium talk award at the Society for Physical Regulation in Medicine and Biology meeting in Miami. She, Kristen Lee, and Matthew Downs all re-

Research snapshot

ceived travel fellowships as well.

The senior design 2010 team Procar took second place at the NCIIA BMEStart competition.

Andrea Tan was accepted into the New York Alpha Chapter of Tau Beta Pi.

Danny Kelly received a Fulbright fellowship and a European Research Council grant.

Kristen Moffat received the Orthopaedic Research Society New Investigator Recognition Award (NIRA), for her innova-tive work on biphasic, nanofiber scaffolds.

Student awards

NEWS

The Jan. 2011 Issue of the Journal of Biomechanics has a letter to the editor from Amit Gefen that shows Columbia University’s Biomedical Engineering Department ranked first in measures including grants, awards, doctorates awarded, etc. based on a 2008 US Center for Measuring Uni-versity Performance study.

Professor Sam Sia was named by NASA as one of ten innova-tors in human health and sustainability (October 2010). He was also a featured speaker at MIT Emerging Technologies Conference, and a keynote speaker at the Henry Wheeler Center for Emerging and Neglected Diseases UC Berkeley.

Professor Clark Hung was named to the Editorial Board for the Journal, Tissue Engineering from Jan. 1, 2011-Dec. 31, 2014.

A new Science & Engineering Library at Columbia Uni-versity has opened in the newly-opened Northwest Corner Building.

Shelly Liu Ping fellowships will be awarded starting this year to truly exceptional students at the rate of one per year and at $50,000 per fellowship.

From left to right: BME PhD students Nora Khanarian, Molly Flexman and

Yuri Plotkin speak to Dr. Michael Soltz from Covidien.

(cont’d from front cover)

analyze the enormous amount of image data produced by genome-scale RNA interference (RNAi) screens. During my tenure I also ran several large-scale RNAi screens in search of phenotypic abnormalities which we could isolate to specific genes. Analyzing such a large number of images would be impractical for humans. However, using CellProfiler we were able to extract this data and link several genes that pro-duce the same phenotype. This work was exciting and chal-lenging which led me to apply to the Biomedical Engineering Masters to PhD program at Columbia University.

I began my studies at Columbia University in 2007. I joined the laboratory of Dr. Barclay Morrison III, PhD who focuses on the prevention and treatment of Traumatic Brain Injury (TBI). About 1.5 million people per year are subject to TBI and many require lifelong treatment. The economic costs exceed $60 billion per year which does not account for social and emotional costs to patients and families. Therefore it is vital that we reduce the incidence of TBI and research poten-tial treatments for these patients.

have already been FDA approved to treat the injured tissue and mitigate the effects of injury. I will be using several methods including immunofluorescence, electrophysiology, and electro-chemistry to determine if our treatments are improving both cell viability and neural circuit function in injured tissue.

PAGE 6 BME INSIGHTS

Hippocampal slice culture on a microelectrode array.

SEM image of Vertically Aligned Carbon Nanofiber Arrays. Courtesy of Timothy E. McKnight, Oak Ridge National Laboratory.

GRADUATE STUDENT PROFILE: MICHAEL LAMPRECHT

Our laboratory is proficient at producing organotypic brain slice cultures of the rat hippocampus. We are able to remove an intact piece of tissue from the brain, culture it, and keep the organization and cellular makeup of that tissue intact for several weeks. This powerful method is conducive to large scale in vitro experiments that otherwise would take much longer or be impossible via in vivo methods. Another advan-tage is that we can reproducibly injure the tissue with well characterized injuries and outcomes. With this powerful tech-nique I am investigating the role of interneurons before and after injury. I plan to test combinations of therapeutics that

20X confocal image of transverse hippocampal slice stained for cell

nuclei (blue) and somatostatin posi-tive interneurons (green).

I am also working on a novel electrode technology, Vertically Aligned Carbon Nanofiber (VACNF) arrays, in collaboration with Oak Ridge National Laboratory. These arrays are con-structed from carbon fiber which is extremely biocompatible. Because of their small size, the arrays offer spatial advantages to typical electrode arrays. The major benefit of using carbon fiber is the ability to sense both electrical and chemical responses. Our laboratory has successfully used this technology to record electri-cal response from our organotypic brain slice cultures. I have successfully recorded dopamine concentrations, a major neuro-transmitter in the brain, with these electrodes. I will continue working on this technology with the goal of simultaneously re-cording electrical and chemical signals from our brain slice cul-tures.

The experiences I have had as a Biomedical Engineering student at Columbia University have been great. I want to thank all of the faculty and staff who have supported me during my research, especially my advisor, Dr. Morrison. I must also thank all of the members of my laboratory who have made this experience fun and entertaining throughout the past few years. Thank you!

(Cont’d from page 3)

How do you combine the two worlds of a startup company and an aca-demic research laboratory?

I love being an entrepreneur--it was one of the main things I missed when I left Sarnoff. I recently formed a company called Neuromatters LLC which is building systems based on the corti-cally-coupled computer vision technology developed in my lab. I am not involved in day to day operations of the company, so the key is to find a strong management team who you trust, has the right technical expertise, and a vision and drive that syn-ergizes with you. I am lucky in that I have found that and can focus my efforts on providing a grand vision for the technol-ogy . I also get to see how my research can be used for practical applications, which is very rewarding. Columbia is largely very supportive of entrepreneurial efforts of its faculty and I see en-trepreneurship as almost as a job requirement for being a fac-ulty in biomedical engineering.

On January 9, 2011, Professor Christopher Jacobs (below)completed the Disney marathon in 4 hours, 42 minutes, 47 seconds as a member of the Leukemia and Lymphoma Soci-ety’s (LLS) Team in Training to raise funds to fight cancer. His efforts raised over $ 6,500 to further the mission of LLS.

PAUL SAJDA

FACULTY AWARDS A team of engineers including Professor Barclay Morrison has been awarded $ 6 million to study the effects of blast waves on neural function from the DoD’s MURI program.

Professor Edward Guo received an NIH grant for over $ 3.7 million to study clinical bone mechanics using advanced imag-ing methods.

Professor Elizabeth Olson (left) received a NIH grant for over $ 1.7 million to study cochlear physiology.

Professor Paul Sajda received a Phase 3 DARPA grant for over $ 1.5 million to exam-ine cortically-coupled computer vision.

Professor Nicolas Chbat (right) was pro-moted to Principal Member Research at Philips North America and recently won a $1 million two-year NIH grant with Mayo Clinic’s Pulmonary & Critical Care Dept. on “In Silico Model for Acute Lung Injury Prediction and Clinical Trial Design.” O. Gajic, MD, Mayo Clinic, is co-PI.

Professor Helen H. Lu was elected fellow of the American Institute for Medical and Biological Engineering (AIMBE) for “groundbreaking research and extraordinarily high levels of mentoring in interface tissue engineering”.

Professor Gerard Ateshian was elected as a Biomedical Engi-neering Society Fellow.

Professor Gordana Vunjak-Novakovic received over $ 2 million in grants from the New York State Department of Health as well as a Helmsley Stem Cell Starter Grant to study maturation of cardiomyocytes and the differentiation of stem cells into cardiac tissues. Dr Vunjak-Novakovic also received the 2010 Clemson award of the Society of Biomaterials “for significant contributions to the literature on the science or tech-nology of biomaterials”

Professor Elisa Konofagou received a $1.4 million, 4-year renewal of her original NIH grant on early detection of cardiac disease using Myocardial Elastography. Prof. Konofagou was also awarded a seed grant by the Kavli Foundation for pre-clinical applications of ultrasound-induced opening of the blood-brain barrier. Prof. Vincent Ferrera in the department of Neu-roscience is co-PI.

Professors Clark Hung (left) and Gerard Ateshian received an NIH grant for over $1.5 million to examine nutrient supply methods for large tissue-engineered cartilage grafts. Co-PIs are Profs. Guo and Vunjak-Novakovic.

Professor Andreas Hielscher received a collaborative Department of Defense grant for

$ 3.3 million to treat bone and cartilage trauma.

PAGE 7 VOLUME 3, ISSUE 1

CHRIS JACOBS RUNS AGAINST CANCER

Key Dates January 18, 2011

Spring Classes Begin

March 14-18, 2011

Spring Break

March 24, 2011

Last Day to Drop Classes

May 2, 2011

Last Day of Classes

May 6-13, 2011

Final Examination Period

May 18, 2011

Commencement

PAGE 8 BME INSIGHTS

V I S I T U S AT H T T P : / / B M E . C O L U M B I A . E D U

BME Insights An annual publication of the

Biomedical Engineering Department

Hayden Huang Elisa E. Konofagou

Robert Foster Questions or comments?

Contact: Hayden Huang (hayden.huang@columbia.edu)

Content Contributors

Genevieve Brown, X. Edward Guo, Christopher Jacobs, Nora Khanarian,

Michael Lamprecht, Helen Lu, Van Mow, Paul Sajda, Siddarth

Subramony, Andrea Tan, Gordana Vunjak-Novakovic

March 7, 2011* “In-vivo optical imaging: From animal to man” Elizabeth Hillman, PhD; Assistant Professor, Biomedical Engineering, FF SEAS, Columbia University *This session will be held in the Irving Institute Conference Room (PH-10-204) March 21, 2011 “Elasticity imaging and therapeutics: Recent advances in medical ultrasound” Elisa E. Konofagou, PhD; Associate Professor, Biomedical Engineering and Radiology Director, Ultrasound and Elasticity Imaging Laboratory, Columbia University April 4, 2011 “Advances in Quantitative Analysis of Medical Images: Func-tional imaging of the Heart, Brain and Vasculature” Andrew Laine, DSc; Vice-Chair, Professor, Biomedical Engineering and Radiology, FF SEAS, Columbia University May 2, 2011 “PET/CT in oncology: Development of a cancer phenotype imaging agent from bench to clinical use” Chaitanya Divgi, MD; Visiting Professor, Kreitchman PET Center, Co-lumbia University June 6, 2010 “Application of PET Imaging to Neuroscience Research” J. John Mann, MD; Paul Janssen Professor of Translational Neurosci-ence in Psychiatry and Radiology, Columbia University All seminars (except 3/7) will be held: 12:00 – 1:00p Irving Institute Education Center Classroom (PH-10-405) 622 West 168 Street, Floor 10, Room 405, NYC 10032 Please RSVP to Michelle McClave at mm3098@columbia.edu or (212) 305-9425

CTSA Irving Institute IMAGINg Seminars