Ram Samudrala
Education |
Awards and honours |
Major research resources developed |
Publications |
Presentations |
Professional activities |
Experience |
Contact and personal information
- Professor and Chief, Division of Bioinformatics, University at Buffalo. October 2014-.
- Multiscale modelling of complex atomic, molecular, cellular,
and physiological systems with applications in medicine and
engineering.
- Modelling interactome structure, function, interaction, evolution and design.
- Computational Analysis of Novel Drug Opportunities (CANDO).
- Associate Professor, University of Washington, Seattle. July 2006-September 2014. (Assistant Professor, January 2001-June 2006.)
- Modelling structure, function, expression, interaction, and
evolution of proteins, RNA, DNA, and small molecules.
- Postdoctoral Fellow, Stanford University. September 1997-December 2000.
- Computational biology: Protein folding, structure, function, and evolution; structural and functional genomics.
- Mentor: Michael Levitt
- Ph.D., University of Maryland, College Park. June 1993-August 1997.
- Computational biology: Protein folding and structure prediction using computational approaches.
- Mentor: John Moult.
- B.A., Ohio Wesleyan University. January 1990-May 1993.
- Majors: Computing Science and Genetics.
- Minors: Mathematics and Biology.
- Distinguished Achievement Citation, Ohio Wesleyan University Alumni Association. 2023.
- NCATS ASPIRE Reduction-to-Practice Award. 2022.
- Wiki Science Competition International Prize Winner. 2021.
- Wiki Science Competition National Finalist. 2019.
- NCATS ASPIRE Design Challenge Award. 2019.
- University at Buffalo Exceptional Scholar. 2018-2019.
- Top 200 Applicant, MacArthur Foundation 100&Change Competition. 2016. [One standard deviation better than the median score of the top 200 applicants.]
- NIH Director's Pioneer Award. 2010.
- Best Undergraduate Research Mentor Award, University of Washington. 2010.
- Honorary diplomas from the cities of Casma and Yautan, Peru; as well as an official Decree of Thanks from the Peruvian Minister of Health for research on vaccine discovery. 2008.
- Alberta Heritage Foundation for Medical Research Visiting Scientist Award. 2008.
- NIH Director's Pioneer Award finalist. 2006. [25/465 applicants selected as finalists.] <--- http://compbio.org/presentations/aug092006.ppt -->
- NSF CAREER Award. 2005-2010.
- University of Washington New Investigator Science in Medicine Lecture. 2005. <--- http://compbio.org/presentations/feb172005.ppt -->
- MIT Technology Review TR100. 2003. [Outstanding innovators under 35.]
- Searle Scholar. 2002-2005.
- Washington State Advanced Technology Initiative Faculty. 2001.
- NSF Program in Mathematics and Molecular Biology/Burroughs Wellcome Fund Fellow. 1997-2001.
- University of Maryland Life Technologies Graduate Fellow. 1993-1997.
- Zain-ul-Abedin Memorial Scholarship for Outstanding Graduate Studies in Molecular and Cell Biology. 1993.
- Howard Hughes Internship Award. 1992.
- Dean's List. 1990-1993.
- Wesleyan Scholar and Honours Student at Ohio Wesleyan. 1990-1993.
- Computational analysis of novel drug opportunities (CANDO) platform
<protinfo.org/cando>:
The CANDO multiscale therapeutic discovery, repurposing, and design
platform aims to discover drugs faster and cheaper that are safer
and better, compared to traditional approaches. The platform
contains pipelines that screen every drug/compound against every
indication by using a variety of AI/machine learning and preditive
analytics approaches. The top putative drug candidates are
rigourously benchmarked and verified in the laboratory and clinic by
our collaborators. The project, funded by a 2010 NIH Director's
Pioneer and NCATS
ASPIRE Awards, is an application of our group's basic science
research in protein and proteome structure, function, and
interaction prediction to therapeutic discovery.
- Protinfo structure, function, and interaction prediction web server modules
<protinfo.org>:
The web server consists of modules to predict the protein structure
of individual molecules and complexes (ABCM, PPC), integrate limited
or noisy experimental data with our structure prediction algorithms
(PsiCSI, NMR), score protein structure decoys (SCORE), assign
proteins to particular functional categories and predict
functionally important residues (MFS, FSSA); predict protein ion
binding sites, types, affinities, and specificities from structure
(SOAK); and predict HIV-1 drug resistance/susceptibility (PIRSPred).
Currently structure, function, and interaction predictions for up to
100 molecules/day are performed.
- The Bioverse framework
<bioverse.org>:
The Bioverse provides a framework for exploring the relationships
among the molecular, genomic, proteomic, systems, and organismal
worlds. Our goal is to perform sophisticated analyses and
predictions based on genomic sequence data to annotate and
understand the interaction of protein sequence, structure, and
function, both at the single molecule as well as at the systems
levels. The Bioverse currently consists of more than 50 organismal
proteomes and is used by several hundred visitors accessing more
than 1,000 molecules/day. The current Bioverse 2D is being expanded
into Bioverse 3D and CANDO.
- ``Nutritious Rice for the World'' project
<protinfo.org/rice>:
This project was developed in collaboration with IBM to predict the
structures, functions, and interactions of the rice interactome. More
over 200 media outlets have provided coverage on this project.
Publications
158 total publications (145 scientific + 8 general + 5 patent)
Scientific publications
145 publications listed, a few accepted/in press; many more submitted; * denotes more significant
- Kumari R, Sharma SD, Kumar A, Ende Z, Mishina M, Wang Y, Falls
Z, Samudrala R, Pohl J, Knight PR, Sambhara S. Antiviral
approaches against influenza virus. Clinical Microbiology
Reviews e0004022, 2023. in press
- Bruggemann L, Falls Z, Mangione W, Schwartz SA, Battaglia S,
Aalinkeel R, Mahajan SD, Samudrala R. Multiscale analysis and
validation of effective drug combinations targeting driver KRAS
mutations in non-small cell lung cancer. International
Journal of Molecular Sciences 24: 997, 2023. *
- Mangione W, Falls Z, Samudrala R. Optimal COVID-19 therapeutic
candidate discovery using the CANDO platform. Frontiers in
Pharmacology 13: 970494, 2022. *
- Moukheiber L, Mangione W, Moukheiber M, Maleki S, Falls Z, Gao
M, Samudrala R. Identifying protein features
and pathways responsible for toxicity using machine learning and
tox21: Implications for predictive
toxicology. Molecules 27: 3021, 2022.
- Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu
J, Broderick G, Sethi S, Samudrala R. Proteomic network analysis
of bronchoalveolar lavage fluid in ex-smokers to discover implicated
protein targets and novel drug treatments for chronic obstructive
pulmonary disease. Pharmaceuticals 15: 566, 2022. *
- Falls Z, Fine J, Chopra G, Samudrala R. Accurate prediction of
inhibitor binding to HIV-1 protease using
CANDOCK. Frontiers in Chemistry 9: 775513, 2022.
- Schuler J, Falls Z, Mangione W, Hudson M, Bruggemann L,
Samudrala R. Evaluating performance of
drug repurposing technologies. Drug Discovery Today
27: 49-64, 2022. *
- Overhoff B, Falls Z, Mangione W, Samudrala R. A deep-learning
proteomic-scale approach for drug design. Pharmaceuticals
(Basel) 14: 1277, 2021. *
- Dey-Rao R, Smith GR, Timilsina U, Falls Z, Samudrala R,
Stavrou S, Melendy T. A
fluorescence-based, gain-of-signal, live cell system to evaluate
SARS-CoV-2 main protease inhibition. Antiviral
Research 195: 105183, 2021.
- Palanikumar L, Karpauskaite L, Al-Sayegh M, Chehade I, Alam M,
Hassan S, Maity D, Ali L, Kalmouni M, Hunashal Y, Ahmed J, Houhou T,
Karapetyan S, Falls Z, Samudrala R, Pasricha R, Esposito G,
Afzal AJ, Hamilton AD, Kumar S, Magzoub M. Protein mimetic amyloid
inhibitor potently abrogates cancer-associated mutant p53
aggregation and restores tumor suppressor function. Nature
Communications 12: 3962, 2021.
- Hudson ML, Samudrala R. Multiscale virtual screening
optimization for shotgun drug repurposing using the CANDO
platform. Molecules 26: 2581-2597, 2021.
- Chatrikhi R, Feeney CF, Pulvino MJ, Alachouzos G, MacRae AJ,
Falls Z, Rai S, Brennessel WW, Jenkins JL, Walter MJ, Graubert TA,
Samudrala R, Jurica MS, Frontier AJ, Kielkopf CL. A
synthetic small molecule stalls pre-mRNA splicing by promoting an
early-stage U2AF2-RNA complex. Cell Chemical Biology
28: 1145-1157, 2021.
- Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf
NM, Samudrala R, Mehboob S, Dementiev A, Abad-Zapatero C,
Movahedzadeh F. Rv0100, a proposed acyl carrier protein in
Mycobacterium tuberculosis: expression, purification and
crystallization. Corrigendum. Acta Crystallograpica F
Structural Biology Communications 76: 192-193, 2020.
- Mandloi S, Falls Z, Deng R, Samudrala R, Elkin
PL. Association of C>U RNA editing with human disease
variants. Student Health Technology Informatics 270:
1205-1206, 2020.
- Bruggemann L, Hawthorne C, Samudrala R, Lopez-Campos
GH. Linking genome and exposome: Computational analysis of human
variation in chemical-target interactions. Student Health
Technology Informatics 270: 1331-1332, 2020.
- Mangione W, Falls Z, Chopra G, Samudrala R. cando.py: Open source
software for predictive bioanalytics of large scale
drug-protein-disease data. Journal of Chemical Information
and Modeling 60: 4131-4136, 2020. *
- Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R.
Shotgun drug repurposing
biotechnology to tackle epidemics and pandemics. Drug
Discovery Today 25: 1126-1128, 2020. *
- Fine J, Konc J, Samudrala R, Chopra G. CANDOCK: Chemical atomic
network-based hierarchical flexible docking algorithm using
generalized statistical potentials. Journal of Chemical
Information and Modeling 60: 1509-1527, 2020. *
- Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf
NM, Samudrala R, Mehboob S, Movahedzadeh F. Rv0100, a
proposed acyl carrier protein in Mycobacterium tuberculosis:
expression, purification and crystallization. Acta
Crystallograpica F Structural Biology Communications 75:
646-651, 2019.
- Fine J, Lackner R, Samudrala R, Chopra G. Computational
chemoproteomics to understand the role of selected psychoactives in
treating mental health indications. Scientific
Reports 9, 1315, 2019. *
- Schuler J, Samudrala R. Fingerprinting CANDO:
Increased accuracy with structure and ligand based shotgun drug
repurposing. ACS Omega 4: 17393-17403, 2019. *
- Schuler J, Mangione W, Samudrala R, Ceusters W. Foundations for a
realism-based drug repurposing ontology. Proceedings of the 10th
International Conference on Biomedical Ontology, 2019.
- Falls Z, Mangione W, Schuler J, Samudrala R. Exploration
of interaction scoring criteria in the CANDO platform. BMC
Research Notes 12: 318, 2019. *
- Mangione W, Samudrala R. Identifying protein features
responsible for improved drug repurposing accuracies using the CANDO
platform: Implications for drug design. Molecules 24: 167,
2019. *
- Schuler J, Hudson M, Schwartz D, Samudrala R. A systematic review of
computational drug discovery, development, and repurposing for Ebola
Virus Disease Treatment. Molecules 22: E1777, 2017.
- Hung L-H, Samudrala R. Rice protein models from the
Nutritious Rice for the World Project. bioRxiv 091975; doi:
https://doi.org/10.1101/091975,
2016.
- Chopra C, Kaushik S, Elkin PL, Samudrala R. Combating
Ebola with repurposed therapeutics using the CANDO
platform. Molecules 21: 1537, 2016. *
- Craig JK, Risler JK, Loesch KA, Dong W, Baker D, Barrett LK,
Subramanian S, Samudrala R, Van Voorhis WC. Mycobacterium
cytidylate kinase appears to be an undruggable target. Journal
of Biomolecular Design 21: 695-700, 2016.
- Chopra G, Samudrala R. Exploring polypharmacology in
drug discovery and repurposing using the CANDO
platform. Current Pharmaceutical Design 22: 3109-3123
2016.
- Manocheewa S, Mittler JE, Samudrala R, Mullins
JI. Composite sequence-structure stability models as screening tools
for identifying vulnerable targets for HIV drug and vaccine
development. Viruses 7: 5718-5735, 2015.
- Sethi G, Chopra G, Samudrala R. Multiscale modelling of
relationships between protein classes and drug behavior across all
diseases using the CANDO platform. Mini Reviews in
Medicinal Chemistry 15: 705-717, 2015.
- Matasci N, Hung L-H, ..., Samudrala R, Tian Z, Wu X, Sun
X, Zhang Y, Wang J, Leebens-Mack J, Wong GSK. Data access for the
1,000 Plants (1KP) project. Gigascience 3: 17, 2014.
- Minie M, Chopra G, Sethi G, Horst JA, White G, Roy A, Hatti K,
Samudrala R. CANDO
and the infinite drug discovery frontier. Drug Discovery
Today 19: 1353-1363, 2014. *
- Hung L-H, Samudrala R. fast_protein_cluster: parallel and
optimized clustering of large scale protein modeling
data. Bioinformatics 30: 1774-1776, 2014.
- Minie M. Samudrala R. The promise and challenge of
digital biology. Journal of Bioengineering and Biomedical
Sciences 3: e118, 2013. editorial.
- Lertkiatmongkol P, Assawamakin A, White G, Chopra G,
Rongnoparut P, Samudrala R, Tongsima S. Distal effect of
amino acid substitutions in CYP2C9 polymorphic variants causes
differences in interatomic interactions against
(S)-warfarin. PLoS One 8: e74053, 2013.
- Laurenzi A, Hung L-H, Samudrala R. Structure prediction of
partial length protein sequences: applications in foldability
prediction and EST annotation. International Journal of
Molecular Sciences 214: 14892-14907, 2013.
- Homo-dimerization and ligand binding by the leucine-rich repeat
domain at RHG1/RFS2 underlying resistance to two soybean pathogens.
Afzal AJ, Srour A, Goil A, Vasudaven S, Liu T, Samudrala R,
Dogra N, Kohli P, Malakar A, Lightfoot DA. BMC Plant
Biology 13: 43, 2013.
- Self-assembly of filamentous amelogenin requires calcium and
phosphate: from dimers via nanoribbons to fibrils. Martinez-Avila
O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst
JA, Habelitz S. Biomacromolecules 13: 3494-502, 2012.
- Strategic protein target analysis for developing drugs to stop
dental caries. Horst JA, Pieper U, Sali A, Zhan L, Chopra G,
Samudrala R, Featherstone JD. Advances in Dental
Research 24: 86-93, 2012. *
- Cementomimetics-constructing a cementum-like biomineralized
microlayer via amelogenin-derived peptides. Gungormus M, Oren EE,
Horst JA, Fong H, Hnilova M, Somerman MJ, Snead ML, Samudrala
R, Tamerler C, Sarikaya M. International Journal of Oral
Sciences 2: 69-77, 2012. *
- Goldman AD, Barrows J, Samudrala R. The enzymatic and metabolic
capabilities of early life. PLoS One 7: e39912,
2012. *
- Hung L-H, Samudrala R. Accelerated protein structure
comparison using TM-score-GPU. Bioinformatics 28:
2191-2192, 2012.
- Goldman AD, Horst JA, Hung L-H, Samudrala R. Evolution
of the protein repertoire. Systems Biology: 207-237,
2012. (R Meyers, Editor. Wiley-VCH Wienheim, Germany.)
- Horst JA, Laurenzi A, Bernard B, Samudrala R. Computational multitarget
drug discovery. Polypharmacology 263-301, 2012. *
- An P, Li R, Wang JM, Yoshimura T, Takahashi M, Samudrala
R, O'Brien SJ, Phair J, Goedert JJ, Kirk GD, Troyer JL, Sezgin
E, Buchbinder SP, Donfield S, Nelson GW, Winkler CA. Role of exonic
variation in chemokine receptor genes on AIDS: CCRL2 F167Y
association with pneumocystis pneumonia. PLoS Genetics
7: e1002328, 2011.
- Moughon S, Samudrala R. LoCo: a new backbone-only
scoring function for protein structure prediction. BMC
Bioinformatics 12: 368, 2011.
- Hung LH, Guerquin M, Samudrala R. GPU-Q-J, a fast method
for calculating root mean square deviation (RMSD) after optimal
superposition. BMC Research Notes 4: 97, 2011.
- Horst OV, Horst JA, Samudrala R, Dale BA. Caries
induced cytokine network in the odontoblast layer of human teeth.
BMC Immunology 12: 9, 2011.
- Cunningham ML, Horst JA, Rieder MJ, Hing AV, Stanaway IB, Park
SS, Samudrala R, Speltz ML. IGF1R variants associated with
isolated single suture craniosynostosis. The American Journal
of Human Genetics 155A: 91-97, 2011. [Accompanying cover.]
- McDermott JE, Corrigan A, Peterson E, Oehmen C,
Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R,
Heffron F. Computational prediction of type III and IV secreted
effectors in Gram-negative bacteria. Infection and
Immunity 79: 23-32, 2011.
- Nicholson CO, Costin JM, Rowe DK, Lin L, Jenwitheesuk E,
Samudrala R, Isern S, Michael SF. Viral entry inhibitors block
dengue antibody-dependent enhancement in
vitro. Antiviral Research 89: 71-74, 2010. *
- Wang J, Zhang J, Li R, Zheng H, Li J, Zhang Y, Li H, Ni P, Li
S, Li S, Wang J, Liu D, McDermott JE, Samudrala R, Liu S, Wang
J, Yang H, Yu J, Wong GK. Evolutionary transients in the rice
transcriptome. Genomics Proteomics Bioinformatics 8:
211-228, 2010.
- Notman R, Oren EE, Tamerler C, Sarikaya M, Samudrala R,
Walsh TR. Solution study of engineered quartz binding
peptides using replica exchange molecular dynamics.
Biomacromolecules 11: 3266-3274, 2010.
- Movahedzadeh F, Balasubramanian V, Bernard B,
Iyer S, Samudrala R, Franzblau SG, Balganesh TS.
Anti-tuberculosis agents: A rational approach for discovery and
development. Genomic and computational tools for emerging
infectious diseases, 2010.
- Horst JA, Wang K, Horst OV, Cunningham ML, Samudrala
R. Disease risk of
missense mutations using structural inference from predicted
function. Current Protein & Peptide Science 11:
573-588, 2010. *
- Horst JA, Samudrala R. A protein sequence meta-functional
signature for calcium binding residue prediction. Pattern
Recognition Letters 31: 2103-2112, 2010. *
- Costin JM, Jenwitheesuk E, Lok S-M, Hunsperger E, Conrads KA,
Fontaine KA, Rees CR, Rossmann MG, Isern S, Samudrala R,
Michael SF. Structural optimization and de novo design of
dengue virus entry inhibitory peptides. PLoS Neglected Tropical
Diseases 4: e721, 2010. *
- Oren EE, Notman R, Kim IW, Evans J, Walsh T, Samudrala
R, Tamerler C, Sarikaya M. Probing the molecular mechanisms of
quartz-binding peptides. Langmuir 26: 11003-11009,
2010.
- Borlee BR, Goldman AD, Murakami K, Samudrala R, Wozniak
DJ, Parsek MR. Pseudomonas aeruginosa uses
a cyclic-di-GMP-regulated adhesin to reinforce the biofilm
extracellular matrix. Molecular Microbiology 75:
827-842, 2010. [Accompanying cover.]
- Goldman AD, Samudrala R, Barrows J. The evolution and
functional repertoire of translation proteins following the origin of
life. Biology Direct 5: 15, 2010. *
- Horst JA, Samudrala R. Diversity of protein structures
and difficulties in fold recognition: The curious case of Protein
G. F1000 Biology Reports 1: 69, 2009. *
- Goldman AD, Leigh JA, Samudrala R. Comprehensive computational
analysis of Hmd enzymes and paralogs in methanogenic
Archaea. BMC Evolutionary Biology 9: 199, 2009.
- Liu T, Horst JA, Samudrala R. A novel method for
predicting and using distance constraints of high accuracy for
refining protein structure prediction. Proteins: Structure,
Function, and Bioinformatics 77: 220-234, 2009. *
- Kittichotirat W, Guerquin M, Bumgarner RE, Samudrala R.
Protinfo PPC: A web
server for atomic level prediction of protein complexes.
Nucleic Acids Research 37: W519-W525, 2009. *
- Samudrala R, Heffron F, McDermott JE. Accurate prediction of
secreted substrates and identification of a conserved putative
secretion signal for type III secretion systems. PLoS
Pathogens 5: e1000375, 2009. *
- Bernard B, Samudrala R. A
generalized knowledge-based discriminatory function for biomolecular
interactions. Proteins: Structure, Function, and
Bioinformatics 76: 115-128, 2009. *
- McDermott JE, Ireton R, Montgomery K, Bumgarner R, Samudrala
R (editors). Computational
systems biology. Methods in Molecular Biology 541:
v-ix, 2009. *
- Frazier Z, McDermott JE, Samudrala R. Computational representation of
biological systems. Methods in Molecular Biology
541: 535-549, 2009.
- Guerquin M, McDermott JE, Samudrala R. The Bioverse API and Web
Application. Methods in Molecular Biology 541:
511-534, 2009.
- Rashid I, McDermott JE, Samudrala R. Inferring molecular interaction
pathways from eQTL data. Methods in Molecular
Biology 541: 211-223, 2009.
- Wichadakul D, McDermott JE, Samudrala R. Prediction and
integration of regulatory and protein-protein
interactions. Methods in Molecular Biology 541:
101-143, 2009.
- McDermott JE, Wang J, Yu J, Wong GSK,
Samudrala R. In Rao GP, Wagner C, Singh RK,
editors. Prediction and
annotation of plant protein interaction
networks. Application of Genomics and Bioinformatics in
Plants (Studium Press) 207-238, 2008.
- Wang K, Horst JA, Cheng G, Nickle D, Samudrala R. Protein meta-functional signatures
from combining sequence, structure, evolution and amino acid
property information. PLoS Computational Biology 4:
e1000181, 2008. *
- Samudrala R, Oren EE, Cheng C, Horst, JA, Bernard B,
Gungormus M, Hnilova M, Fong H, Tamerler C, Sarikaya M. Knowledge-based design of
inorganic binding peptides. Proceedings of the conference
on the Foundations of Nanoscience: Self-Assembled Architectures and
Devices, 2008.
- Evans JS, Samudrala R, Walsh TR, Oren EE, Tamerler
C. Molecular design of
inorganic-binding polypeptides. MRS Bulletin 33:
514-518, 2008. [Accompanying
cover and introductory article with biographies on pages 504-512.] *
- Liu T, Guerquin M, Samudrala R. Improving the accuracy of
template-based predictions by mixing and matching between initial
models. BMC Structural Biology 8: 24, 2008.
- Jenkins C, Samudrala R, Geary S, Djordjevic SP.
Structural and functional
characterisation of an organic hydroperoxide resistance (Ohr)
protein from Mycoplasma gallisepticum.
Journal of Bacteriology 190: 2206-2208, 2008.
- Jenwitheesuk E, Horst JA, Rivas KL, Van Voorhis WC, Samudrala
R. Novel paradigms
for drug discovery: Computational multitarget
screening. Trends in Pharmacological Sciences 29:
62-71, 2008. [Accompanying cover.] *
- Ngan S-C, Hung L-H, Liu T, Samudrala R. Scoring functions for de
novo protein structure prediction revisited. Methods
in Molecular Biology 413: 243-282, 2007.
- Oren EE, Tamerler C, Sahin D, Hnilova M, Seker UOS, Sarikaya M,
Samudrala R. A novel
knowledge-based approach for designing inorganic binding
peptides. Bioinformatics 23: 2816-2822, 2007. *
- Jenwitheesuk E, Samudrala R. Identification of potential
HIV-1 targets of minocycline. Bioinformatics 23:
2797-2799, 2007.
- Chevance FFV, Takahashi N, Karlinsey JE, Gnerer J, Hirano T,
Samudrala R, Aizawa S-I, Hughes KT. The mechanism of outer
membrane penetration by the eubacterial flagellum and implications
for spirochete evolution. Genes and Development 21:
2326-2335, 2007.
- McDermott JE, Samudrala R. Bioinformatic characterization
of plant networks. Proceedings of the Asia Pacific Conference
on Plant Tissue Culture and Agrobiotechnology, 2007.
- Bockhorst J, Lu F, Janes JH, Keebler J, Gamain B, Awadalla P, Su
X, Samudrala R, Jojic N, Smith JD. Structural polymorphism
and diversifying selection on the pregnancy malaria vaccine
candidate VAR2CSA. Molecular and Biochemical
Parasitology 155: 103-112, 2007.
- Berube PM, Samudrala R, Stahl DA. Transcription of
amoC is associated with the recovery of Nitrosomonas
europaea from ammonia starvation. Journal of
Bacteriology 89: 3935-3944, 2007.
- Hung L-H, Ngan S-C, Samudrala R. De novo
protein structure prediction. In Xu Y, Xu D, Liang J, editors.
Computational Methods for Protein Structure Prediction and
Modeling 2: 43-64, 2007.
- Hung L-H, Samudrala R. An automated assignment-free
Bayesian approach for accurately identifying proton contacts from
NOESY data. Journal of Biomolecular NMR 36:
189-198, 2006. *
- Wang K, Samudrala R. Incorporating background frequency
improves entropy-based residue conservation measures. BMC
Bioinformatics 7: 385, 2006.
- Liu T, Samudrala R. The effect of experimental
resolution on the performance of knowledge-based discriminatory
functions for protein structure selection. Protein
Engineering, Design and Selection 19: 431-437, 2006.
- Korotkova N, Le Trong I, Samudrala R, Korotkov K, Van
Loy CP, Bui A-L, Moseley SL, Stenkamp RE. Crystal structure and mutational
analysis of the DaaE adhesin of Escherichia
coli. Journal
of Biological Chemistry 281: 22367-22377, 2006.
- Wang K, Samudrala R. Automated functional
classification of experimental and predicted protein
structures. BMC Bioinformatics 7: 278, 2006. *
- Howell DPG, Samudrala R, Smith JD. Disguising itself -
insights into Plasmodium falciparum binding and immune
evasion from the DBL crystal structure. Molecular and
Biochemical Parasitology 148: 1-9, 2006.
- Wang K, Mittler J, Samudrala R. Comment on "Evidence for
positive epistasis in HIV-1". Science 312:848b,
2006.
- Chang AN, McDermott JE, Guerquin M, Frazier Z, Samudrala
R. Integrator: Interactive
graphical search of large protein
interactomes over the Web. BMC Bioinformatics 7:
146, 2006.
- Ngan S-C, Inouye M, Samudrala R. A knowledge-based
scoring function based on residue triplets for protein structure
prediction. Protein Engineering, Design and
Selection 19: 187-193, 2006.
- Jenwitheesuk E, Samudrala R. Heptad-repeat-2 mutations
enhance the stability of the enfuvirtide-resistant HIV-1 gp41
hairpin structure. Antiviral Therapy 10: 893-900,
2005. *
- Cheng G, Qian B, Samudrala R, Baker D. Improvement in
protein functional site prediction by distinguishing structural and
functional constraints on protein family evolution using
computational design. Nucleic Acids Research
33: 5861-5867, 2005. *
- Jenwitheesuk E, Samudrala R. Identification of potential
multitarget antimalarial drugs. Journal of the American
Medical Association 294: 1490-1491, 2005. *
- Wang W, Zheng H, Yang S, Yu H, Li J, Jiang H, Su J, Yang L,
Zhang J, McDermott JE, Samudrala R, Wang J, Yang H, Yu J,
Kristiansen K, Wong GK, Wang J. Origin and evolution of new exons in
rodents. Genome Research 15: 1258-1264, 2005.
- Liu T, Jenwitheesuk E, Teller D, Samudrala R.
Structural insights into the Cellular
Retinaldehyde Binding Protein (CRALBP). Proteins:
Structure, Function, and Bioinformatics 61: 412-422, 2005.
- McDermott JE, Bumgarner RE, Samudrala R. Functional
annotation from predicted protein interaction networks.
Bioinformatics 21: 3217-3226, 2005. *
- McDermott JE, Guerquin M, Frazier Z, Chang AN, Samudrala R.
BIOVERSE: Enhancements to the
framework for structural, functional, and contextual annotations of
proteins and proteomes. Nucleic Acids Research
33: W324-W325, 2005. *
- Hung L-H, Ngan S-C, Liu T, Samudrala R.
PROTINFO: New algorithms for
enhanced protein structure prediction. Nucleic Acids
Research 33: W77-W80, 2005. *
- Wang K, Samudrala R. FSSA: A novel method for
identifying functional signatures from structural
alignments. Bioinformatics 21: 2969-2977, 2005. *
- Jenwitheesuk E, Wang K, Mittler J, Samudrala R.
PIRSpred: A webserver for
reliable HIV-1 protein-inhibitor resistance/susceptibility
prediction. Trends in Microbiology 13: 150-151,
2005. *
- Chang AN, McDermott JE, Samudrala R.
An enhanced java
graph applet interface for visualizing
interactomes. Bioinformatics 21: 1741-1742, 2005.
- Jenwitheesuk E, Samudrala R. Virtual screening of HIV-1
protease inhibitors against human cytomegalovirus protease using
docking and molecular dynamics. AIDS 19: 529-533,
2005.
- Jenwitheesuk E, Samudrala R. Prediction of HIV-1
protease inhibitor resistance using a protein-inhibitor flexible
docking approach. Antiviral Therapy 10: 157-166,
2005. *
- Yu J, Wang J, Lin W, Li S, Li H, Zhou J, ..., McDermott JE,
Samudrala R, Wang J, Wong GK. The genomes of Oryza
sativa: A history of duplications. PLoS
Biology 3: e38, 2005. *
- Ekwa-Ekok C, Diaza GA, Carlson C, Hasegawad T,
Samudrala R, Limf K, Yabug JM, Levya B, Schnapp LM. Genomic organization and sequence
variation of the human integrin subunit 8 gene
(ITGA8). Matrix Biology 23: 487-496, 2004.
- Wang J, Zhang J, Zheng H, Li J, Liu D, Li H, Samudrala
R, Yu J, Wong GK. Mouse
transcriptome: Neutral evolution of "non-coding" complementary
DNAs. Nature 431, 2004.
- Wang K, Samudrala R, Mittler J. HIV-1 genotypic drug resistance
interpretation algorithms need to include hypersusceptibility
mutations. Journal of Infectious Diseases 190:
2055-2056, 2004.
- Wang K, Samudrala R, Mittler J. Antivirogram or PhenoSense: a comparison of
their reproducibility and an analysis
of their correlation. Antiviral Therapy 9: 703-712, 2004.
- Jenwitheesuk E, Wang K, Mittler J, Samudrala R. Improved accuracy of HIV-1
genotypic susceptibility interpretation using a consensus
approach. AIDS 18: 1858-1859, 2004.
- Wang K, Fain B, Levitt M, Samudrala R. Improved protein structure
selection using decoy-dependent discriminatory
functions. BMC Structural Biology 4: 8, 2004. *
- Wang K, Jenwitheesuk E, Samudrala R, Mittler J. Simple linear model provides highly
accurate genotypic predictions of HIV-1 drug
resistance. Antiviral Therapy 9: 343-352, 2004.
- Wang K, Samudrala R, Mittler J. Weak agreement between predictions of
``reduced susceptibility'' from Antivirogram and
PhenoSense assays. Journal of Clinical Microbiology
42: 2353-2354, 2004.
- McDermott JE, Samudrala R. Enhanced functional information from
protein networks. Trends in
Biotechnology 22: 60-62, 2004. *
- Jenwitheesuk E, Samudrala R. Identifying inhibitors of
the SARS coronavirus proteinase. Bioorganic & Medicinal
Chemistry Letters 13: 3989-3992, 2003. [Most Cited Paper
2003 - 2006 Award.] *
- McDermott JE, Samudrala R. BIOVERSE: Functional, structural,
and contextual annotation of proteins and
proteomes. Nucleic Acids Research 31:
3736-3737, 2003. *
- Hung L-H, Samudrala R. PROTINFO: Secondary and
tertiary protein structure prediction. Nucleic Acids
Research 31: 3296-3299, 2003. *
- Jenwitheesuk E, Samudrala R. Improved prediction of
HIV-1 protease-inhibitor binding energies by molecular dynamics
simulations. BMC Structural Biology 3: 2, 2003. *
- Hung L-H, Samudrala R. Accurate and automated
classification of protein secondary structure with
PsiCSI. Protein Science 12: 288-295, 2003. *
- Jenkins C, Samudrala R, Anderson I, Hedlund BP, Petroni
G, Michailova N, Pinel N, Overbeek R, Rosati G, Staley JT. Genes for the cytoskeletal protein
tubulin in the bacteria genus Prosthecobacter.
Proceedings of the National Academy of Sciences 99:
17049-17054, 2002.
- McDermott JE, Samudrala R. The Bioverse: An object-oriented
genomic database and webserver written in
Python. In Proceedings of the conference on Objects in
Bio- & Chem-Informatics, 2002.
- Samudrala R, Levitt M. A comprehensive analysis of 40
blind protein structure predictions. BMC Structural
Biology 2: 3-18, 2002. *
- Van Loy CP, Sokurenko EP, Samudrala R, Moseley S.
Identification of a DAF binding
domain in the Dr adhesin. Molecular Microbiology
45: 439-452, 2002.
- Samudrala R. Modelling genome structure and
function. Pure and Applied Chemistry 6: 907-914, 2002.
- Samudrala R. Lessons from blind protein structure
prediction experiments. In Grohima M, Selvaraj S,
editors. Recent Research Developments in Protein Folding,
Stability, and Design 123-139, 2002.
- Xia Y, Huang ES, Levitt M, Samudrala R. Ab initio
construction of protein tertiary structures using a hierarchical
approach. Journal of Molecular Biology 300:
171-185, 2000. *
- Samudrala R, Levitt M. Decoys 'R' Us: A database of
incorrect protein conformations to improve protein structure
prediction. Protein Science 9: 1399-1401, 2000.
<
http://dd.compbio.org
>
- Huang ES, Samudrala R, Park BH. Scoring functions
for ab initio protein structure prediction. Methods
in Molecular Biology 143: 223-245, 2000.
- Samudrala R, Huang ES, Koehl P, Levitt M. Constructing
side chains on near-native main chains for ab initio protein
structure prediction. Protein Engineering 7:
453-457, 2000.
- Samudrala R, Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R.
Probing structure-function
relationships of the DNA polymerase
alpha-associated zinc-finger protein using computational
approaches. In Altman R, Dunker K, Hunter L,
Klein T, Lauderdale K, editors. Proceedings of the Pacific
Symposium on Biocomputing 179-189, 2000.
- Huang ES, Samudrala R, Ponder JW. Ab initio fold
prediction of small helical proteins using distance geometry and
knowledge-based scoring functions. Journal of Molecular
Biology 290:267-281, 1999.
- Samudrala R, Xia Y, Huang ES, Levitt M. Ab initio prediction of
protein structure using a combined hierarchical
approach. Proteins: Structure, Function, and Genetics
S3: 194-198, 1999. *
- Samudrala R, Xia Y, Levitt M, Huang ES. A combined approach for ab
initio construction of low resolution protein tertiary
structures from sequence. In Altman R, Dunker K, Hunter L,
Klein T, Lauderdale K, editors. Proceedings of the Pacific
Symposium on Biocomputing 505-516, 1999.
- Huang ES, Samudrala R, Ponder JW. Distance geometry generates native-like
folds for small helical proteins using
the consensus distances of predicted protein
structures. Protein Science 7: 1998-2003, 1998.
- Samudrala R, Moult J. Determinants of side chain
conformational preferences in protein
structures. Protein Engineering 11: 991-997, 1998.
- Samudrala R, Moult J. A graph-theoretic algorithm for
comparative modelling of protein structure. Journal of
Molecular Biology 279: 287-302, 1998. *
- Samudrala R, Moult J. An all-atom distance-dependent
conditional probability discriminatory function for protein
structure prediction. Journal of Molecular Biology
275: 893-914, 1998. *
- Samudrala R, Moult J. Handling context-sensitivity
in protein structures using graph theory: bona fide
prediction. Proteins: Structure, Function, and
Genetics 29S: 43-49, 1997. *
- Samudrala R. A
graph-theoretic solution to the context-sensitivity problem in
protein structure prediction. PhD thesis, 1997.
- Samudrala R, Pedersen JT, Zhou H, Luo R, Fidelis K,
Moult J. Confronting the
problem of interconnected structural changes in the comparative
modelling of proteins. Proteins: Structure, Function, and
Genetics 23: 327-336, 1995.
- Samudrala R. Book
review: Discovering Genomics,
Proteomics, and Bioinformatics by A. Malcolm Campbell
and Laurie Heyer. Cell Biology Education 2: 222-223,
2003.
- Samudrala R. Book Review: Structural
Bioinformatics by Philip E. Bourne and Helge
Weissig. Briefings in Bioinformatics 4: 299-301, 2003.
- Samudrala R. Taking the
cost out of firewalls. LinuxWorld
Magazine 1: 58-59, 2003.
- Samudrala R. Linux
Cluster HOWTO, 2003.
- Samudrala R. Installing and
using RAID. In Danesh A, Das G, editors. Special
Edition Using Linux System Administration, Que Publishing,
2000.
- Samudrala R. Creativity
and ownership: where is the balance?. In Blondeau O, Latrive F,
editors. Libres Enfants Du Savoir Numérique,
129-140, éditions de l'éclat, 2000.
- Samudrala R. The future of
music. In
Blondeau O, Latrive F, editors. Libres Enfants Du Savoir
Numérique, 447-462, éditions de l'éclat,
2000.
- Samudrala R. The free music philosophy.
In Blondeau O, Latrive F, editors. Libres Enfants Du Savoir
Numérique, 463-478, éditions de l'éclat,
2000.
Patent publications
4 listed; 4 more provisional applications or ROIs submitted
- Oren EE, Tamerler C, Sarikaya M, Samudrala R. Method and
system for designing polypeptides and polypeptide-like polymers with
specific chemical and physical characteristics. Priority date:
September 17, 2008.
- Michael SF, Isern S, Costin J, Jenwitheesuk E, Samudrala
R. Optimized
dengue virus entry inhibitory peptide (1OAN1). Priority date:
July 13, 2007.
- Jenwitheesuk E, Michael SF, Isern S, Garry R, Costin J,
Samudrala R. Dengue virus entry
inhibitory peptide (DN81). Priority date: July 13,
2007.
- Jenwitheesuk E, Lagunoff M, Van Voorhis W, Samudrala
R. Compositions and
methods for predicting inhibitors of protein targets. Priority
date: July 7, 2006.
- Prediction of co-prescription induced drug events using the
CANDO platform. University at Buffalo Clinical and Translational
Sciences Institute Pilot Studies Colloquium. Buffalo, NY. December
15, 2022. invited.
- Distinctive dialogues: How healthcare data will change the
world. University at Buffalo, Buffalo, NY. November 10,
2022. panel.
- Proteomusic: converting protein structures to complex music
patterns. Sigma Xi STEM Art and Film Festival. November 5-7,
2021. exhibit.
- Recent developments in bioinformatics. National Library of
Medicine/National Center for Biotechnology Information
workshop. March 12, 2022. invited.
- Broad spectrum coronavirus therapeutic discovery using the
CANDO platform. Louisiana Biomedical Research Network Annual
Meeting. February 13, 2021. keynote.
- Computational Analysis of Novel Drug Opportunities
(CANDO). International Conference on Protein and RNA Structure
Prediction. Punta Cana, Dominican Republic. December 3,
2019. invited.
- Optimum analgesic discovery by multiscale interactomic
profiling. NIH NCATS ASPIRE Design Challenge Winners
Conference. Bethesda, MD. October 28, 2019. invited.
- Computational Analysis of Novel Drug Opportunities
(CANDO). Center for Leading Innovation & Collaboration (CLIC)
Un-meeting. Rochester, NY. June 1, 2019. invited.
- The comprehensive solution to characterise and treat
disease. Louisiana Biomedical Research Network Annual Meeting. Baton
Rouge, LA. January 19, 2019. keynote.
- AI-based shotgun drug discovery, repurposing, and
design. Research Areas Ready for Acceleration and Growth, University
at Buffalo, Buffalo, NY. September 13, 2018. invited.
- AI-based shotgun drug discovery to characterise and treat
disease. SUNY Germination Space Artificial Intelligence
Program. Buffalo, NY. May 6, 2018. invited.
- Grant application strategies. Research fundamentals
workshop. University at Buffalo, Buffalo, NY. January 21,
2018. panel.
- The comprehensive solution to characterise and treat every
disease. International Conference on Protein and RNA Structure
Prediction. Montego Bay, Jamaica. December 5, 2017. invited.
- The comprehensive solution to characterise and treat every
disease. Clinical Sciences and Drug Discovery. Washington,
DC. November 9, 2017. keynote.
- The comprehensive solution to characterise and treat every
disease. Conference on Computational Biology and Bioinformatics. New
Orleans, LA. April 7. 2017. keynote.
- The comprehensive solution to characterise and treat every
disease. International Conference on Genetic and Protein
Engineering. Atlanta, GA. November 14, 2016. keynote.
- Interactomics: Computational Analysis of Novel Drug
Opportunities (CANDO). Annual Mayo Clinic Individualizing
Medicine Conference. Rochester, MN. October 7, 2016. invited.
- Interactome based drug discovery and disease-disease
connections. Intelligent Systems in Molecular Biology. Orlando,
FL. July 12, 2016. invited; presented by Gaurav Chopra.
- Interactomics: Computational Analysis of Novel Drug
Opportunities. International conference on Clinical Sciences and
Drug Discovery. Balitmore, MD. November 2-4, 2015. invited.
- Multiscale modelling of relationships between protein classes
and drug behavior across all diseases using the cando
platform. International Conference on Protein Engineering. Chicago,
IL. October 26-28, 2015. invited.
- Interactomics: Computational Analysis of Novel Drug
Opportunities. International Conference on Protein
Engineering. Chicago, IL. October 26-28, 2015. keynote.
- Interactome based drug discovery. Intelligent Systems in
Molecular Biology. Dublin, Ireland. July 10-14, 2015. invited;
presented by Gaurav Chopra.
- Interactomics: Computational Analysis of Novel Drug
Opportunities. Significant Advances in Bioengineering. Philadelpha,
PA. April 28, 2015. keynote.
- Multiscale modelling of relationships between protein classes
and drug behavior across all diseases using the cando platform.
Significant Advances in Bioengineering. Philadelpha, PA. April 27,
2015. invited.
- Interactomics: Computational Analysis of Novel Drug
Opportunities. NIH Common Fund High-Risk High-Reward
Symposium. Washington, DC. December 15, 2014. invited.
- Interactomics: Atomic systems biology translated to drug
discovery. From High-throughput Structural Bioinformatics to
Integrative Systems Biology - Network Tools and Applications in
Biology (NETTAB) Conference. Turin, Italy. October 16-18, 2014.
invited keynote and workshop.
- Interactomics: Computational Analysis of Novel Drug
Opportunities. Systems Biology of Infectious Diseases. Seattle,
WA. August 20, 2014. invited; presented by Geetika Sethi.
- Interactomics: Computational Analysis of Novel Drug
Opportunities. Michael Levitt Nobel Memorial Symposium. Stanford,
CA. September 11, 2014. invited.
- Interactomics: Computational Analysis of Novel Drug
Opportunities. Intelligent Systems in Molecular Biology. Boston,
MA. July 13, 2014. invited.
- Interactomics. Zing Protein Folding Conference. Dominican
Republic. July 16-19, 2014. invited; presented by Gaurav
Chopra.
- Interactomics:
Computational analysis of novel drug opportunities. Zing Protein
and RNA Structure Prediction Conference. Xcaret, Mexico. December 4,
2013. invited.
- Interactomics:
Computational analysis of novel drug
opportunities. International Conference on Pattern Recognition
in Bioinformatics (PRIB). Nice, France. June 18,
2013. keynote.
- Interactomics:
Computational analysis of novel drug opportunities. Genoa
Computational Biology Workshop. Genoa, Italy. June 14,
2013. keynote.
- Interactomics.
International Union of Pure and Applied Chemistry
Conference. Chonburi, Thailand. January 24, 2013. keynote.
- Interactomics. International
Conference on Bioinformatics (InCoB). Bangkok, Thailand. October 4,
2012. keynote; presented by Gaurav Chopra.
- Interactomics:
Discovering drugs against infectious and neoplastic disease using a
shotgun computational multitargeting approach. Mahidol
International Conference on Infections and Cancers. Bangkok,
Thailand. February 8, 2012. keynote.
- Interactomics. Pacific
Symposium on Biocomputing. Kona, HI. January 5,
2012. invited.
- Computational
analysis of novel drug opportunities (CANDO). Seventh Annual NIH
Director Pioneer's Award Symposium. Bethesda, MD. September 21,
2011. invited.
- Shotgun
multitarget computational drug discovery. World DNA and Genome
Day. Dalian, China. April 27, 2011. invited.
- Understanding
life at the atomic level. Paws-on-Science Huskies Weekend at the
Pacific Science Center. Seattle, WA. April 9, 2011. exhibit;
presented with four undergraduate students.
- Shotgun
multitarget computational drug discovery. Pepcon: Emerging
Leaders in Protein and Peptide Science. Beijing, China. March 25,
2011. invited.
- Computational
Vaccine Discovery. World Congress on Vaccines. Beijing,
China. March 23, 2011. invited.
- Modelling
structeomes. Undergraduate Research Program Research Exposed
series. University of Washington, Seattle, WA. January 19,
2011. invited.
- IGF1R
variants associated with isolated single suture craniosynostosis.
Ninth Critical Assessment of Structure Prediction (CASP9). Asilomar,
CA. December 8, 2010. refereed; presented by Jeremy Horst.
- Research authorship. Biomedical Research Integrity Discussion.
University of Washington, Seattle, WA. August 3, 2010. two
panels.
- Understanding
life at the atomic level. Paws-on-Science Huskies
Weekend at the Pacific Science Center. Seattle, WA. April 10,
2010. exhibit.
- In
silico design of solid binding peptides as molecular building
blocks in technology and medicine. ACS 237th National
Meeting. Salt Lake City, UT. March 24, 2009. invited;
presented by Ersin Emre Oren.
- Protein
structure refinement. Eighth Critical Assessment of Structure
Prediction (CASP8). Asilomar, CA. December 7, 2008. refereed.
- Protein
folding algorithms. Melbourne, Australia. October 16, 2008. keynote.
- Modelling
interactomes. BioC 2008. Fred Hutchinson Cancer
Research Center, Seattle, WA. July 28, 2008. invited.
- Modelling
the Bartonella interactome. Meeting on discovery of a
vaccine for Bartonella bacilliformis. National Institutes of
Health, Lima, Peru. June 26, 2008. invited.
- Modelling
interactomes. U.S.-India Joint Training Program Workshop on
Global Infectious Diseases. Hyderabad, India. January 22,
2008. invited.
- Modelling
interactomes. The 4th Solanaceae Genome Workshop. Jeju Island,
Korea. Sep 10, 2007. invited.
- Modelling
interactomes. 21st Symposium of the Protein Society. Boston,
MA. July 24, 2007. invited.
- Modelling
interactomes. Asia Pacific Conference on Plant Tissue Culture
and Agrobiotechnology. Kuala Lumpur, Malaysia. June 19,
2007. invited.
- Computational
engineering of bionanostructures. Foundations of
Nanoscience: Self-assembled Architectures and Devices
Conference. Snowbird, UT. April 21, 2007. invited.
- Shotgun
structural proteomics. Seventh Critical Assessment of Structure
Prediction (CASP7). Asilomar, CA. November 30, 2006. invited.
- Modelling
proteomes. Molecular Biomimetics and Bionanotechnology
conference. Istanbul, Turkey. November 13, 2006. invited.
- Designing
inorganic binding proteins. First workshop on Molecular
Biomimetics. Friday Harbour, WA. September 6, 2006. invited.
- Modelling
proteomes. Oral Biology Research Symposium. Seattle, WA. October
7, 2005. invited.
- Modelling
proteomes. BioC. Seattle, WA. August 17, 2005. invited.
- Modelling
proteomes: Application to understanding HIV disease progression.
Center for AIDS Research Symposium. Seattle, WA. May 27,
2005. invited.
- Modelling
proteomes. Fifth Annual Northwest Gene Expression
Conference. Seattle, WA. May 26, 2005. invited.
- Computational
engineering of bionanostructures. Foundations of
Nanoscience: Self-assembled Architectures and Devices
Conference. Snowbird, UT. April 25, 2005. invited.
- Modelling
proteomes. Searle Scholars Meeting. Chicago, IL. April 12,
2005. invited.
- An
integrated computational framework for systems biology
research. LabAutomation Conference. San Jose, CA. February 3,
2005. refereed.
- Protinfo/Samudrala:
New automated methods for CASP6. Sixth Critical Assessment of
Structure Prediction (CASP6). Gaeta, Italy. December 6,
2004. refereed; presented by Ling-Hong Hung.
- Structural
Bioinformatics. American Crystallographic Association Annual
Meeting. Chicago, IL. July 22, 2004. invited.
- Modelling
proteomes. Fourth Annual Northwest Gene Expression
Conference. Seattle, WA. August 28, 2003. invited.
- Predicting
protein structure from sequence. Biothailand 2003 Post-Congress
Workshop. Bangkok, Thailand. July 22, 2003. invited.
- Modelling
the rice proteome. Conference on Rice Biotechnology
2003. Pattaya, Thailand. July 18, 2003. invited.
- Modelling,
comparison and analysis of proteomes from different
organisms. International Conference on Biodiversity and
Bioactive Compounds. Pattaya, Thailand. July 17, 2003. invited.
- Violent
vs. non-violent approaches to global conflict resolution. Time
of Reflection: The War in Iraq symposium. Seattle, WA. April
23,2003. invited.
- Modelling
proteomes. The International Conference on Bioinformatics
2002. Bangkok, Thailand. February 8, 2002. invited.
- Protein
Structure Prediction. The International Conference on
Bioinformatics (InCoB). Bangkok, Thailand. February 5,
2002. keynote.
- Modelling
genome structure and function. Statistical Genetics and
Computational Molecular Biology Symposium. Seattle, WA. December
2001. invited.
- Protein structure prediction: progress and prospects. At the
Interface of Biology, Mathematics and Physics Symposium. Tucson,
AZ. March 2001. invited.
- Protein structure prediction: progress and
prospects. Biomedical Computation at Stanford 2000
Symposium. Stanford, CA. October 2000. invited.
- Computational biology: from gene to structure to
function. Intelligent Systems in Molecular Biology. San Diego, CA.
August 2000. invited.
- Computational biology: from gene to structure to
function. Mathematical and Computational Challenges in Molecular and
Cell Biology Symposium. Berkeley, CA. June 2000. invited.
- Probing structure-function relationships of proteins using
computational approaches. Pacific Symposium on
Biocomputing. Honolulu, HI. January 2000. refereed.
- Heterogeneous clusters and computational biology. Mellon
Institute's Developing and Using Clusters as a Biomedical Research
Tool Conference. Pittsburgh, PA. June 1999. invited.
- The triumph of technology: the defeat of copyright law. Second
Annual MP3 Summit. San Diego, CA. June 1999. invited.
- Applying the Cathedral and Bazaar paradigms to the music
industry. Alliance for Converging Technologies Lighthouse
Conference. Berkeley, CA. March 9, 1999. invited.
- Combining an all-atom conditional probability discriminatory
function and exhaustive enumeration techniques for protein structure
prediction. NSF Program in Mathematics and Molecular Biology meeting
VI. Santa Fe, NM. January 1999. invited.
- A combined approach for ab initio construction of low
resolution protein tertiary structures from sequence
.
Pacific Symposium on Biocomputing. Kona, HI. January
1999. refereed.
- Bona fide ab initio prediction of protein structures by
exhaustive enumeration and successive filtering using
knowledge-based scoring functions. Third Critical Assessment of
Structure Prediction. Asilomar, CA, December 16,
1998. refereed.
- Free Music Philosophy. First Annual MP3 Summit. San Diego, CA.
June 1998. invited.
- An all-atom conditional probability discriminatory
function for protein structure prediction. Burroughs Wellcome
Fund's Doing Science at the Interface. Berkeley, CA. June
1998. invited.
- Creativity and ownership: where is the balance? Third Annual
Ethics and Technology Conference. Santa Clara, CA. June
1998. refereed.
- Confronting the problem of interconnected structural changes in
the comparative modelling of proteins. NSF Program in Mathematics
and Molecular Biology meeting V. Santa Fe, NM. January
1997. invited.
- A graph theoretic approach to handle the problem of
interconnectedness in the comparative modelling of proteins.
Second Critical Assessment of Structure Prediction. Asilomar,
CA. December 13, 1996. refereed.
- Comparative modelling of the Histidine-containing
Phosophocarrier protein, the Cellular Retinoic Acid-binding Protein,
and the Eosinophil Derived Neurotoxin. First Critical Assessment of
Structure Prediction. Asilomar, CA, December 5, 1994. refereed.
- Adjunct faculty, Department of Pharmacology and Toxicology,
State University of New York, Buffalo. 2015-.
- Member, Structural Biology, Faculty Opinions. June 1, 2002-.
- Affiliate faculty, Department of Microbiology, University of
Washington, Seattle. 2015-2016.
- Adjunct faculty, Department of Biology, University
of Washington, Seattle. 2004-2014.
- Adjunct faculty, Department of Oral Biology, University
of Washington, Seattle. 2006-2014.
- Member, Interdisciplinary Program in Pathobiology,
University of Washington, Seattle. 2012-2014.
- Member, Computational Molecular Biology Program, University of
Washington, Seattle. 2001-2014.
- Member, Molecular and Cellular Biology Program, University of
Washington, Seattle. 2001-2014.
- Member, Nanotechnology Program, University of Washington,
Seattle. 2001-2014.
- Member and co-investigator, Clinical and Translational Research
Center, Buffalo, NY. 2016-.
- Member and co-director, Bioinformatics and Biostatics Core,
UB-UR Center for AIDS Research, Rochester, NY. 2017.
- Member and co-investigator, Genetically Engineering Materials
Science and Engineering Centre. 2007-2014.
- Member, Center for Ecogenetics and Environmental Health,
University of Washington, Seattle. 2001-2014.
- Member, Keck Center for Microbial Pathogens, University of
Washington, Seattle. 2004.
- Member, External Advisory Committee, Louisiana Biomedical
Research Network. 2017-.
- Member, Organising Committee, Drug Screening and Pharmacology
Summit. Boston, MA. 2023.
- Member, International Advisory Committee, 18th IEEE
International Conference on Computational Intelligence in
Bioinformatics and Computational Biology. Victoria, Australia. 2021.
- Member, Organising Committee, International conference on
Clinical Sciences and Drug Discovery. Washington, DC. 2017.
- Member, Organising Committee, International Conference on
Genetic and Protein Engineering, Las Vegas, NV. 2017.
- Member, Organising Committee, International Conference on
Genetic and Protein Engineering, Atlanta, GA. 2016.
- Member, Organising Committee, International conference on
Clinical Sciences and Drug Discovery. Dundee, Scotland. 2016.
- Member, Program Committee, Biomedical Expo, Houston, TX. 2015.
- Chair, Scientific Session, Clinical Sciences in Drug Discovery,
Balitmore, MD. 2015.
- Chair, Young Investigator Forum, International Conference in
Protein Engineering, Chicago, IL. 2015.
- Member, Program Committee, International Conference in Protein
Engineering, Chicago, IL. 2015.
- Member, Program Committee, International Conference in
Biomedical Engineering, Philadelpha, PA. 2015.
- Member, Program Committee, Intelligent Systems in Molecular
Biology, Dublin, Ireland. 2011.
- Member, Program Committee, Network Tools and Applications in
Biology (NETTAB) Conference, Turin, Italy. 2014.
- Member, Program Committee, Intelligent Systems in Molecular
Biology, Vienna, Austria. 2011.
- Member, Bioconductor Advisory Board, Fred Hutchinson Cancer
Research Center, Seattle, WA. 2006-2011.
- Member, Biocommons Computing Center Advisory Board,
University of Washington, Seattle, WA. 2003-2006.
- Member, Scientific committee for the International Conference on
Bioinformatics, Bangkok, Thailand. 2002.
- Member, Promotions and Tenure Committee, Jacobs School of
Medicine and Biomedical Sciences, University at Buffalo,
NY. 2020-.
- Member, Awards Committee, Jacobs School of Medicine and
Biomedical Sciences, University at Buffalo, NY. 2023-.
- Member, Steering Committee, PhD Program in Biomedical Sciences
(PPBS), University at Buffalo, NY. 2022-.
- Alternate member, Faculty Council, Jacobs School of
Medicine and Biomedical Sciences, University at Buffalo, NY. 2016-.
- Member, faculty and administrator hiring search committees,
Department of Biomedical Informatics, University at Buffalo,
NY. 2022.
- Reviewer, CLIMB UP for Summer Research, University at Buffalo,
NY. 2019.
- Member, Scientific Leadership Committee, Drug Development Core,
UB Clinical and Translational Research Center, Buffalo,
NY. 2017-2020.
- Member, Admissions Committee, PhD Program in Biomedical
Sciences (PPBS), University at Buffalo, NY. 2016-2019.
- Moderator, Undergraduate Research Symposium, Undergraduate
Research Program, University of Washington, Seattle. 2011.
- Member, Levinson Scholarship Review Committee, University of
Washington, Seattle. 2010.
- Member, Undergraduate Award Committee, Department of
Microbiology, University of Washington, Seattle. 2010.
- Consulant, National Centre for Genetic Engineering and
Biotechnology (BIOTEC), Thailand. December, 2009.
- Chair and member, Admissions Committee, Department of
Microbiology, University of Washington, Seattle. 2004-2008.
- Ad hoc grant application reviewer for Natural Sciences and
Engineering Research Council of Canada (NSERC), Agency for Science,
Technology and Research (A*STAR) Singapore, Burroughs Wellcome Fund,
Genome Canada, Natural Sciences and Engineering Research Council of
Canada, Israel Science Foundation, UW Royalty Research Fund, FL
Department of Health, PA Department of Health, UB Clinical and
Translational Research Center, and several others. 2000-.
- Member, ten NIH ad hoc study sections/special emphasis panels. 2003-.
- Member eight NSF review panels. 2003-.
- Associate Editor, Frontiers in Chemistry, 2022-.
- Editorial Board, Biology. 2020-.
- Associate Editor, BMC Systems Biology. 2012-.
- Associate Editor, BMC Bioinformatics. 2010-.
- Editorial Board, Journal of Bioengineering & Biomedical
Sciences. 2010-.
- Editor in Chief, Interactome. 2013-2014.
- Manuscript reviewer for
Bioinformatics,
BMC Bioinformatics,
BMC Structural Biology,
Drug Discovery Today,
Frontiers in Chemistry,
Frontiers in Pharmacology,
Journal of Molecular Biology,
Nucleic Acids Research,
Proteins: Structure, Function, and Bioinformatics,
Protein Science,
and several others.
- Professor and Chief of the Division of Bioinformatics at the
State University of New York at Buffalo developing and leading a
comprehensive bioinformatics research and training programme on
multiscale modelling of complex biological systems. October 2014-.
- Principal Investigator, at the University of Washington, of a
computational genomics research group investigating protein
structure and function; bioinformatics/data mining; predicting
membrane protein structure; protein design; docking; evolution; and
understanding higher level organisation of protein pathways in the
cell and simulating their behaviour. February 2001-September 2014.
- Postdoctoral Fellow at Stanford University working on methods
to sample main chain conformations
in comparative modelling and ab initio scenarios,
continued development of all-atom discriminatory functions and side
chain prediction methods, comparative modelling and ab initio
prediction for the third and fourth Critical Assessment of
Structure Prediction (CASP3 and 4) experiments, and computational
aspects of structural and functional genomics. With Michael Levitt. September
1997-January 2001.
- Graduate Research Fellow at the Centre for Advanced Research in
Biotechnology working on modelling protein
structure primarily using graph theoretic methods, development of an
all-atom conditional-probability discriminatory function,
development of algorithms for side chain prediction, and comparative
modelling for the first and second Critical Assessment of Structure
Prediction (CASP1 and 2) experiments.
With John Moult. August 1993-August 1997.
- Research Intern at East Carolina University, Greenville, NC
doing theoretical and experimental work on analysing
genetic relationships between the Herpes Simplex Virus and the
Pseudo Rabies Virus. With Nels Pederson. Summer 1992.
- Research Intern at USDA laboratories, Delaware, Ohio performing
computational analysis of the performance of various drugs that
prevent Dutch Elm disease. With Steve Ishita. Spring 1992.
- Programming languages, operating systems, computer
architecture, structured computer organisation, artificial
intelligence, algorithms and data structures, mathematical
foundations of computing science, compiler theory and design, linear
algebra, numerical analysis, and combinatorics and graph theory.
- Programming languages: experience with several procedural
languages such as C/C++, FORTRAN, and Perl; functional languages such as
Lisp; and formatting languages such as TeX/LaTeX and SGML/HTML.
- Operating systems: experience with several flavours of Unix
(mainly Linux, Irix, OSF/1, and AIX), networking protocols, and
systems programming.
- Software: I have written several general freeware programs that
are used by the Internet community. As part of my research, I have
written programs that been used extensively in-house, and are
available as a freeware distribution, for prediction of protein
structure and function, both at the single molecule as well as the
genomic levels.
- Solved several computing problems working as a computing
consultant for Information Systems, The Writing Resource Centre, and
the Politics and Government Department at Ohio Wesleyan (1990-1993),
and at the Centre for Advanced Research in Biotechnology
(1993-1997). Designed and implemented high-performance Linux-based
computing clusters at Stanford University (1997-2001) and the
University of Washington (2001-present).
- Artificial intelligence in biology; bioinformatics; biomedical
informatics; biophysical modeling; computational biology;
computational chemistry; computational drug discovery; drug design;
drug development; drug discovery; genomics and proteomics; molecular
and cellular biology; nanotechnology; protein folding; protein
function and structure; proteomics; structural biology;
translational research.
- Molecular and population genetics, developmental biology,
bacterial physiology, plant structure function and systematics,
evolution, developmental biology, chemistry of nucleic acids,
protein chemistry and enzymic catalysis, protein structure and
function, cell biology, and biophysics and theoretical/computational
biology.
- Computational techniques: experience with modelling of DNA, RNA,
protein, and organismal structure, function, and evolution by simulation.
- Experimental techniques: experience with recombinant DNA technology
(cloning, expression, analysis of genetic material).
Date of birth: March 23, 1972
Ram Samudrala, PhD
Professor and Chief, Division of Bioinformatics
Department of Biomedical Informatics
School of Medicine and Biomedical Sciences
State University of New York (SUNY)
Buffalo, NY 14620
V: 1-206-251-8852
F: 1-206-260-8979
E: <ram@compbio.org>
W: <compbio.org>