BALTIMORE, June 4, 2014 – InSilico Medicine, Inc. announced today that Charles Cantor, Ph.D. will chair its Scientific Advisory Board.
Dr. Cantor, one of the leaders of the Human Genome Project, has published more than 400 peer-reviewed articles, authored and co-authored more than 50 U.S. and international patents. He is also an author of the first genomics textbook, “Genomics: The Science and Technology of the Human Genome Project” and the three-volume textbook “Biophysical Chemistry”.
“Professor Cantor’s discoveries and leadership are already helping save lives and improve human health span. What is less known is his interest in areas related to aging including the complex and multi-year research projects in isotopically-fortified organic compounds and advanced diagnostics using the cell-free nucleic acids. He is the role model for the many research scientists aspiring to utilize resources available in the private sector, accelerate scientific research without the many formal constraints and budgetary limitations of academia and turn their discoveries into practical projects. We are honored to have Charles join our advisory board”, said Alex Zhavoronkov, PhD, CEO of InSilico Medicine, Inc.
Dr. Cantor is the co-founder of Sequenom, Inc, a company engaged in non-invasive prenatal diagnostics and co-founder of Retrotope, a company developing isotopically-fortified organic compounds to bolster stress resistance and combat age-related diseases and acts as a consultant for several companies within the biotechnology industry. He is professor emeritus at the Boston University, distinguished adjunct professor at the University of California Irvine and adjunct professor at the Moscow Institute of Physics and Technology and at Scripps Research Institute. Dr. Cantor was previously the chair and professor of the department of biomedical engineering and biophysics, and director of the Center for Advanced Biotechnology at Boston University, and his research laboratory remains active.
“Aging is one of the most pressing problems facing the economies of the developed countries and there is an urgent need for new ways to increase productive longevity and screening the known drugs for their geroprotective properties and personalizing anti-cancer and aging-suppressive regiments using genetic and epigenetic analysis is one of the low hanging fruits in applied aging research. I am pleased to join the SAB of this international team dedicated to develop working solutions for both aging and age-related diseases”, said Charles Cantor, PhD, chair of the Science Advisory Board of InSilico Medicine, Inc.
Dr. Cantor was the chairman of Genetics and Development at Columbia University College of Physicians & Surgeons, and Professor of Molecular Biology, University of California, Berkeley.
He earned his bachelor’s degree in chemistry at Columbia College, and his doctorate at the University of California Berkeley.
About InSilico Medicine, Inc.
Insilico Medicine, Inc. is a Baltimore-based bioinformatics and drug discovery company specializing in cancer and aging research and personalized medicine in age-related diseases. The company is developing models and softwares to predict the efficacy of the various targeted drugs in oncology and extrapolated these methods to evaluate the possible geroprotective properties of the many drugs with known molecular targets. The mission of InSilico Medicine is to find working solutions to treat, cure and prevent age-related diseases and aging itself through excellence in knowledge management, machine learning and bioinformatics, relentless pursuit for new drug, omics and clinical outcomes data, development of reliable in silico drug screening methods, novel validation approaches and strong international partnerships in personalized medicine. This mission will be achieved within the regulatory frameworks as well as the legal and ethical boundaries and by working with the outstanding scientists, academic and medical institutions and pharmaceutical companies of impeccable credibility. For more information please visithttp://www.InSilicoMedicine.com
Press release at Reuters.com
BALTIMORE, May 30, 2014 – InSilico Medicine, Inc, engaged in cancer and aging research for drug discovery and developing personalized approaches to extending productive longevity is proud to announce the addition of Prof. Bud Mishra to its board of scientific advisors.
“Dr. Alex Zhavoronkov is a fascinating young scientist, seriously engaged in modeling the future of aging and various diseases that accompany it. He has assembled a dream team, especially with a leading visionary, Dr. Charles Cantor, who has “disrupted” the way we think about biology, biotechnology and bioinformatics. With a group like this, I hope to engage in a collective ‘head-banging’ against amazingly challenging biomedical problems – using some of the most advanced science and technologies”, said professor Bud Mishra.
“It is a pleasure to be involved in this innovative enterprise that can potentially really optimize individual medical care. I look forward to working with some of the outstanding participants in this endeavor. In particular I have long hoped for an opportunity to do something direct with bud Mishra and now that he has also joined the SAB of Insilico Medicine we have a forum to promote brain storming and interactions”, said Dr. Charles Cantor, a professor at Boston University, the former director of the Human Genome Project with the Department of Energy and the chair of the science advisory board of InSilico Medicine, Inc.
Prof. Bhubaneswar (Bud) Mishra is a professor of computer science and mathematics at NYU’s Courant Institute of Mathematical Sciences, professor of human genetics at Mt. Sinai School of Medicine, and a professor of cell biology at NYU School of Medicine. He founded the NYU/Courant Bioinformatics Group, a multi-disciplinary group working on research at the interface of computer science, applied mathematics and biology. His primary research subfield is “applied algorithmics,” but has ranged more generally from compilers, algorithms and complexity, logic, and algebra to robotics, finance, Internet, and biology.
Dr. Mishra published over three hundred high-impact publications on subjects ranging from mathematics, computer science and robotics to causality of cancer and genetics. His works were cited over five thousand times by other scientists and led to the many successful businesses and practical implementations.
“The sole fact that computer science juggernauts like Dr. Bud Mishra, whose research fuelled the computer, the Internet and the genomics revolutions are now working on aging research gives me a lot of hope for the future. These luminaries are creating the new level of abstraction on top of the laboratory science and using the rapidly expanding knowledge base to find practical applications that may rapidly translate into clinical practice. Our goal is to prove to the academic community, pharmaceutical companies, regulators and policy makers that it is possible to significantly streamline aging research for drug repurposing, drug discovery and personalization. Extending productive longevity is no longer a dream, but a clearly achievable objective”, said Alex Zhavoronkov, PhD, CEO of InSilico Medicine, Inc.
Press release at MarketWatch.com
Baltimore, May 20, 2014 – InSilico Medicine, Inc, the aging and longevity bioinformatics and drug discovery company, today announced the opening of its office in Baltimore within the Emerging Technology Centers (ETC) at Johns Hopkins University Eastern Campus.
InSilico Medicine, Inc is a Baltimore-based bioinformatics and drug discovery company specializing in cancer, aging research and personalized medicine in age-related diseases. The company developed methods and software tools to predict the effectiveness of the various targeted drugs in oncology and extrapolated these methods to evaluate the possible geroprotective properties of the many drugs with known molecular targets. The mission of InSilico Medicine is to find working solutions to treat, cure and prevent age-related diseases and aging itself through excellence in knowledge management, machine learning and bioinformatics, relentless pursuit for new drug, omics and clinical outcomes data, development of reliable in silico drug screening methods, novel validation approaches and strong international partnerships in personalized medicine.
“The state of the whole area of biomedical sciences today resembles that of the dawn of the personal computing in the 80′s or Internet in the 90′s. And as some of the discoveries transition from the laboratory into clinical practice and mainstream use, Baltimore may eclipse Silicon Valley. Baltimore is one of the few rapidly regenerating and developing cities with highly qualified labor and cost-effective infrastructure and we are proud to join this thriving community. ETC allows the innovative companies to develop within the Johns Hopkins ecosystem and move fast into the emerging areas of science and technology while absorbing the culture of excellence,” said Alex Zhavoronkov, PhD, CEO of InSilico Medicine, Inc.
To participate in the rapidly growing science and technology hub in Baltimore and to take advantage of the innovation-friendly environment developed by the community of the top industry captains, InSilico Medicine selected the Emerging Technology Centers at Johns Hopkins Eastern Campus as the optimal location for its research and development operations. This location provides access to thousands of highly educated bioinformatics professionals and interns to work on the highly-ambitious high-impact projects.
“We are extremely excited to welcome Insilico Medicine as an ETC portfolio company,” said Deborah Tillett, ETC’s President. “Their amazing research in productive longevity promises to change the future for all of us; they are a great addition to ETC and the City,” she concluded.
“Proximity to the major academic institutions like the Johns Hopkins University, Johns Hopkins Medicine, National Institute on Aging and University of Maryland will allow us to hire the recent graduates and interns as well as collaborate with some of the world’s most advanced geneticists, bioinformaticians and computer scientists. We aim to be a driver of change in medicine embracing the concept of productive longevity and shifting the paradigms from treatment to personalized prevention. Our approach to evaluating the ability of drugs to slow down the age-related processes and possibly repair the accumulated damage is unique and we would be very proud if it becomes one of the many breakthroughs originating from this Mecca of biomedicine”, said Qingsong Zhu, PhD, COO of InSilico Medicine, Inc.
“Many things are aligned in Baltimore to propel innovative start-up companies in healthcare. Access to world-class researchers and talent in biomedicine, technology and healthcare here in Maryland is unparalleled. If you couple that intellectual asset with a growing entrepreneurial base, a robust investment community, and the active involvement of large prominent institutions like the Johns Hopkins University, Johns Hopkins Medicine, BioHealth Innovation, and Northrop Grumman, as seen in the recent successful launch of DreamIT Health Baltimore, Baltimore’s first health accelerator, you start to see the initial sparks to what will undoubtedly lead to an explosion of innovations. We already see those sparks developing rapidly and InSilico Medicine is a testament to the growing prominence of Baltimore for innovative international companies. Its aim of combating cancer and aging through the use of genomics and novel bioinformatics comes at a very exciting and opportune time,” states Benjamin Seo, a Partner at emocha Mobile Health Inc. – a company, spun-out of technology developed at Johns Hopkins, offering a mobile health platform for remote patient management on a global scale.
Full press release at StreetInsider.com
BALTIMORE, Apr 09, 2014 – Today Insilico Medicine, Inc., a Baltimore-based company using advances in genomics to discover new therapies to target aging and age-related diseases, announced the appointment of cancer genomics expert Dr. Qingsong Zhu to the position of Chief Operating Officer (COO).
Dr. Zhu holds a bachelors degree in biology from the Beijing Forestry University in Beijing. He obtained his Ph.D. in Biochemistry under Dr. Karl Kramer and Dr. Subaratnam Muthurishnan from Kansas State University Manhattan, Kansas US where his research focused on insect genome sequencing, annotation and new gene identification. Dr. Zhu spent seven years as a postdoctoral research fellow at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University where he worked with Dr. Nancy Davidson in the breast cancer program and Dr. Robert Arceci in pediatric oncology. He was experienced in biomarker identification and drug development using both microarray and next generation sequencing techniques. Dr. Zhu has a broad professional network in the US and internationally and is fluent in Mandarin Chinese.
Insilico Medicine, Inc. holds an exclusive license to drug discoveries made using Hong Kong based Pathway Pharmaceuticals’ OncoFINDER tool, which predicts drug efficacy through a proprietary gene expression analysis algorithm. Dr. Qingsong Zhu will be responsible for operations and drug discovery research initiatives. He has over 15 years of experience in genomics with an emphasis on bioinformatics and the use of microarray and next generation sequencing (NGS) in cancer research. He has been involved in the identification of several novel drug targets and preclinical development programs. In addition, he has over three years experience managing clinical trials.
His latest entrepreneurial endeavors focused on improving the early diagnosis and personalized treatment of cancer and other diseases. He published his research in reputable peer-reviewed journals including Nature and as the first author in PNAS and Bioinformatics.
“The capabilities of drug discovery and personalized medicine companies are no longer constrained by the ability to afford and operate expensive sequencing equipment, but by the ability to interpret the data, make connections and extract valuable knowledge. Building on years of research in bioinformatics and equipped with powerful resources like the OncoFINDER and GeroScope, Insilico Medicine has set itself the most challenging of goals possible in biomedical research: finding drugs that combat age-related diseases and even aging itself. I am very excited to join this fast-paced and ambitious company and contribute to the revolution in cancer and aging research”, said Qingsong Zhu, PhD, Chief Operating Officer of Insilico Medicine, Inc.
Insilico Medicine, Inc. joins Google Ventures’s Calico and Craig Venter’s Human Longevity. Inc. in the hunt for novel solutions to age-related disease.
Dr Zhu notes that “Whilst other recently announced companies plan to use Big Data to find solutions for healthy aging without clearly defining the methods, Insilico Medicine, Inc has a very specific approach to high-throughput in silico drug discovery, screening and ranking of the many potential drugs and drug combinations.”
“We are very excited about Dr. Zhu joining our team. He spent many years working at the top cancer lane at Johns Hopkins Medicine as well as an independent consultant on application of NGS to diagnostic and personalized medicine. His philosophy of combining corporate goals with academic excellence is aligned with the spirit of Insilico Medicine, Inc. Dr. Zhu will coordinate the internal team as well as the sponsored research projects and collaborations with our partners. Together we will relentlessly pursue the ambitious goals of the company to discover new drugs and drug combinations to combat age-related diseases and develop new methods for tailoring drug regiments of the individual patients”, commented Professor Alex Zhavoronkov, PhD, Chief Executive Officer of Insilico Medicine, Inc.
Press release at MarketWatch.com
Requires subscription to GenomeWeb.
BALTIMORE, March 6, 2014 – In Silico Medicine Inc, developing novel computer-assisted methods for drug discovery in aging research, has officially launched in the US. InSilico Medicine draws on years of research and software development expertise of its partner, Pathway Pharmaceuticals in Hong Kong, which employs its state of the art OncoFinder platform to select and rate personalized cancer therapies, and identify new drug candidates in oncology.
Population aging is one of the major internal threats to the economies, cultures and social structures in developed countries. Increasing productive longevity of the working population may not only be the major new source of economic growth, but the only altruistic way to save the debt-laden economies from collapsing. And while aging is a very complex multifactorial process that cannot be stopped or reversed by a simple combination of drugs, the pharmaceutical industry needs a platform to screen and predict the effectiveness of possible aging-suppressive drugs in a high-throughput environment to at least slow some of the aging processes
One of the reasons why pharmaceutical companies failed to develop business models for increasing productive human longevity is because human lifespans are much longer than that of the many model organisms and it takes decades to evaluate the effects of any drug. Some of the known drugs have been on the market for many decades and only recently scientists started finding clues to their oncoprotective, cardioprotective and geroprotective effects. Moreover, many drugs that work on model organisms including mice do not have the same effects in humans. There is an urgent need for intelligent systems that will cost-effectively predict the effectiveness of the many drugs on the population, but also on the individual levels.
“We built our platform on years of experience of a large international team who specialize in using gene expression data from individual patient’s tumor to predict the effectiveness of targeted compounds and improve clinical decision making. We are reinventing this system for drug discovery in cancer and aging,” said Alex Zhavoronkov, PhD, the CEO of In Silico Medicine. “The recent wave of startups looking to employ big data to find solutions for aging, including the Google’s Calico and Human Longevity, should give everyone hope that we may see the time when both the medical institutions and pharmaceutical companies will start saving lives so every human being on the planet will benefit.”
Some of the ideas behind the company’s drug discovery platforms for both cancer and aging are rather simple: analyze the genetic and epigenetic profiles of young and normal cells, run computer simulations to see what drugs make the old or malignant cell get as close to the norm as possible and then validate the results on human cells and model organisms. The same approach may be employed to personalize the drug regimen for individual patients. The core expertise of In Silico Medicine is in all-inclusive gene expression analysis and development of various algorithms that minimize the difference between the “young” and “old” signaling pathway activation profiles, and they are actively adding new modules that can be used with the drug databases. These include microRNA, methylation and proteomics modules among others.
Read this press release at Reuters
Alex Zhavoronkov, PhD
Chief Executive Officer
Prior to co-founding In Silico Medicine Dr. Zhavoronkov held numerous positions in academia as well as the senior management positions in both IT and biotechnology private and publicly-traded companies in Canada, USA, Germany, Russia and China.
He started his career in telecommunications semiconductors the product marketing engineer with PMC-Sierra (Nasdaq:PMCS) in Burnaby, then progressed from the business manager of desktop business unit to the director of Central and Eastern Europe at ATI Technologies (Nasdaq: AMD), a publicly- traded in computer graphics acquired by AMD.
He served as the CEO of Mediox, Inc, the developer of the many popular multimedia interactive display devices and as the director of GTCBio, a biotechnology conference management company. Together with scientists from Canada, Russia and the US, he co-founded the First Oncology Research and Advisory Center, a personalized medicine organization providing contract research services to oncologists interested in gene expression and activated signaling pathway analysis and predicted effectiveness of targeted drugs to improve clinical decision making in oncology. The company was later acquired by Pathway Pharmaceuticals, Limited in Hong Kong.
Dr. Zhavoronkov is the adjunct professor of the Moscow Institute of Physics and Technology. He is a member of the editorial boards of Drug Discovery International and Frontiers in Molecular Diagnostics journals. He is the author of over thirty research articles, analytical reports, white papers and several books including the biotechnology bestseller “The Ageless Generation: How biomedical advances will transform the global economy”.
Dr. Qingsong Zhu
Chief Operating Officer
Dr. Qingsong Zhu is responsible for Insilico Mecine, Inc operations and drug discovery research initiatives. He has over 15 years of experience in genomics research with the emphasis on bioinformatics and the use of microarray and next generation sequencing (NGS) in cancer research and drug target identification and evaluation using in vitro and in vivo models. In addition, he has over three years of clinical trials experience. His latest entrepreneurial endeavors focused on improving the early diagnosis and personalized treatment of cancer and other diseases.
Dr. Zhu spent six years as the post doctoral research associate in the leading labs at the Johns Hopkins School of Medicine in Baltimore. He published extensively in reputable peer-reviewed journals including Nature and as the first author in PNAS and Bioinformatics.
Dr Zhu holds the bachelor degree in biology from the Beijing Forestry University in Beijing, a masters degree in biochemistry and a Ph.D. degree from the Kansas State University in Manhattan, US. from the He obtained his Ph.D. in Biochemistry under Dr. Karl Kramer and Dr. Subaratnam Muthurishnan from Kansas State University where his research focused on insect genome sequencing, annotation and new gene identification. He received his postdoctoral training in the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University. He worked with Dr. Nancy Davidson in the breast cancer program and Dr. Robert Arceci in pediatric oncology. He was experienced in biomarker identification and drug development using both microarray and next generation sequencing techniques. Dr. Zhu has a broad professional network in the US and internationally and is fluent in Mandarin Chinese.
Research and Development Team
In Silico Medicine is built on the scientific platform constructed by over a hundred scientists internationally. It draws on the research and software development expertise of its partner, Pathway Pharmaceuticals in Hong Kong. The companies share management and the Scientific Advisory Board.
The company is actively hiring and we are actively searching for experts in bioinformatics in the areas of:
Anton Buzdin, PhD, DSc
Prof. Anton Buzdin, PhD, Doctor of Sciences, is the head of the Group for Genomic Analysis of Cell Signaling Systems at the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry in Moscow. He also supervises a Laboratory of Bioinformatics at the Federal Clinical Research Center for Pediatric Hematology, Oncology and Immunology in Moscow and works as the invited professor at the Federal Medico-Biological Agency of Russia. He is also a director of the First Oncology Research and Advisory Center, a Russia-based innovative company aimed at the application of research in bioinformatics to clinical medicine.
His primary research interests are focused on genomics, molecular genetics and bioinformatics, translation medicine, include systems biology of carcinogenesis, high-throughput analysis of biological and biomedical information and finding molecular targets for the development of new drugs.
He was graduated from Lomonosov Moscow State University at 1999. Dr. Buzdin was acknowledged by a Golden Medal of the Russian Academy of Sciences, by a Medal of the Academia Europaea, by a Medal of the Timofeev-Ressovsky International Society of Genetics and by many other awards. Mr. Buzdin is author of more than 70 scientific works.
Sergey Roumiantsev, MD, PhD, DSc
Prof. Sergey A. Roumiantsev, MD, PhD, DSc, is the Head of Research and Education programs at the Federal Clinical Research Center of Pediatric Hematology, Oncology and Immunology, and a Professor at the Russian National Research Medical University(Department of Oncology and Hematology, Pediatric Faculty). He also heads the faculty of regenerative and translational medicine at the Moscow Institute of Physics and Technology.
He has more than 160 scientific publications in medical journals.
His primary research interests include molecular diagnostics, regenerative medicine, immunobiology and immunopharmacology, biology of neoplastic growth, properties of leukemic and normal blood and bone marrow cells, normal and leukemic hematopoiesis, stem cell banking, angiogenesis, oncogenetic, target therapy, and blood doping.
Nikolay Borisov, PhD, DSc
Head of Laboratory for Oncological Bioinformatics and Systems Biology of Cell Signaling Pathways, Federal Biophysical Center A.I. Burnazyan of Federal Biomedical Agency (Moscow).
Head of Department of Medical Physics, Biophysics and X-ray Planning in Institute of Professional Education, Federal Biophysical Center A.I. Burnazyan.
Graduate of Department of Biophysics, Radiation Physics and Ecology, National Research Nuclear University “MEPhI” (1996). Passed his doctoral internship (over 5 years) in Thomas Jefferson University, Philadelphia, and IRSN, Fontenay-aux-Roses, France.
Collaborates with University College Dublin (Ireland) and Pittsburg University (USA).
Mr. Borisov is author of more than 80 works regarded to methods of computing mathematics in molecular oncology and radiation physics. Expert of International Atomic Energy Agency in medical physics and molecular oncology (2011). Was acknowledged by medal V.I.Korogodin “Life phenomenon” (2009). Honored by commendation of Biological Sciences Department of the Russian Academy of Sciences for studies of molecular-kinetik fundaments of blastomatosis with domain-oriented approach.
We will announce the Science Advisory Board shortly. It will be comprised of the distinguished scientists including the former director of the Human Genome Project at DOE, professor of the Boston University, Charles Cantor, PhD and many other scientists and medical doctors as well as the representatives of the pharmaceutical industry.
SILENCING AML1-ETO GENE EXPRESSION LEADS TO SIMULTANEOUS ACTIVATION OF BOTH PRO-APOPTOTIC AND PROLIFERATION SIGNALING PV SPIRIN, TD LEBEDEV, NN ORLOVA, AS GORNOSTAEVA, MM PROKOFJEVA, NA NIKITENKO, SE DMITRIEV, AA BUZDIN, NM BORISOV, AM ALIPER, AV GARAZHA, PM RUBTSOV, C STOCKING AND VS PRASSOLOV LEUKEMIA (14 APRIL 2014) | DOI:10.1038/LEU.2014.130 HTTP://WWW.NATURE.COM/LEU/JOURNAL/VAOP/NCURRENT/FULL/LEU2014130A.HTML
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A. BUZDIN, E. KOVALSKAYA-ALEXANDROVA, E. GOGVADZE, E. SVERDLOV (2006) GREM, A TECHNIQUE FOR GENOME-WIDE ISOLATION AND QUANTITATIVE ANALYSIS OF PROMOTER ACTIVE REPEATS. NUCLEIC ACIDS RES., 34(9): E67.
I. V. KHOLODENKO, A. A. BUZDIN, R. V. KHOLODENKO, J. A. BIBIKOVA, V. F. SOROKIN, V. N. YARYGIN, AND E. D. SVERDLOV (2006) MOUSE RETINAL PROGENITOR CELL (RPC) COCULTIVATION WITH RETINAL PIGMENT EPITHELIAL CELL CULTURE AFFECTS FEATURES OF RPC DIFFERENTIATION. BIOCHEMISTRY (MOSCOW) 71(7):767-74.
KOVALSKAYA, E., BUZDIN, A., GOGVADZE, E., VINOGRADOVA, T., SVERDLOV, E.D. (2006) FUNCTIONAL HUMAN ENDOGENOUS RETROVIRAL LTR TRANSCRIPTION START SITES ARE LOCATED BETWEEN THE R AND U5 REGIONS. VIROLOGY, MAR 15; 346(2):373-378.
BUZDIN, A. (2006) TRANSPOSABLE ELEMENTS AND THEIR USE FOR TARGET SITE SPECIFIC GENE DELIVERY. CURRENT PHARMACOGENOMICS, MARCH; 4(1): 1-8.
GOGVADZE, E., BUZDIN, A. (2005) NEW MECHANISM OF RETROGENE FORMATION IN MAMMALIAN GENOMES: IN VIVO RECOMBINATION DURING RNA REVERSE TRANSCRIPTION. MOLECULAR BIOLOGY (MOSCOW), MAY-JUN;39(3):364-373.
BUZDIN, A., VINOGRADOVA, T., LEBEDEV, Y., SVERDLOV, E. (2005) GENOME-WIDE EXPERIMENTAL IDENTIFICATION AND FUNCTIONAL ANALYSIS OF HUMAN SPECIFIC RETROELEMENTS. CYTOGENET. GENOME RES.;110(1-4):468-474., IN THE SPECIAL ISSUE: “RETROTRANSPOSABLE ELEMENTS AND GENOME EVOLUTION”
GOGVADZE, E., BUZDIN, A., SVERDLOV, E. (2005) MULTIPLE TEMPLATE SWITCHES DURING LINE DIRECTED REVERSE TRANSCRIPTION IS A GENERAL MECHANISM OF THE CHIMERIC RETROELEMENT FORMATION IN MAMMALS. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY, 31(1):82-89
CHALAYA T., GOGVADZE E., BUZDIN A., KOVALSKAYA E., SVERDLOV E.D. (2004). IMPROVING SPECIFICITY OF DNA HYBRIDIZATION-BASED METHODS. NUCLEIC ACIDS RES., 32(16):E130.
BUZDIN, A. (2004) RETROELEMENTS AND FORMATION OF CHIMERIC RETROGENES. CMLS, CELL. MOL. LIFE SCI. 61(16):2046-2059
BUZDIN, A., GOGVADZE, E., KOVALSKAYA, E., VOLCHKOV, P., USTYUGOVA, S., ILLARIONOVA, A., FUSHAN, A., VINOGRADOVA, T., SVERDLOV, E. (2003) THE HUMAN GENOME CONTAINS MANY TYPES OF CHIMERIC RETROGENES GENERATED THROUGH IN VIVO RNA RECOMBINATION. NUCLEIC ACIDS RES., 31(15):4385-4390.
BUZDIN, A., LEBEDEV, YU., SVERDLOV, E. (2003) HUMAN SPECIFIC HERV-K LTRS IN GENE INTRONS HAVE A NON-RANDOM ORIENTATION AND, POSSIBLY, PARTICIPATE IN ANTISENSE REGULATION OF THE GENE EXPRESSION. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY, 29(1):103-106.
BUZDIN, A., USTYUGOVA, S., KHODOSEVICH, K., MAMEDOV, I., LEBEDEV, Y., HUNSMANN, G., SVERDLOV, E. (2003) HUMAN-SPECIFIC SUBFAMILIES OF HERV-K (HML-2) LONG TERMINAL REPEATS: THREE MASTER GENES WERE ACTIVE SIMULTANEOUSLY DURING BRANCHING OF HOMINOID LINEAGES. GENOMICS, 81(2):149-156.
BUZDIN, A., USTYUGOVA, S., GOGVADZE, E., LEBEDEV, Y., HUNSMANN, G., SVERDLOV, E. (2003) GENOME-WIDE TARGETED SEARCH FOR HUMAN SPECIFIC AND POLYMORPHIC L1 INTEGRATIONS. HUMAN GENETICS, 112(5-6):527-533.
BUZDIN, A., USTYUGOVA, S., GOGVADZE, E., VINOGRADOVA, T., LEBEDEV, Y., SVERDLOV, E. (2002) A NEW FAMILY OF CHIMERIC RETROTRANSCRIPTS FORMED BY A FULL COPY OF U6 SMALL NUCLEAR RNA FUSED TO THE 3′ TERMINUS OF L1. GENOMICS, 80(4):402-406.
MAMEDOV, I., BATRAK, A., BUZDIN, A., ARZUMANYAN, E., LEBEDEV, Y., SVERDLOV, E. (2002) GENOME-WIDE COMPARISON OF DIFFERENCES IN THE INTEGRATION SITES OF INTERSPERSED REPEATS BETWEEN CLOSELY RELATED GENOMES. NUCLEIC ACIDS RES., 30(14):E71.
BUZDIN, A., REVINA, L., KOSTINA, L., ZALUNIN, I., CHESTUKHINA, G. (2002) INTERACTION OF 65- AND 62-KD PROTEINS FROM THE APICAL MEMBRANES OF THE AEDES AEGYPTI LARVAE MIDGUT EPITHELIUM WITH CRY4B AND CRY11A ENDOTOXINS OF BACILLUS THURINGIENSIS. BIOCHEMISTRY (MOSCOW), 67(5):540-546.
BUZDIN, A., KHODOSEVICH, K., MAMEDOV, I., VINOGRADOVA, T., LEBEDEV, Y., HUNSMANN, G., SVERDLOV, E. (2002) A TECHNIQUE FOR GENOME-WIDE IDENTIFICATION OF DIFFERENCES IN THE INTERSPERSED REPEATS INTEGRATIONS BETWEEN CLOSELY RELATED GENOMES AND ITS APPLICATION TO DETECTION OF HUMAN-SPECIFIC INTEGRATIONS OF HERV-K LTRS. GENOMICS, 79(3):413-422.
KRIEGER, I., REVINA, L., KOSTINA, L., BUZDIN, A., ZALUNIN, I., CHESTUKHINA, G., STEPANOV, V. (1999) MEMBRANE PROTEINS OF AEDES AEGYPTI LARVAE BIND TOXINS CRY4B AND CRY11A OF BACILLUS THURINGIENSIS SSP. ISRAELENSIS. BIOCHEMISTRY (MOSCOW), 64(10):1163-1168.
FREQUENT ALLELIC LOSSES IN TUMOR-ASSOCIATED STROMAL CELLS AND TUMOR EPITELIUM OF PROSTATE CANCER. KEKEEVA TV, POPOVA OP, SHEGAĬ PV, ZAVALISHINA LE, ANDREEVA IUIU, ZALETAEV DV, NEMTSOVA MV. MOL BIOL (MOSK). 2008 JAN-FEB;42(1):96-101.
ABBERANT METHYLATION OF P16, HIC1, N33 AND GSTP1 GENES IN TUMOR EPITELIUM AND TUMOR-ASSOCIATED STROMAL CELLS OF PROSTATE CANCER. KEKEEVA TV, POPOVA OP, SHEGAĬ PV, ALEKSEEV BIA, ADNREEVA IUIU, ZALETAEV DV, NEMTSOVA MV. MOL BIOL (MOSK). 2007 JAN-FEB;41(1):79-85.
KUZMINA N.B., BORISOV N.M. HANDLING COMPLEX RULE-BASED MODELS OF MITOGENIC CELL SIGNALING (ON THE EXAMPLE OF ERK ACTIVATION UPON EGF STIMULATION. INTERNATIONAL PROCEEDINGS OF CHEMICAL, BIOLOGICAL AND ENVIROMENTAL ENGINEERING, 2011, V. 5, P. 76-82.
BORISOV N., AKSAMITIENE A., KIYATKIN A., LEGEWIE S., BERKHOUT J., MAIWALD TH., KAIMACHNIKOV N., TIMMER J., HOEK J., KHOLODENKO B. SYSTEMS-LEVEL INTERACTIONS BETWEEN INSULIN – EPIDERMAL GROWTH FACTOR NETWORKS AMPLIFY MITOGENIC SIGNALING. MOLECULAR SYSTEMS BIOLOGY, 2009, V.5, ARTICLE 256.
BORISOV N.M., CHISTOPOLSKY A.S., FAEDER J.R. AND KHOLODENKO B.N. DOMAIN-ORIENTED REDUCTION OF RULE-BASED NETWORK MODELS. IET SYSTEMS BIOLOGY, 2008, V. 2, P. 342-351.
KIYATKIN A., AKSAMITIENE E., MARKEVICH N.I., BORISOV N.M., HOEK J.B., KHOLODENKO B.N. SCAFFOLDING PROTEIN GAB1 SUSTAINS EPIDERMAL GROWTH FACTOR-INDUCED MITOGENIC AND SURVIVAL SIGNALING BY MULTIPLE POSITIVE FEEDBACK LOOPS. JOURNAL OF BIOLOGICAL CHEMISTRY, 2006, V. 281, P.19925-19938.
BORISOV N.M., MARKEVICH N.I., HOEK J.B., KHOLODENKO B.N. TRADING THE MICRO-WORLD OF COMBINATORIAL COMPLEXITY FOR THE MACRO-WORLD OF PROTEIN INTERACTION DOMAINS. BIOSYSTEMS, 2006, V. 83, P. 152-166.
BORISOV N.M., MARKEVICH N.I., HOEK J.B., KHOLODENKO B.N. SIGNALLING THROUGH RECEPTORS AND SCAFFOLDS: INDEPENDENT INTERACTIONS REDUCE COMBINATORIAL COMPLEXITY. BIOPHYSICAL JOURNAL, 2005, V. 89, P. 951-966.
JONES RB, SONG H, XU Y, GARRISON KE, BUZDIN AA, ANWAR N, HUNTER DV, MUJIB S, MIHAJLOVIC V, MARTIN E, LEE E, KUCIAK M, RAPOSO RA, BOZORGZAD A, MEIKLEJOHN DA, NDHLOVU LC, NIXON DF, OSTROWSKI MA. LINE-1 RETROTRANSPOSABLE ELEMENT DNA ACCUMULATES IN HIV-1-INFECTED CELLS. J VIROL. 2013 DEC;87(24):13307-20. DOI: 10.1128/JVI.02257-13.
BRAIN-COMPUTER INTERFACE BASED ON GENERATION OF VISUAL IMAGES, BOBROV P, FROLOV A, CANTOR C, FEDULOVA I, BAKHNYAN M, ZHAVORONKOV A. PLOS ONE. 2011;6(6):E20674. EPUB 2011 JUN 10.
ZHAVORONKOV A, CANTOR CR., METHODS FOR STRUCTURING SCIENTIFIC KNOWLEDGE FROM MANY AREAS RELATED TO AGING RESEARCH. PLOS ONE. 2011;6(7):E22597. EPUB 2011 JUL 22.
MOSKALEV AA, SMIT-MCBRIDE Z, SHAPOSHNIKOV MV, PLYUSNINA EN, ZHAVORONKOV A, BUDOVSKY A, TACUTU R, FRAIFELD VE. GADD45 PROTEINS: RELEVANCE TO AGING, LONGEVITY AND AGE-RELATED PATHOLOGIES. AGEING RES REV. 2012 JAN;11(1):51-66. EPUB 2011 OCT 5
MOSKALEV AA, SHAPOSHNIKOV MV, PLYUSNINA EN, ZHAVORONKOV A, BUDOVSKY A, YANAI H, FRAIFELD VE.THE ROLE OF DNA DAMAGE AND REPAIR IN AGING THROUGH THE PRISM OF KOCH-LIKE CRITERIA. AGEING RES REV. 2012 FEB 14.
ZABOLOTNEVA AA, ZHAVORONKOV A, GARAZHA AV, ROUMIANTSEV SA, BUZDIN AA. CHARACTERISTIC PATTERNS OF MICRORNA EXPRESSION IN HUMAN BLADDER CANCER. . FRONT GENET. 2013 JAN 4;3:310. DOI: 10.3389/FGENE.2012.00310.
BASKAEV KK, KHOLODENKO RV, MALAKHOVA GV, GAĬFULLIN NM, KORZENEVA EA, SUNTSOVA MV, BUZDIN AA. EXPERIMENTAL ANALYSIS OF HUMAN SPECIFIC PROTEIN CODING OPEN READING FRAME C11ORF72. BIOORG KHIM. 2013 MAR-APR;39(2):151-8.
NEPOMNYASHCHAYA YN, ARTEMOV AV, ROUMIANTSEV SA, ROUMYANTSEV AG, ZHAVORONKOV A. NON-INVASIVE PRENATAL DIAGNOSTICS OF ANEUPLOIDY USING NEXT-GENERATION DNA SEQUENCING TECHNOLOGIES, AND CLINICAL CONSIDERATIONS. CLIN CHEM LAB MED. 2012 SEP 29;0(0):1-14.
ZHAVORONKOV A, SMIT-MCBRIDE Z, GUINAN KJ, LITOVCHENKO M, MOSKALEV A. POTENTIAL THERAPEUTIC APPROACHES FOR MODULATING EXPRESSION AND ACCUMULATION OF DEFECTIVE LAMIN A IN LAMINOPATHIES AND AGE-RELATED DISEASES. J MOL MED (BERL). 2012 OCT 23.
MOSKALEV A, PLYUSNINA E, SHAPOSHNIKOV M, SHILOVA L, KAZACHENOK A, ZHAVORONKOV A. THE ROLE OF D-GADD45 IN OXIDATIVE, THERMAL AND GENOTOXIC STRESS RESISTANCE. CELL CYCLE. 2012 OCT 24;11(22).
ZABOLOTNEVA AA, ZHAVORONKOV AA, SHEGAY PV, GAIFULLIN NM, ALEKSEEV BY, ROUMIANTSEV SA, GARAZHA AV, KOVALCHUK O, ARAVIN A, BUZDIN AA. A SYSTEMATIC EXPERIMENTAL EVALUATION OF MICRORNA MARKERS OF HUMAN BLADDER CANCER. FRONT GENET. 2013 NOV 15;4:247. DOI: 10.3389/FGENE.2013.00247
BOOKS AND CHAPTERS:
RECENT INSERTS OF TRANSPOSABLE ELEMENTS AFFECT STRUCTURE AND FUNCTIONS OF HUMAN GENOME. ANTON BUZDIN, MARIA SUNTSOVA, OLGA BANTYSH, ELENA ALEKSANDROVA, ANASTASIA ZABOLOTNEVA, ELENA GOGVADZE, AND NURSHAT GAIFULLIN (2012) CHAPTER NO. 23 IN “RADIOBIOLOGY AND ENVIRONMENTAL SECURITY”, EDS. C.E. MOTHERSILL, V. KOROGODINA AND C.B. SEYMOUR. SPRINGER, ISBN 978-94- 007-1999-6 (PB) P: 269-297.
D.A. GHILAROV, A.А. BUZDIN. ENDOGENOUS RETROVIRAL SEQUENCES CONTROL THE TRANSCRIPTION OF MANY HOST GENES IN EUKARYOTES (2009). CHAPTER IN “VIRAL GENOMES: DIVERSITY, PROPERTIES AND PARAMETERS” NOVA SCIENCE PUBLISHERS (USA) PAGES: 35-63. ISBN: 978-1-60741-067-6.
MONOGRAPH “NUCLEIC ACIDS HYBRIDIZATION: MODERN APPLICATIONS”. EDS. : ANTON BUZDIN, SERGEY LUKYANOV; SPRINGER (2007) ISBN 978-1-4020-6039-7.
NUCLEIC ACIDS HYBRIDIZATION: POTENTIALS AND LIMITATIONS (ANTON BUZDIN)
CHAPTER IN “NUCLEIC ACIDS HYBRIDIZATION: MODERN APPLICATIONS”. EDS.: ANTON BUZDIN, SERGEY LUKYANOV, SPRINGER (2007) ISBN 978-1-4020-6039-7.
SELECTIVE SUPPRESSION OF POLYMERASE CHAIN REACTION AND ITS MOST POPULAR APPLICATIONS (SERGEY LUKYANOV, KONSTANTIN LUKYANOV, NADEZHDA GURSKAYA, EKATERINA BOGDANOVA, ANTON BUZDIN).
SUPPRESSION SUBTRACTIVE HYBRIDIZATION (SERGEY LUKYANOV, DENIS REBRIKOV, ANTON BUZDIN).
STEM-LOOP OLIGONUCLEOTIDES AS HYBRIDIZATION PROBES AND THEIR PRACTICAL USE IN MOLECULAR BIOLOGY AND BIOMEDICINE (ANTON BUZDIN, SERGEY LUKYANOV).
COINCIDENCE CLONING: ROBUST TECHNIQUE FOR ISOLATION OF COMMON SEQUENCES (ANTON BUZDIN).
DNA HYBRIDIZATION IN SOLUTION FOR MUTATION DETECTION (ANTON BUZDIN).
CURRENT ATTEMPTS TO IMPROVE THE SPECIFICITY OF NUCLEIC ACIDS HYBRIDIZATION (ANTON BUZDIN).
Our investors are:
Deep Knowledge Ventures, Hong Kong
Deep Knowledge Ventures is a Hong Kong-based venture fund management company focusing on mid- to long-term biotechnology investments at both seed and venture stage.
Pathway Pharmaceuticals, Hong Kong
Pathway Pharmaceuticals is a Hong Kong-based research company focusing on personalized medicine, oncology and age-related diseases.
We prefer candidates from the BWI area with the ability to work full-time in Baltimore.
From the schemes below you can investigate resources of In Silico drug discovery.
Below you can see the scheme of Drug Discovery Complex and all of its databases interactions.
We offer three possible ways of cooperation for pharma and research companies.
Model 1: Pharma Company provides patient’s clinical datasets to In Silico Medicine, which investigates these datasets through unique Cloud intelligence algorithm and forms ranked list of relevant drugs for current clinical case.
Model 2: Pharma Company provides In Silico Medicine uncategorized drug list. List is being examined through Cloud Intelligence Service and the most efficient drugs are given as a result to Pharma company.
Model 3: Pharma Company provides In Silico Medicine inquiry for perspective compounds, all peculiarities of each compound are being analyzed through Cloud Intelligence Service. The investigation of given compounds results in list of the most efficient variants of compounds combinations.
Our mission statement and our pledge to our investors, friends and families:
Through excellence in knowledge management, machine learning and bioinformatics, relentless pursuit for new drug, omics and clinical outcomes data, development of reliable in silico drug screening methods, novel validation approaches and strong international partnerships in personalized medicine we strive to find real working solutions to cure and prevent age-related diseases and aging itself.
This mission will be achieved within within the regulatory frameworks as well as the legal and ethical boundaries and by working with the outstanding scientists, academic and medical institutions and pharmaceutical companies of impeccable credibility.
Our goals are:
Some of our near-term milestones are:
Since 2008 the In Silico Medicine research team worked hard to develop a comprehensive database of tissue-specific gene expression profiles from a large number of healthy patients, who lost their lives in accidents. This database was thoroughly analyzed, categorized and annotated. In parallel, we constructed multiple databases of gene expression from the many cancer biopsies, before and after treatment.
We developed tools to map gene expression data onto signaling signaling pathways and developed algorithms for evaluating the individual pathway activation strengths and to analyze and measure the state of the overall signaling pathway cloud.
We then developed an annotated database of just over 150 targeted compounds acting on various molecular targets and network elements. We developed another set of algorithms to evaluate the activity of these drugs on the signaling pathway cloud to predict the effectiveness of these drugs on each patient’s tumor. This research laid the foundation for the development of the OncoFinder (OncoFinder.com), which was purchased by and is now the flagship product of the Hong Kong-based, Pathway Pharmaceuticals, the main research and business partner of In Silico Medicine. The OncoFinder was validated internally with over 220 patients with excellent and yet unpublished results and led to further improvements in the algorithms. The tool is now used to provide medical doctors with a research tool, which may improve their clinical decision making.
The concept of a signaling pathway cloud analysis for aging research. Source: “Signaling pathway cloud regulation for in silico screening and ranking of the potential geroprotective drugs”, Alex Zhavoronkov, Anton Buzdin, Andrey Garazha, Nikolay Borisov, Alexey Moskalev, Frontiers in Genetics, Accepted, In print
In Silico Medicine took the concept of OncoFinder further, but instead of the normal and cancer cells, we evaluate the effects of various drugs on the pathway cloud constructed from gene expression and epigenetic data from cells taken from the old patients with those taken from the young patients with the intent to bring the state of the “old cells” as close to the signaling pathway cloud activation profile of the young cells.
Our original modus operandi was illustrated in the recent perspective publication in the reputable open access journal, Frontiers in Genetics.
Many high net-worth individuals with excellent management skills donate billions of dollars to research via foundations and fellowships, without being directly involved with the research projects. These foundations are typically set up to address a broad cause and usually do not have a core goal-oriented project.
A team of experts is hired to supervise research activities and provide grants to scientists who are usually already funded by the government, academia or industry. Some high net-worth individuals besides donating to basic research would also like to solve personal medical problems and steer some of the research effort. These individuals often have excellent project management and organizational skills, but lack the scientific background and confidence to start their own research projects. In contrast, many young scientists and medical doctors would like to apply their skills to conduct cutting edge research and work with patients, but thus lack management expertise. Personalized science projects could bridge this gap and link patients with management expertise with teams of scientists and physicians who are interested in pursuing goal-oriented science, the patient provides research grants, samples and management expertise. The team of physicians and research scientists executes research projects that address the patient’s future needs and research interests.
To test this personalized science concept, we organized a group of young scientists and physicians with over five hundred active members and conducted a series of thirty weekly lectures on regenerative medicine. In parallel we used social media to create multidisciplinary teams of biophysicists, biologists, geneticists and physicians to work on twenty five research projects with topics spanning from metastatic mineralization of the connective tissue to bioinformatics approaches to personalized medicine in oncology. Using this pool of scientists and physicians it became possible to launch research-personalized science projects to address both patient research interests and needs. Whenever a high net-worth individual with medical problems or would like to prevent possible future medical problems becomes interested in pursuing a research project, the project is announced to the community to form a core team that is funded and co-managed by that individual. These small, goal-oriented teams dedicated to solving specific patient problems may be more effective than large foundations or industries.
Patients provide grant funding to a research organization. The organization provides funding and research infrastructure to young researchers. The research team then interacts with the patient and leading experts in the field to provide care.
When it comes to testing the effects of a drug on patients with diagnosed pathologies clinical outcomes are among many measurable factors and incremental increases in the size of the the study group lead to higher confidence in the results. But how do we test the effectiveness of a treatment on patients when the only pathologic process they have is aging and it is not classified as the disease?
There are many ways to approach this problem and the concept of personalized science, when the team of experts works with a single patient to find optimal individual geroprotector regiments for the benefit of the patient and mankind as the whole.
The first phase of the project may include using the patient’s own cells to validate the individual predicted efficacy and toxisity of the various drugs. These may be as simple as a vitamin or aspirin and statins to new chemical substances. No recommendations should be made to the patient. In the case that the patient’s doctor makes a decision to prescribe some of these drugs, it may be possible to analyze a very large number of changes in the bodily fluids, gene expression and epigenetic data in various tissues, physical condition and even locomotive activity to evaluate the dynamic effects of the drug. Even though the regular tests on a single patient may be expensive, even one patient may help validate the effectiveness of a geroprotector. With time and more patients this model may lead to significant advances in aging research for drug discovery.
Personalized longevity science: personalized biomarker tracking, drug and therapy selection and drug discovery.