Computational Biology     


Computational Biology Publications


EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets
Kalen Cantrell, Marcus W Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu, Erfan Sayyari, Jamie Morton, Anupriya Tripathi, Julia M Gauglitz, Clarisse Marotz, Nathaniel L Matteson, Cameron Martino, Jon G Sanders, Anna Paola Carrieri, Se Jin Song, Austin D Swafford, Pieter Dorrestein, Kristian G Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vazquez-Baeza, Rob Knight
mSystems 6(2), e01216-20, 2021
Abstract   Learn more:

Negative symptoms and speech pauses in youths at clinical high risk for psychosis
Emma R. Stanislawski, Zarina R. Bilgrami, Cansu Sarac, Sahil Garg, Stephen Heisig, Guillermo A. Cecchi, Carla Agurto & Cheryl M. Corcoran
npj Schizophrenia, 2021

Learning Brain Dynamics with Coupled Low-dimensional Nonlinear Oscillators and Deep Recurrent Networks
German Abrevaya, Guillaume Dumas, Aleksandr Y. Aravkin, Peng Zheng, Jean-Christophe Gagnon-Audet, James Kozloski, Pablo Polosecki, Guillaume Lajoie, David Cox, Silvina Ponce Dawson, Guillermo Cecchi, Irina Rish
Neural Computation , 2021

Annotations of Recurrent Structural Variant Events in Pan-Cancer Whole Genome Data for Precision Medicine
Koyama T, Hasegawa T, Kasajima R, Shimizu E, Tokumasu R, Yokoyama K, Yamaguchi K, Tojo A, Furukawa Y, Weeraratne D, Willis V, Snowdon J, Nakagawa H, Miyano S, Parida L, Yamaguchi R, Imoto S.
Research Square Preprint, 2021

Introductions and evolutions of SARS-CoV-2 strains in Japan
Tokumasu R, Weeraratne D, Snowdon J, Parida L, Kudo M, Koyama T.
medRxiv 2021.02.26.21252555

Monitoring the microbiome for food safety and quality using deep shotgun sequencing
Kristen L. Beck*, Niina Haiminen*, David Chambliss, Stefan B Edlund, Mark Kunitomi, B. Carol Huang, Nguyet Kong, Balasubramanian Ganesan, Robert Baker, Peter Markwell, Ban Kawas, Matthew Davis, Robert J. Prill, Harsha Krishnareddy, Edward Seabolt, Carl H. Marlowe, Sophie Pierre, Andre Quintanar, Laxmi Parida, Geraud Dubois, James Kaufman, Bart C. Weimer, Consortium for Sequencing the Food Supply Chain
npj Science of Food 5(3), 2021
Abstract   Blog:

Re-purposing software for functional characterization of the microbiome
L.-J. Gardiner, N. Haiminen, F. Utro, L. Parida, E. Seabolt, R. Krishna and J.H. Kaufman
Microbiome, 2021

Functional profiling of COVID-19 respiratory tract microbiomes
N. Haiminen, F. Utro, E. Seabolt, L. Parida
Scientific Reports11, 2021

Barriers to Prescribing Targeted Therapies for NSCLC Patients with Highly Actionable Gene Variants in the Veterans Affairs National Precision Oncology Program
Vashistha V, Armstrong J, Winski D, Poonnen PJ, Hintze B, Price M, Snowdon JL, Weeraratne D, Brotman D, Jackson GP, Kelley MJ.
Journal of Clinical Oncology (JCO) Oncology Practice, 2021

Switching Cytolytic Nanopores into Antimicrobial Fractal Ruptures by a Single Side Chain Mutation
Katharine Hammond, Flaviu Cipcigan, Kareem Al Nahas, Valeria Losasso, Helen Lewis, Jehangir Cama, Fausto Martelli, Patrick W. Simcock, Marcus Fletcher, Jascindra Ravi, Phillip J. Stansfeld, Stefano Pagliara, Bart W. Hoogenboom, Ulrich F. Keyser, Mark S. P. Sansom, Jason Crain, and Maxim G. Ryadnov
ACS Nano, 2021
Front cover article

Challenges in benchmarking metagenomic profilers
Zheng Sun, Shi Huang, Meng Zhang, Qiyun Zhu, Niina Haiminen, Anna-Paola Carrieri, Yoshiki Vazquez-Baeza, Laxmi Parida, Ho-Cheol Kim, Rob Knight, Yang-Yu Liu
Nature Methods, 2021
Abstract   CMI blog:


IBM Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale
Ed Seabolt, Gowri Nayar, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Eser Kandogan, Mark Kuntomi, Mary Roth, Ignacio Terrizzano, James Kaufman, Vandana Mukherjee
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1-1, 2020
Abstract   metacyc, relational database, functional genomics, kegg, central dogma of molecular biology, cloud computing, ibm, genome, computational biology, computer science

Linguistic markers predict onset of Alzheimer's disease
Elif Eyigoz, Sachin Mathur, Mar Santamaria, Guillermo Cecchi, Melissa Naylor
Lancet eClinical Medicine, 2020

COSIFER: a python package for the consensus inference of molecular interaction networks
Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow, Mehmet Eren Ahsen, Gustavo A Stolovitzky, Maria Rodriguez Martinez
Bioinformatics, 2020

Genetic Determinants and Evolutionary History of Richters Syndrome
E.M. Parry, R. Guieze, I. Leshchiner, D. Rosebrock, B. Persaud, C.K. Lemvigh, E. Tausch, M.S. Davids, J. Bloehdorn, C. Schneider, L. Elagina, A.Z. Martinez, A. Taylor-Weiner, N. Jain, W.G. Wierda, L.Z. Rassenti, T.J. Kipps, J. Broseus, F. Cymbalista, N.E. Kay, K.J. Livak, S. Li, T. Huang, N. Purroy, A.J. Anandappa, S.M. Fernandes, F. Utro, K. Rhrissorrakrai, C. Levovitz, B Danish, K. Slowik, S.A. Parikh, J.R. Brown, L. Parida, D.S. Neuberg, S. Stilgenbauer, G. Getz, C.J. Wu
Blood, ASH, 136, 47-48, 2020

Estimation of lesion-specific mutation shedding in cfDNA from rapid autopsy study
F. Utro, K. Rhrissorrakrai, C. Levovitz, I. Leshchiner, L. Martin, C. Chen, C. Pinto, B. Danysh, K. Slowik, L. Goyal, R. Allen, M.W. Broudo, D. Juric, G. Getz, L. Parida
Cancer Research, AACR, 80, 1509-1509, 2020

Targeting Proteases for Treating COVID-19
Binquan Luan, Tien Huynh, Xuemei Cheng, Ganhui Lan, Hao-Ran Wang
Journal of Proteome Research 19(11), 4316-4326, 2020
Abstract   viral entry, proteases, viral protein, protease, virus, pathogenesis, virology, tmprss2, endogeny, medicine

Pre-training Protein Language Models with Label-Agnostic Binding Pairs Enhances Performance in Downstream Tasks
Modestas Filipavicius, Matteo Manica, Joris Cadow, Maria Rodriguez Martinez
MLSB NeurIPS, 2020

Structural Basis of the Potential Binding Mechanism of Remdesivir to SARS-CoV-2 RNA-Dependent RNA Polymerase
Leili Zhang, Ruhong Zhou
Journal of Physical Chemistry B 124(32), 6955-6962, 2020
Abstract   rna dependent rna polymerase, polymerase, rna polymerase, rna, binding site, transcription, homology modeling, ligand, biochemistry, chemistry

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age
Shi Huang, Niina Haiminen, Anna-Paola Carrieri, Rebecca Hu, Lingjing Jiang, Laxmi Parida, Baylee Russell, Celeste Allaband, Amir Zarrinpar, Yoshiki V\'azquez-Baeza, Pedro Belda-Ferre, Hongwei Zhou, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Zhenjiang Zech Xu
mSystems 5(1), American Society for Microbiology Journals, 2020

In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers
David R Bell, Jeffrey K Weber, Wang Yin, Tien Huynh, Wei Duan, Ruhong Zhou
Proceedings of the National Academy of Sciences of the United States of America 117(15), 8486-8493, 2020
Abstract   aptamer, systematic evolution of ligands by exponential enrichment, in silico, virtual screening, rational design, isothermal titration calorimetry, docking, nucleic acid, computational biology, chemistry

Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme
Ruiqiong Guo, Zixuan Cang, Jiaqi Yao, Miyeon Kim, Erin Deans, Guowei Wei, Seung-gu Kang*, Heedeok Hong*
Proceedings of the National Academy of Sciences, National Academy of Sciences, 2020

Loss of nucleus accumbens low-frequency fluctuations is a signature of chronic pain
Meena M Makary, Pablo Polosecki, Guillermo A Cecchi, Ivan E DeAraujo, Daniel S Barron, Todd R Constable, Peter G Whang, Donna A Thomas, Hani Mowafi, Dana M Small, Paul Geha
Proceedings of the National Academy of Sciences, 2020

Automated extraction of chemical synthesis actions from experimental procedures
Alain C. Vaucher, Federico Zipoli, Joppe Geluykens, Vishnu H. Nair, Philippe Schwaller, Teodoro Laino
Nature Communications 11(1), 2020


Analysis of Chinese acral and mucosal melanoma patient genomic and neoantigen profiles in cancer vaccine development: A pilot study
Guo X, Gao S, Yang L, Fang J, Wei G, Ma X, Zhao Z, Weeraratne SD, Snowdon J, Wang S, Qing X.
J Clin Oncol 37, 2019 (suppl; abstr e14300).

Food authentication from shotgun sequencing reads with an application on high protein powders
Niina Haiminen, Stefan Edlund, David Chambliss, Mark Kunitomi, Bart C. Weimer, Balasubramanian Ganesan, Robert Baker, Peter Markwell, Matthew Davis, B. Carol Huang, Nguyet Kong, Robert J. Prill, Carl H. Marlowe, Andre Quintanar, Sophie Pierre, Geraud Dubois, James H. Kaufman, Laxmi Parida, Kristen L. Beck
npj Science of Food 3(24), Springer Nature, 2019
Abstract   Blog:

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer
Johanna Wagner, Maria Anna Rapsomaniki, Stephane Chevrier, Tobias Anzeneder, Claus Langwieder, August Dykgers, Martin Rees, Annette Ramaswamy, Simone Muenst, Savas Deniz Soysal, Andrea Jacobs, Jonas Windhager, Karina Silina, Maries van den Broek, Konstantin Johannes Dedes, Maria Rodriguez Martinez, Walter Paul Weber, Bernd Bodenmiller
Cell 177(5), 1330-1345. e18, 2019

Dark-matter matters: Discriminating subtle blood cancers using the darkest DNA
L. Parida, C. Haferlach, K. Rhrissorrakrai, F. Utro, C. Levovitz, W. Kern, N. Nadarajah, S. Twardziok, S. Hutter, M. Meggendorfer, W. Walter, C. Baer, T. Haferlach
PLoS Comput Biology 15(8), 2019

PIMKL: Pathway-Induced Multiple Kernel Learning
Matteo Manica, Joris Cadow, Roland Mathis, Maria Rodriguez Martinez
npj Systems Biology and Applications 5(1), 8, Nature Publishing Group, 2019

Mitochondrial origins of fractional control in regulated cell death
Luis C. Santos, Robert Vogel, Jerry E. Chipuk, Marc R. Birtwistle, Gustavo Stolovitzky, Pablo Meyer
Nature Communications 10(1), 2019
Abstract   programmed cell death, phenotype, organelle, mitochondrion, genetics, explained variation, cell, cancer, biology, apoptosis

Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata
M. Klaas, N. Haiminen, J. Grant, P. Cormican, J. Finnan, S.K. Arojju, F. Utro, T. Vellani, L. Parida, S. Barth
Annals of botany, 2019

Differential Impact of Cognitive Computing Augmented by Real World Evidence on Novice and Expert Oncologists
McNamara D, Goldberg SL, Latts L, Graham D, Waintraub SE, Norden AD, Landstrom C, Pecora AL, Hervey J, Schultz E, Wang CK, Jungbluth N, Francis PM, Snowdon JL
Cancer Medicine, 2019

Detecting and discriminating between different types of bacteria with a low-cost smartphone based optical device and neural network models
Venkat Balagurusamy; Vince Siu; Ashwin Dhinesh Kumar; Sahil Dureja; Joseph Ligman; Prabhakar Kudva; Matt Tong; Donna Dillenberger
Proceedings Volume 11087, Biosensing and Nanomedicine XII, 2019

Signatures of Low-Dimensional Neural Predictive Manifolds
S. Recanatesi, M. Farrell, G Lajoie, S. Deneve, M. Rigotti, E. Shea-Brown
Computational and Systems Neuroscience (Cosyne), 2019

The Geometry of Abstraction in Hippocampus and Pre-Frontal Cortex
S. Bernardi, M.K. Benna, M. Rigotti, J. Munuera, S. Fusi, C.D. Salzman
Computational and Systems Neuroscience (Cosyne), 2019

Measuring Prefrontal Representational Geometry: fMRI Adaptation vs Pattern Analysis
A. Bhandari, M.K. Benna, M. Rigotti, S. Fusi, D. Badre
2019 Conference on Cognitive Computational Neuroscience, Cognitive Computational Neuroscience

fMRI Adaptation vs Pattern Analysis: Evaluating Methods for Measuring Human PFC Representational Geometry and Dimensionality
A. Bhandari, Y. Braverman, M.K. Benna, M. Rigotti, S. Fusi, D. Badre
Society for Neuroscience Meeting, Society for Neuroscience, 2019

Transient, Consequential Increases in Extracellular Potassium Ions Accompany Channelrhodopsin2 Excitation.
Octeau JC, Gangwani MR, Allam SL, Tran D, Huang S, Hoang-Trong TM, Golshani P, Rumbell TH, Kozloski JR, Khakh BS.
Cell Reports, 2019

Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders
Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Saez-Rodriguez, Maria Rodriguez-Martinez
Molecular Pharmaceutics, 2019
PMID: 31618586

Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer
Ali Oskooei, Matteo Manica, Roland Mathis, Maria Rodriguez-Martinez
Scientific Reports 9(1), 15918, 2019

Association of Mutational Profile and Human Papillomavirus Status in Patients with Head and Neck Squamous Cell Carcinoma
Doerstling S, Winski D, Hintze B, Poonnen PJ, Duffy JE, Snowdon JL, George J, Jackson GP, Weeraratne D, Spector NL, Kelley MJ, Vashistha V
Journal of Molecular Diagnostics 21(6), 1250-1266, 2019

Signal Enrichment of Metagenome Sequencing Reads using Topological Data Analysis
Aldo Guzman-Saenz, Niina Haiminen, Saugata Basu and Laxmi Parida
BMC Genomics 20(194), 2019

Haplotype assembly of autotetraploid potato using integer linear programming
Enrico Siragusa, Niina Haiminen, Richard Finkers, Richard Visser, Laxmi Parida
Bioinformatics 35(18), 3279-3286, 2019


T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable
Alok V. Joglekar, Zhe Liu, Jeffrey K. Weber, Yong Ouyang, John D. Jeppson, Won Jun Noh, Pedro A. Lamothe-Molina, Huabiao Chen, Seung-gu Kang, Michael T. Bethune, Ruhong Zhou, Bruce D. Walker, David Baltimore
Proceedings of the National Academy of Sciences of the United States of America 115(8), 1877-1882, 2018
Abstract   t cell, natural killer t cell, epitope, cd8, cytokine secretion, t cell receptor, cytotoxicity, in vitro, molecular biology, chemistry

T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable
Alok V Joglekar, Zhe Liu, Jeffrey K Weber, Yong Ouyang, John D Jeppson, Won Jun Noh, Pedro A Lamothe-Molina, Huabiao Chen, Seung-gu Kang, Michael T Bethune, others
Proceedings of the National Academy of Sciences 115(8), 1877--1882, National Academy of Sciences, 2018

Self-organized criticality and pattern emergence through the lens of tropical geometry
Nikita Kalinin, Aldo Guzm\'an-S\'aenz, Yulieth Prieto, Mikhail Shkolnikov, Vera Kalinina, Ernesto Lupercio
Proceedings of the National Academy of Sciences 115(35), E8135--E8142, National Acad Sciences, 2018

PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks
Ali Oskooei, Jannis Born, Matteo Manica, Vigneshwari Subramanian, Julio Saez-Rodriguez, Maria Rodriguez Martinez
Machine Learning for Molecules and Materials NIPS 2018 Workshop

Inference of the three-dimensional chromatin structure and its temporal behavior
Bianca-Cristina Cristescu, Zalan Borsos, John Lygeros, Maria Rodriguez Martinez, Maria Anna Rapsomaniki
Machine Learning for Molecules and Materials NeurIPS 2018 Workshop

Gaussian Process regressions for inverse problems and parameter searches in models of ventricular mechanics
P. Di Achille, A. Harouni, S. Khamzin, O. Solovyova, J.J. Rice, V. Gurev
Frontiers in Physiology9, 1002, Frontiers, 2018

Baseline multimodal information predicts future motor impairment in premanifest Huntington's disease
Castro, Eduardo and Polosecki, Pablo and Rish, Irina and Pustina, Dorian and Warner, John H and Wood, Andrew and Sampaio, Cristina and Cecchi, Guillermo A
NeuroImage: Clinical, Elsevier, 2018

Efficient algorithms for polyploid haplotype phasing
Dan He, Subrata Saha, Richard Finkers, Laxmi Parida
BMC genomics19:2, BioMed Central, 2018

Accelerating molecular discovery through data and physical sciences: Applications to peptide-membrane interactions
Cipcigan, Flaviu and Carrieri, Anna Paola and Pyzer-Knapp, Edward O and Krishna, Ritesh and Hsiao, Ya-Wen and Winn, Martyn and Ryadnov, Maxim G and Edge, Colin and Martyna, Glenn and Crain, Jason
The Journal of Chemical Physics 148(24), 241744, AIP Publishing, 2018

Inhibition of CYP2C8 by metallofullerenol Gd@ C82 (OH) 22 through blocking substrate channels and substrate recognition sites
Ma, Dongfang and Meng, Xuan-Yu and Bell, David R and Liu, Shengtang and Zhou, Ruhong
Carbon127, 667--675, Elsevier, 2018

Concentration-dependent binding of CdSe quantum dots on the SH3 domain
Bell, David R and Kang, Seung-Gu and Huynh, Tien and Zhou, Ruhong
Nanoscale 10(1), 351--358, Royal Society of Chemistry, 2018

Cooperative Modes of Action of Antimicrobial Peptides Characterized with Atomistic Simulations: a Study on Cecropin B
Hsiao, Ya-Wen and Hedstr{\"o}m, Magnus and Losasso, Valeria and Metz, Sebastian and Crain, Jason and Winn, Martyn D
The Journal of Physical Chemistry B, ACS Publications, 2018

Broad/IBM Project: Discovery of treatment resistance mechanisms through use of liquid biopsy genomics services
G. Getz, C. Cibulskis, I. Leshchiner, M. Hanna, D. Livitz, K. Slowik, C. Levovitz, F. Utro, K. Rhrissorrakrai, D. Rotem, and others
Cancer Research, AACR, 2018

The Binding Specificity Determines the Cytochrome P450 3A4-Mediated Enantioselective Metabolism of Metconazole
Shulin Zhuang, Leili Zhang, Tingjie Zhan, Liping Lu, Lu Zhao, Haifei Wang, Joseph A Morrone, Weiping Liu, Ruhong Zhou
The Journal of Physical Chemistry B, ACS Publications, 2018

Learning Oscillatory Brain Dynamics: van der Pol Meets LSTM
Abrevaya, German and Aravkin, Alexandr and Cecchi, Guillermo and Polosecki, Pablo and Rish, Irina
Computational Neuroscience - CNS 2018 (accepted)

The number of titrated microRNA species dictates ceRNA regulation
Hua-Sheng Chiu, Maria Rodriguez Martinez, Elena V Komissarova, David Llobet-Navas, Mukesh Bansal, Evan O Paull, Jose Silva, Xuerui Yang, Pavel Sumazin, Andrea Califano
Nucleic Acids Research, 2018

A dual role for the N-terminal domain of the IL-3 receptor in cell signalling
Broughton, Sophie E and Hercus, Timothy R and Nero, Tracy L and Kan, Winnie L and Barry, Emma F and Dottore, Mara and Shing, Karen S Cheung Tung and Morton, Craig J and Dhagat, Urmi and Hardy, Matthew P and others
Nature communications 9(1), 386, Nature Publishing Group, 2018

Brain and psychological determinants of placebo pill response in chronic pain patients
E Vachon-Presseau, SE Berger, TB Abdullah, L Huang, GA Cecchi, JW Griffith, TJ Schnitzer, AV Apkarian
Nature Communications 9(3397), 2018

An entropic barriers diffusion theory of decision-making in multiple alternative tasks
Diego Fernandez Slezak, Mariano Sigman, Guillermo Cecchi
PLoS Computational Biology14 (3), e1005961, 2018

CellCycleTRACER accounts for cell cycle and volume in mass cytometry data
Maria Anna Rapsomaniki, Xiao-Kang Lun, Stefan Woerner, Marco Laumanns, Bernd Bodenmiller, María Rodríguez-Martínez
Nature Communications9, 2018

Shared neural coding for social hierarchy and reward value in primate amygdala
J. Munuera, M. Rigotti, C.D. Salzman
Nature Neuroscience, 1, Nature Publishing Group, 2018

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries
Yixiao Gong, Charalampos Lazaris, Theodore Sakellaropoulos, Aurelie Lozano, Prabhanjan Kambadur, Panagiotis Ntziachristos, Iannis Aifantis, Aristotelis Tsirigos
Nature Communications, 9(1), p.542., 2018

Computational Approaches to Behavior Analysis in Psychiatry
Corcoran, Cheryl M and Cecchi, Guillermo A
Neuropsychopharmacology 43(1), 225, Nature Publishing Group, 2018

Data-driven Modeling of Hemodynamics and its Role on Thrombus Size and Shape in Aortic Dissections
A. Yazdani, H. Li, M.R. Bersi, P. Di Achille, J. Insley, J.D. Humphrey, G.E. Karniadakis
Scientific Reports 8(1), 2515, Nature Publishing Group, 2018

DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes
R. Giancarlo, S.E. Rombo, F. Utro
Theoretical Computer Science, 2018

Essential Simplices in Persistent Homology and Subtle Admixture Detection
S. Basu, F. Utro, L. Parida
18th International Workshop on Algorithms in Bioinformatics (WABI 2018), pp. 14:1-14:10


Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
McIntyre, Alexa BR and Ounit, Rachid and Afshinnekoo, Ebrahim and Prill, Robert J and H{\'e}naff, Elizabeth and Alexander, Noah and Minot, Samuel S and Danko, David and Foox, Jonathan and Ahsanuddin, Sofia and others
Genome biology 18(1), 182, BioMed Central, 2017

Classification of Cardiovascular Proteins Involved in Coronary Atherosclerosis and Heart Failure Using Watson’s Cognitive Computing Technology
Ruff, Christian T and Lacoste, Alix and Nordio, Francesco and Fanola, Christina L and Silverman, Michael G and Argentinis, Elenee and Spangler, Scott and Sabatine, Marc S
2017 - Am Heart Assoc, Am Heart Assoc

Artificial intelligence in neurodegenerative disease research: use of IBM Watson to identify additional RNA-binding proteins altered in amyotrophic lateral sclerosis
Bakkar, Nadine and Kovalik, Tina and Lorenzini, Ileana and Spangler, Scott and Lacoste, Alix and Sponaugle, Kyle and Ferrante, Philip and Argentinis, Elenee and Sattler, Rita and Bowser, Robert
Acta neuropathologica, 1--21, Springer, 2017

Alignment-free inference of hierarchical and reticulate phylogenomic relationships
Bernard, Guillaume and Chan, Cheong Xin and Chan, Yao-ban and Chua, Xin-Yi and Cong, Yingnan and Hogan, James M and Maetschke, Stefan R and Ragan, Mark A
Briefings in bioinformatics, 2017

A colored graph approach to the perfect phylogeny with persistent characters
Bonizzoni P., Carrieri A.P., Della Vedova G., Trucco, G.
Theoretical Computer Science658, 60-73, 2017

Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations
Bell, David R and Cheng, Sara Y and Salazar, Heber and Ren, Pengyu
Scientific Reports7, 45812, Nature Publishing Group, 2017

A communal catalogue reveals Earth’s multiscale microbial diversity
Thompson, Luke R and Sanders, Jon G and McDonald, Daniel and Amir, Amnon and Ladau, Joshua and Locey, Kenneth J and Prill, Robert J and Tripathi, Anupriya and Gibbons, Sean M and Ackermann, Gail and others
Nature 551(7681), Nature Publishing Group, 2017

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City
Maritz, Julia M and Sullivan, Steven A and Prill, Robert J and Aksoy, Emre and Scheid, Paul and Carlton, Jane M
PloS one 12(4), e0175527, Public Library of Science, 2017

Analysis of blood-based gene expression in idiopathic Parkinson disease
Shamir, Ron and Klein, Christine and Amar, David and Vollstedt, Eva-Juliane and Bonin, Michael and Usenovic, Marija and Wong, Yvette C and Maver, Ales and Poths, Sven and Safer, Hershel and others
Neurology 89(16), 1676--1683, AAN Enterprises, 2017

Learning stable and predictive network-based patterns of schizophrenia and its clinical symptoms
Mina Gheiratmand, Irina Rish, Guillermo A Cecchi, Matthew RG Brown, Russell Greiner, Pablo I Polosecki, Pouya Bashivan, Andrew J Greenshaw, Rajamannar Ramasubbu, Serdar M Dursun
npj Schizophrenia 3(1), 22, Nature Publishing Group, 2017

Wafer-scale integration of sacrificial nanofluidic chips for detecting and manipulating single DNA molecules
Wang, Chao and Nam, Sung-Wook and Cotte, John M and Jahnes, Christopher V and Colgan, Evan G and Bruce, Robert L and Brink, Markus and Lofaro, Michael F and Patel, Jyotica V and Gignac, Lynne M and others
Nature communications8, 14243, Nature Publishing Group, 2017

Application of genome wide association and genomic prediction for improvement of cacao productivity and resistance to black and frosty pod diseases
J. Alberto Romero Navarro, Wilbert Wilbert Phillips-Mora, Adriana Arciniegas-Leal, Allan Mata-Quiros, Niina Haiminen, Guiliana Mustiga, Donald Livingstone III, Harm Van bakel, David Kuhn, Laxmi Parida, Andrew Kasarskis and Juan Carlos Motamayor
Frontiers in Plant Science, 2017

Broken flow symmetry explains the dynamics of small particles in deterministic lateral displacement arrays
Kim, Sung-Cheol and Wunsch, Benjamin H and Hu, Huan and Smith, Joshua T and Austin, Robert H and Stolovitzky, Gustavo
Proceedings of the National Academy of Sciences, 201706645, National Acad Sciences

Automated Detection of Malarial Retinopathy in Digital Fundus Images for Improved Diagnosis in Malawian Children with Clinically Defined Cerebral Malaria
Joshi, Vinayak and Agurto, Carla and Barriga, Simon and Nemeth, Sheila and Soliz, Peter and MacCormick, Ian J and Lewallen, Susan and Taylor, Terrie E and Harding, Simon P
Scientific Reports7, Nature Publishing Group, 2017

Bio-inspired silicon nanospikes fabricated by metal-assisted chemical etching for antibacterial surfaces
Hu, Huan and Siu, Vince S and Gifford, Stacey M and Kim, Sungcheol and Lu, Minhua and Meyer, Pablo and Stolovitzky, Gustavo A
Applied Physics Letters 111(25), 253701, AIP Publishing, 2017

Host phenotype prediction from differentially abundant microbes using RoDEO
A.P. Carrieri*, N. Haiminen*, L. Parida
In: Bracciali A., Caravagna G., Gilbert D., Tagliaferri R. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics, Lecture Notes in Computer Science, pp. 27-41, Springer, 2017

Characterizing human prefrontal cortex representations with fMRI
A. Bhandari, M. Rigotti, C. Gagne, S. Fusi, D. Badre
Society for Neuroscience Meeting (Washington DC), 2017

Predicting human olfactory perception from chemical features of odor molecules
A. Keller, R.C. Gerkin, Y. Guan, A. Dhurandhar, G. Turu, B. Szalai, J.D. Mainland, Y. Ihara, C. Wen Yu, R. Wolfinger, C. Vens, L. Schietgat, K. De Grave, R. Norel, DREAM Cons., G. Stolovitzky, G.A. Cecchi, L. Vosshal, P. Meyer
Science, 10.1126/science.aal2014, 2017

CuII(atsm) improves the neurological phenotype and survival of SOD1G93A mice and selectively increases enzymatically active SOD1 in the spinal cord.
Hilton JB, Mercer SW, Lim NKH, Faux NG, Buncic G, Beckman JS, Roberts BR, Donnelly PS, White AR, Crouch PJ.
Science Reports 7(42292), 2017

Emergence of Alternative Structures in Amyloid Beta 1-42 Monomeric Landscape by N-terminal Hexapeptide Amyloid Inhibitors
Chakraborty, Srirupa and Das, Payel
Scientific reports 7(1), 9941, Nature Publishing Group, 2017

Autism Classification Using Brain Functional Connectivity Dynamics and Machine Learning
Ravi Tejwani, Adam Liska, Hongyuan You, Jenna Reinen, Payel Das
NIPS Big Neuro Workshop, 2017

Structural perturbations on huntingtin N17 domain during its folding on 2D-nanomaterials
Leili Zhang, Mei Feng, Ruhong Zhou, Binquan Luan
Nanotechnology 28(35), 354001, IOP Publishing, 2017


Response of single bacterial cells to stress gives rise to complex history dependence at the population level
Mathis, Roland and Ackermann, Martin
Proceedings of the National Academy of Sciences 113(15), 4224--4229, National Acad Sciences, 2016

Homology model and ligand binding interactions of the extracellular domain of the human a4b2 nicotinic acetylcholine receptor
Shu Mao, Hui Wen Ng, Michael Orr, Heng Luo, Hao Ye, Weigong Ge, Weida Tong, Huixiao Hong
Journal of Biomedical Science and Engineering 9(01), 41, Scientific Research Publishing, 2016

Automated evolutionary optimization of ion channel conductances and kinetics in models of young and aged rhesus monkey pyramidal neurons
Rumbell, Timothy H and Dragulji{'c}, Danel and Yadav, Aniruddha and Hof, Patrick R and Luebke, Jennifer I and Weaver, Christina M
Journal of Computational Neuroscience 41(1), 65--90, Springer, 2016

HLA-B*59:01: a marker for Stevens--Johnson syndrome/toxic epidermal necrolysis caused by methazolamide in Han Chinese
Fanping Yang, Jiekun Xuan, Junyi Chen, Hailei Zhong, Heng Luo, Peng Zhou, Xinghuai Sun, Lin He, Sheng-an Chen, Zhihao Cao, Xiaoqun Luo, Qinghe Xing
The pharmacogenomics journal 16(1), 83--87, Nature Publishing Group, 2016

Large-scale cortical models towards understanding relationship between brain structure abnormalities and cognitive deficit
Yasunori Yamada
the 25 th Annual Computational Neuroscience Meetihg (CNS-16), 2016

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
Sieberts, Solveig K and Zhu, Fan and Garc{'i}a-Garc{'i}a, Javier and Stahl, Eli and Pratap, Abhishek and Pandey, Gaurav and Pappas, Dimitrios and Aguilar, Daniel and Anton, Bernat and Bonet, Jaume and others
Nature communications7, Nature Research, 2016

Crowdsourcing biomedical research: leveraging communities as innovation engines
Saez-Rodriguez, Julio and Costello, James C and Friend, Stephen H and Kellen, Michael R and Mangravite, Lara and Meyer, Pablo and Norman, Thea and Stolovitzky, Gustavo
Nature Reviews Genetics 17(8), 470--486, Nature Publishing Group, 2016

Predicting Alzheimer' s disease from a blood-based biomarker profile: a 54 month follow up
Burnham SC, Rowe CC, Baker D, Bush AI, Doecke JD, Faux NG, Laws SM, Martins RN, Maruff P, Macaulay S, Rainey-Smith S, Savage G, Ames D, Masters CL, Wilson W, Villemagne VL
Neurology 87(11), 1093-1101, 2016

Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins
Waks, Zeev and Weissbrod, Omer and Carmeli, Boaz and Norel, Raquel and Utro, Filippo and Goldschmidt, Yaara
Scientific Reports6, Nature Publishing Group, 2016

Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins
Z. Waks, O. Weissbrod, B. Carmeli, R. Norel, F. Utro, Y. Goldschmidt
Scientific Reports 6, 38988, Nature Publishing Group, 2016

Different states of synaptotagmin regulate evoked versus spontaneous release
Hua Bai, Renhao Xue, Huan Bao, Leili Zhang, Arun Yethiraj, Qiang Cui, Edwin R Chapman
Nature communications7, 10971, Nature Publishing Group, 2016

Nanoscale lateral displacement arrays for the separation of exosomes and colloids down to 20 nm
B. H. Wunsch*, J. T. Smith*, S. M. Gifford, C. Wang, M. Brink, R. L. Bruce, R. H. Austin, G. Stolovitzky, Y. Astier, * Equal contribution
Nature Nanotechnology11, 936-940, 2016

Cortico-hippocampal contribution to the generation of contextual information
S. Bernardi, J. Munuera, M. Rigotti, S. Fusi, C. D. Salzman
Society for Neuroscience Meeting (San Diego CA), Society for Neuroscience, 2016

Neurophysiological mechanisms for representing abstract components of mental states
J. Munuera, M. Rigotti, S. Fusi, C. D. Salzman
Society for Neuroscience Meeting (San Diego CA), Society for Neuroscience, 2016

DPDR-CPI, a server that predicts Drug Positioning and Drug Repositioning via Chemical-Protein Interactome
Heng Luo, Ping Zhang, Xi Hang Cao, Dizheng Du, Hao Ye, Hui Huang, Can Li, Shengying Qin, Chunling Wan, Leming Shi, Lin He, Lun Yang
Scientific Reports6, 35996, Springer Nature, 2016

HLA-B*51:01 is strongly associated with clindamycin-related cutaneous adverse drug reactions
Ying Yang, Sheng-an Chen, Fanping Yang, Lirong Zhang, Gil Alterovitz, Huizhong Zhu, Jiekun Xuan, Xicheng Yang, Heng Luo, Jian Mu, Lin He, Xiaoqun Luo, Qinghe Xing
The Pharmacogenomics Journal0, 1-5, Springer Nature, 2016

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis
Noren, David P and Long, Byron L and Norel, Raquel and Rrhissorrakrai, Kahn and Hess, Kenneth and Hu, Chenyue Wendy and Bisberg, Alex J and Schultz, Andre and Engquist, Erik and Liu, Li and others
PLoS Comput Biol 12(6), e1004890, Public Library of Science, 2016

Inferring causal molecular networks: empirical assessment through a community-based effort
Hill, Steven M and Heiser, Laura M and Cokelaer, Thomas and Unger, Michael and Nesser, Nicole K and Carlin, Daniel E and Zhang, Yang and Sokolov, Artem and Paull, Evan O and Wong, Chris K and others
Nature methods 13(4), 310--318, Nature Publishing Group, 2016

sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides
Heng Luo, Hao Ye, Hui Wen Ng, Sugunadevi Sakkiah, Donna Mendrick, Huixiao Hong
Scientific Reports6, 32115, Nature Publishing Group, 2016


Performance evaluation of different encoding strategies for quantitative genetic trait prediction
Ogundijo, Oyetunji E and He, Dan and Parida, Laxmi
Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on, pp. 1--6

Noise-Driven Causal Inference in Biomolecular Networks
Prill, Robert J and Vogel, Robert and Cecchi, Guillermo A and Altan-Bonnet, Gr{'e}goire and Stolovitzky, Gustavo
PloS one 10(6), e0125777, Public Library of Science, 2015

Summary of the DREAM8 parameter estimation challenge: toward parameter identification for whole-cell models
Karr, Jonathan R and Williams, Alex H and Zucker, Jeremy D and Raue, Andreas and Steiert, Bernhard and Timmer, Jens and Kreutz, Clemens and Wilkinson, Simon and Allgood, Brandon A and Bot, Brian M and others
PLoS Comput Biol 11(5), e1004096, Public Library of Science, 2015

Variable-Selection Emerges on Top in Empirical Comparison of Whole-Genome Complex-Trait Prediction Methods
Haws, David C and Rish, Irina and Teyssedre, Simon and He, Dan and Lozano, Aurelie C and Kambadur, Prabhanjan and Karaman, Zivan and Parida, Laxmi
PloS one 10(10), e0138903, Public Library of Science, 2015

Functional consequences of age-related morphologic changes to pyramidal neurons of the rhesus monkey prefrontal cortex
Coskren, Patrick J and Luebke, Jennifer I and Kabaso, Doron and Wearne, Susan L and Yadav, Aniruddha and Rumbell, Timothy and Hof, Patrick R and Weaver, Christina M
Journal of Computational Neuroscience 38(2), 263--283, Springer, 2015

A platform for leveraging next generation sequencing for routine microbiology and public health use
Laura I Rusu, Kelly L Wyres, Matthias Reumann, Carlos Queiroz, Alexe Bojovschi, Tom Conway, Saurabh Garg, David J Edwards, Geoff Hogg, Kathryn E Holt
Health Information Science and Systems 3(1), 1, BioMed Central, 2015

Computational modeling of seizure dynamics using coupled neuronal networks: factors shaping epileptiform activity
Naze, Sebastien and Bernard, Christophe and Jirsa, Viktor
PLoS Comput Biol 11(5), e1004209, Public Library of Science, 2015

Surface curvature relation to protein adsorption for carbon-based nanomaterials
Gu, Zonglin and Yang, Zaixing and Chong, Yu and Ge, Cuicui and Weber, Jeffrey K and Bell, David R and Zhou, Ruhong
Scientific reports5, 10886, Nature Publishing Group, 2015

Topological Signatures for Population Admixture
Parida L., Utro F., Yorukoglu D., Carrieri A.P., David Kuhn D., Basu S.
In: Research in Computational Molecular Biology, RECOMB 2015, Lecture Notes in Computer Science, Teresa M. Przytycka (Ed.), pp. 261-275, Springer

Self-organization of computation in neural systems by interaction between homeostatic and synaptic plasticity
Sakyasingha Dasgupta, Christian Tetzlaff, Tomas Kulvicius, Florentin Woergoeter
24th Annual Computational Neuroscience Meeting: CNS*2015, pp. O5, BioMed Central Ltd

Extensive capsule locus variation and large-scale genomic recombination within the Klebsiella pneumoniae clonal group 258.
Wyres, K.L., Gorrie, C., Edwards, D.J., Wertheim, H.F.L., Hsu, L.Y., Van Kinh, N., Zadoks, R., Baker, S. and Holt, K.E.
Genome Biology and Evolution 7(5), 1267-1279, 2015

Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments
Maria Anna Rapsomaniki, Eugenio Cinquemani, Nickolaos Nikiforos Giakoumakis, Panagiotis Kotsantis, John Lygeros, Zoi Lygerou
Bioinformatics 31(3), 355--362, 2015

An Efficient Nonlinear Regression Approach for Genome-Wide Detection of Marginal and Interacting Genetic Variations
S. Lee, A. Lozano, P. Kambadur, and E. P. Xing
19th International Conference on Research in Computational Molecular Biology (RECOMB 2015)

Development and validation of a gene expression tumour classifier for cancer of unknown primary
Richard W Tothill, Fan Shi, Lisa Paiman, Justin Bedo, Adam Kowalczyk, Linda Mileshkin, Evangeline Buela, Robert Klupacs, David Bowtell, Keith Byron
Pathology-Journal of the RCPA 47(1), 7--12, LWW, 2015

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis
R. Giancarlo, D. Scaturro, F. Utro
Computer Methods and Programs in Biomedicine, Elsevier, 2015

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge
K. Rhrissorrakrai, V. Belcastro, E. Bilal, R. Norel, C. Poussin, C. Mathis, R. H. Dulize, N. V. Ivanov, L. Alexopoulos, J. J. Rice, M. C. Peitsch, G. Stolovitzky, P. Meyer, J. Hoeng
Bioinformatics 31(4), 471--483, 2015

A crowd-sourcing approach for the construction of species-specific cell signaling networks
E. Bilal, T. Sakellaropoulos, I. N. Melas, D. E. Messinis, V. Belcastro, K. Rhrissorrakrai, P. Meyer, R. Norel, A. Iskandar, E. Blaese, J. J. Rice, M. C. Peitsch, J. Hoeng, G. Stolovitzky, L. G. Alexopoulos, C. Poussin
Bioinformatics 31(4), 484--491, 2015

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge
M. Biehl, P. Sadowski, G. Bhanot, E. Bilal, A. Dayarian, P. Meyer, R. Norel, K. Rhrissorrakrai, M. D. Zeller, S. Hormoz
Bioinformatics 31(4), 453--461, 2015

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge
A. Dayarian, R. Romero, Z. Wang, M. Biehl, E. Bilal, S. Hormoz, P. Meyer, R. Norel, K. Rhrissorrakrai, G. Bhanot, F. Luo, A. L. Tarca
Bioinformatics 31(4), 462--470, 2015

Inter-species pathway perturbation prediction via data-driven detection of functional homology
C. Hafemeister, R. Romero, E. Bilal, P. Meyer, R. Norel, K. Rhrissorrakrai, R. Bonneau, A. L. Tarca
Bioinformatics 31(4), 501--508, 2015

Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression
R. Kuffner, N. Zach, R. Norel, J. Hawe, D. Schoenfeld, L. Wang, G. Li, L. Fang, L. Mackey, O. Hardiman, M. Cudkowicz, A. Sherman, G. Ertaylan, M. Grosse-Wentrup, T. Hothorn, J. van Ligtenberg, J. H. Macke, T. Meyer, B. Scholkopf, L. Tran, R. Vaughan, G. S
Nat. Biotechnol. 33(1), 51--57, 2015

Host Trait Prediction of Metagenomic Data for Topology-based Visualization
L. Parida, N. Haiminen, D. Haws, J. Suchodolski
Lecture Notes in Computer Science 8956, 134-149 , Springer, 2015

High performance computing enabling exhaustive analysis of higher order single nucleotide polymorphism interaction in Genome Wide Association Studies
Benjamin Goudey, Mani Abedini, John L Hopper, Michael Inouye, Enes Makalic, Daniel F Schmidt, John Wagner, Zeyu Zhou, Justin Zobel, Matthias Reumann
Health Information Science and Systems 3(1), 1, BioMed Central, 2015


Resolving ambiguity in genome assembly using high performance computing
Mahtab Mirmomenia, Thomas Conwaya, Matthias Reumannb, Justin Zobelc
Australasia’s big data in biomedicine \& healthcare conference, 36, 2014

The species translation challenge—a systems biology perspective on human and rat bronchial epithelial cells
Carine Poussin, Carole Mathis, Leonidas G Alexopoulos, Dimitris E Messinis, R\'emi HJ Dulize, Vincenzo Belcastro, Ioannis N Melas, Theodore Sakellaropoulos, Kahn Rhrissorrakrai, Erhan Bilal, others
Scientific Data1, Nature Publishing Group, 2014

Inter-species Inference of Gene Set Enrichment in Lung Epithelial Cells from Proteomic and Large Transcriptomic Data Sets
Sahand Hormoz, Gyan Bhanot, Michael Biehl, Erhan Bilal, Pablo Meyer, Raquel Norel, Kahn Rhrissorrakrai, Adel Dayarian
Bioinformatics, btu569, Oxford Univ Press, 2014

Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors
Tatiana Tatarinova, Bilal Salih, Jennifer Dien Bard, Irit Cohen, Alexander Bolshoy
Hindawi, 2014

The Challenges of Systems Biology
Pablo Meyer and Guillermo A. Cecchi
Practical Applications of Sparse Modeling, pp. 7-15, MIT Press, 2014

Reliability Estimation and Enhancement via Spatial Smoothing in Sparse fMRI Modeling
Carroll, Melissa K., Guillermo A. Cecchi, Irina Rish, Rahul Garg, Marwan Baliki, and A. Vania Apkarian
Practical Applications of Sparse Modeling, pp. 123-150, MIT Press, 2014

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia
Thomas Trimarchi, Erhan Bilal, Panagiotis Ntziachristos, Giulia Fabbri, Riccardo Dalla-Favera, Aristotelis Tsirigos, Iannis Aifantis
Cell 158(3), 593--606, Elsevier, 2014

Comparative exomics of Phalaris cultivars under salt stress
N. Haiminen, M. Klaas, Z. Zhou, F. Utro, P. Cormican, T. Didion, C. Sig Jensen, C.E. Mason, S. Barth, L. Parida
BMC Genomics 15(Suppl 6), S18, BioMed Central Ltd, 2014

Redundancy-weighting for better inference of protein structural features
Chen Yanover, Natalia Vanetik, Michael Levitt, Rachel Kolodny, Chen Keasar
Bioinformatics, btu242, Oxford Univ Press, 2014

BAC Sequencing Using Pooled Methods
CA Saski, FA Feltus, L Parida, N Haiminen
Bacterial Artificial Chromosomes, in Methods in Molecular Biology 1227(3), Springer, 2014

Practical Applications of Sparse Modeling
A book edited by I. Rish, G. Cecchi, A.C. Lozano, A. Niculecu-Mizil
MIT Press, 2014

Best-Fit in Linear Time for Non-generative Population Simulation
Niina Haiminen, Claude Lebreton, Laxmi Parida
Algorithms in Bioinformatics, in Lecture Notes in Computer Science 8701, 247-262, Springer, 2014

Augmented Human: Human OS for Improved Mental Function
Steve Heisig, Guillermo A. Cecchi, Ravi Rao and Irina Rish
AAAI'14 Workshop on Cognitive Computing for Augmented Human Intelligence, 2014

A Window into the Intoxicated Mind? Speech as an Index of Psychoactive Drug Effects
Bedi G, Cecchi G A, Fernandez Slezak D, Carrillo F, Sigman M, de Wit H
Neuropsychopharmacology, 2014

Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome
Annelyse Thevenin, Liat Ein-Dor, Michal Ozery-Flato, Ron Shamir
Nucleic acids research, gku667, Oxford Univ Press, 2014


Multi-step loading of human minichromosome maintenance proteins in live human cells
Ioanna-Eleni Symeonidou, Panagiotis Kotsantis, Vassilis Roukos, Maria Anna Rapsomaniki, Hernán E. Grecco, Philippe Bastiaens, Stavros Taraviras, Zoi Lygerou
Journal of Biological Chemistry 288(50), 35852--35867, 2013

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
P. Meyer, G. Siwo, D. Zeevi, E. Sharon, R. Norel, E. Segal, G. Stolovitzky, G. Siwo, A. K. Rider, A. Tan, R. S. Pinapati, S. Emrich, N. Chawla, M. T. Ferdig, Y. A. Tung, Y. S. Chen, M. J. Chen, C. Y. Chen, J. M. Knight, S. M. Sahraeian, M. S. Esfahani, R.
Genome Res. 23(11), 1928--1937, 2013

The Three Steps of Clustering In The Post-Genomic Era
R. Giancarlo, G. Lo Bosco, L. Pinello, F. Utro
Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data, pp. 519--556, Wiley Online Library, 2013

MINT: Mutual Information based Transductive Feature Selection for Genetic Trait Prediction
D. He, I. Rish, D. Haws, S.Teyssedre, Z. Karaman, L. Parida
The Seventh International Workshop on Machine Learning in Systems Biology (MLSB 2013),

Functional MRI Analysis with Sparse Models
I. Rish
Invited paper at NECTAR track of the European Conference on Machine Learning (ECML-2013)

sbv IMPROVER Diagnostic Signature Challenge: Design and results
Kahn Rhrissorrakrai, J Jeremy Rice, Stephanie Boue, Marja Talikka, Erhan Bilal, Florian Martin, Pablo Meyer, Raquel Norel, Yang Xiang, Gustavo Stolovitzky, others
Systems Biomedicine 1(4), 3--14, Landes Bioscience, 2013

Polymorphisms in the F8 gene and MHC-II variants as risk factors for the development of inhibitory anti-factor VIII antibodies during the treatment of hemophilia A: a computational assessment
Gouri Shankar Pandey, Chen Yanover, Tom E Howard, Zuben E Sauna
PLoS computational biology 9(5), e1003066, Public Library of Science, 2013

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color
J.C. Motamayor*, K. Mockaitis*, J. Schmutz*, N. Haiminen*, D. Livingstone, O.E. Cornejo, S. Findley, P. Zheng, F. Utro, S. Royaert, C. Saski, J. Jenkins, R. Podicheti, M. Zhao, B. Scheffler, others
Genome Biology 14(6), R53, BioMed Central Ltd, 2013
Abstract   IBM 100 Icons of Progress:

iXora: Exact haplotype inferencing and trait association
F. Utro, N. Haiminen, D. Livingstone, O.E. Cornejo, S. Royaert, R. Schnell, J.C. Motamayor, D.N. Kuhn, L. Parida
BMC Genetics 14(1), 48, BioMed Central Ltd, 2013

BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters
H. Huang, S. Tata, R.J. Prill
Bioinformatics 29(1), 135--136, Oxford Univ Press, 2013

Sum of parts is greater than the whole: inference of common genetic history of populations
F. Utro, M. Pybus, L. Parida
BMC Genomics 14(Suppl 1), S10, BioMed Central Ltd, 2013

Evaluation of methods for modeling transcription factor sequence specificity
M.T. Weirauch, A. Cote, R. Norel, M. Annala, Y. Zhao, T.R. Riley, J. Saez-Rodriguez, T. Cokelaer, A. Vedenko, S. Talukder, others
Nature biotechnology, Nature Publishing Group, 2013

Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition
Sarah C Atkinson, Con Dogovski, Matthew T Downton, Peter E Czabotar, Renwick CJ Dobson, Juliet A Gerrard, John Wagner, Matthew A Perugini
Plant molecular biology 81(4-5), 431--446, Springer, 2013


easyFRAP: an interactive, easy-to-use tool for qualitative and quantitative analysis of FRAP data
Maria Anna Rapsomaniki, Panagiotis Kotsantis, Ioanna-Eleni Symeonidou, Nickolaos-Nikiforos Giakoumakis, Stavros Taraviras, Zoi Lygerou
Bioinformatics 28(13), 1800--1801, 2012

Wisdom of crowds for robust gene network inference
D. Marbach, J.C. Costello, R. Kuffner, N.M. Vega, R.J. Prill, D.M. Camacho, K.R. Allison, The DREAM5 Consortium, M. Kellis, J.J. Collins, G. Stolovitzky
Nature Methods, Nature Publishing Group, 2012

Levodopa and the feedback process on set-shifting in parkinson's disease
W.L. Au, J. Zhou, P. Palmes, Y.Y. Sitoh, L. Tan, J.C. Rajapakse
Human brain mapping, Wiley Online Library, 2012

The folding transition state of Protein L is extensive with non-native interactions (and not small and polarized)
T.Y. Yoo, A. Adhikari, Z. Xia, T. Huynh, K.F. Freed, R. Zhou, T.R. Sosnick
Journal of Molecular Biology, Elsevier, 2012

Stability-Based Model Selection for High Throughput Genomic Data: An Algorithmic Paradigm
R. Giancarlo, F. Utro
Artificial Immune Systems, pp. 260--270, Springer, 2012

GenomicTools: an open source platform for developing high-throughput analytics in genomics
A. Tsirigos, N. Haiminen, E. Bilal, F. Utro
Open source software in life science research: Practical solutions to common challenges in the pharmaceutical industry and beyond, Woodhead Publishing Series in Biomedicine No. 16, 2012

ARG-based genome-wide analysis of cacao cultivars
F. Utro, O.E. Cornejo, D. Livingstone, J.C. Motamayor, L. Parida
BMC Bioinformatics 13(Suppl 19), S17, BioMed Central Ltd, 2012

Slowing and controlling the translocation of DNA in a solid-state nanopore
B. Luan, G Stolovitzky, G Martyna
Nanoscale 4(4), 1068-1077, The Royal Society of Chemistry, 2012

Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis
M. Rodríguez-Martínez, A. Corradin, U. Klein, M.J. Alvarez, G.M. Toffolo, B. di Camillo, A. Califano, G.A. Stolovitzky
Proceedings of the National Academy of Sciences 109(7), 2672-2677, 2012

Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol
B. Luan, D. Wang, R. Zhou, S. Harrer, H. Peng, G. Stolovitzky
Nanotechnology 23(45), 455102, IOP Publishing, 2012

Crystal, solution and in silico structural studies of dihydrodipicolinate synthase from the common grapevine
Sarah C Atkinson, Con Dogovski, Matthew T Downton, F Grant Pearce, Cyril F Reboul, Ashley M Buckle, Juliet A Gerrard, Renwick CJ Dobson, John Wagner, Matthew A Perugini
PLoS One 7(6), e38318, Public Library of Science, 2012

Enzymology of bacterial lysine biosynthesis
Con Dogovski, SC Atkinson, SR Dommaraju, M Downton, L Hor, S Moore, JJ Paxman, MG Pevereli, TW Qiu, M Reumann, others
Biochemistry, pp. 225--262, InTech, 2012

In Silico Cardiac Risk Assessment in Patients With Long QT SyndromeType 1: Clinical Predictability of Cardiac Models
Ryan Hoefen, Matthias Reumann, Ilan Goldenberg, Arthur J Moss, O Jin, Yiping Gu, Scott McNitt, Wojciech Zareba, Christian Jons, Jorgen K Kanters, others
Journal of the American College of Cardiology 60(21), 2182--2191, Am Coll Cardio Found, 2012

Exploiting the brainÿ s network structure in identifying ADHD subjects
Soumyabrata Dey, A.Ravishankar Rao, Mubarak Shah
Frontiers in Systems Neuroscience, Frontiers, 2012

A computational model of early visual cortex using konio-cellular pathway projections
A. Ravishankar Rao, Youping Xiao
International Joint Conference on Neural Networks, pp. 1-8, IEEE, 2012

Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data
D. He, B. Han, E. Eskin
Research in Computational Molecular Biology, pp. 64--78, 2012

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification
P. Meyer, J. Hoeng, J. J. Rice, R. Norel, J. Sprengel, K. Stolle, T. Bonk, S. Corthesy, A. Royyuru, M. C. Peitsch, G. Stolovitzky
Bioinformatics 28(9), 1193--1201, 2012

Discovering Patterns in Gene Order
Laxmi Parida, Niina Haiminen
Evolutionary Genomics, in Methods in Molecular Biology 855(3), 431-455, Springer, 2012

GenomicTools: a computational platform for developing high-throughput analytics in genomics
A. Tsirigos, N. Haiminen, E. Bilal, F. Utro
Bioinformatics 28(2), 282--283, Oxford University Press, 2012

Textual data compression in computational biology: Algorithmic techniques
R Giancarlo, D Scaturro, F Utro
Computer Science Review, Elsevier, 2012

Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia
P. Ntziachristos, A. Tsirigos, P. Van Vlierberghe, J. Nedjic, T. Trimarchi, M. Sol Flaherty, D. Ferres-Marco, V. da Ros, Z. Tang, J. Siegle, others
Nature medicine 18(2), 298--303, Nature Publishing Group, 2012

Network-Induced Classification Kernels for Gene Expression Profile Analysis
O. Lavi, G. Dror, R. Shamir
Journal of Computational Biology 19(6), 694-709, Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA, 2012

Circulating branched-chain amino acid concentrations are associated with obesity and future insulin resistance in children and adolescents
SE McCormack, O. Shaham, MA McCarthy, AA Deik, TJ Wang, RE Gerszten, CB Clish, VK Mootha, SK Grinspoon, A. Fleischman
Pediatric Obesity, Wiley Online Library, 2012


Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers
Chen Yanover, Philip Bradley
Nucleic acids research 39(11), 4564--4576, Oxford Univ Press, 2011

Machine learning competition in immunology--Prediction of HLA class I binding peptides
Guang Lan Zhang, Hifzur Rahman Ansari, Phil Bradley, Gavin C Cawley, Tomer Hertz, Xihao Hu, Nebojsa Jojic, Yohan Kim, Oliver Kohlbacher, Ole Lund, others
Journal of immunological methods 374(1), 1--4, Elsevier, 2011

Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA
Joseph D Shih, Zeev Waks, Nancy Kedersha, Pamela A Silver
Nucleic acids research 39(17), 7740--7749, Oxford Univ Press, 2011

Cell-to-cell variability of alternative RNA splicing
Zeev Waks, Allon M Klein, Pamela A Silver
Molecular systems biology 7(1), Wiley Online Library, 2011

Molecular profiling of a lethal tumor microenvironment, as defined by stromal caveolin-1 status in breast cancers.
Agnieszka K Witkiewicz, Jessica Kline, Maria Queenan, Jonathan R Brody, Aristotelis Tsirigos, S Pavlides, F Sotgia, MP Lisanti
Cell cycle (Georgetown, Tex.) 10(11), 2011

Structural Properties of the Caenorhabditis elegans Neuronal Network
L. R. Varshney, B. L. Chen, E. Paniagua, D. H. Hall, and D. B. Chklovskii
PLoS Computational Biology 7(2), e1001066, Public Library of Science, 2011

Informational Limits of Neural Circuits
L. R. Varshney and D. Shah
Proceedings of the Forty-Ninth Annual Allerton Conference on Communication, Control, and Computing, pp. 1757-1763, 2011

Neural Reconstruction with Approximate Message Passing (NeuRAMP)
A. K. Fletcher, S. Rangan, L. R. Varshney, and A. Bhargava
Proceedings of the Twenty-Fifth Annual Conference on Neural Information Processing Systems (NIPS), 2011

Speeding up the Consensus Clustering methodology for microarray data analysis
R Giancarlo, F Utro
Algorithms for Molecular Biology 6(1), 1, BioMed Central Ltd, 2011

J Bernauer, S Flores, X Huang, S Shin, R Zhou
Pacific Symposium on Biocomputing, pp. 80, 2011


A novel pipeline method for the preprocessing of Mass spectrometry proteomics data
Maria Anna V. Rapsomaniki, Panagiotis G. Zerefos, Konstantinos Theofilatos, Spiridon D. Likothanassis, Athanasios K. Tsakalidis, Seferina P. Mavroudi
Information Technology and Applications in Biomedicine (ITAB), 2010 10th IEEE International Conference on, pp. 1--4, IEEE

Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures (Extended Abstract)
D Corona, V Di Benedetto, A Gabriele, R Giancarlo, F Utro
Structure Discovery in Biology: Motifs, Networks & Phylogenies, 2010

Plugging into Proteins: Poisoning Protein Function by a Hydrophobic Nanoparticle
G Zuo, Q Huang, G Wei, R Zhou, H Fang
ACS nano, 1027--1030, ACS Publications, 2010

A New Method to Reconstruct Recombination Events at a Genomic Scale
Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit, The Genographic Consortium
PLoS Comput Biol 6(11), e1001010, Public Library of Science, 2010

An Evaluation of Feature Sets and Sampling Techniques for De-identification of Medical Records
James Gardner, Li Xiong, Fusheng Wang, Andrew Post, Joel Saltz, Tyrone Grandison
1st ACM International Health Informatics Symposium, ACM, 2010

The Quality Preserving Database: A Computational Framework for Encouraging Collaboration, Enhancing Power and Controlling False Discovery
E Aharoni, H Neuvirth, S Rosset
IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics, Published by the IEEE Computer Society, 2010

Recombinomics: population genomics from a recombination perspective
Asif Javed, Laxmi Parida
C3S2E '10: Proceedings of the Third C* Conference on Computer Science and Software Engineering, pp. 129--137, ACM, 2010

Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study)
M. Zazzi, R. Kaiser, A. Sonnerborg, D. Struck, A. Altmann, M. Prosperi, M. Rosen-Zvi, A. Petroczi, Y. Peres, E. Schulter, C. Boucher, F. Brun-Vezinet, R. Harigan, L. Morris, M. Obermeier, C. F. Perno, R. Shafer, A. Vandamme, K. van Laethem, A. Wensing, T.
HIV Medicine pp. 1468-1293, 2010

Single Mutation Effects on Conformational Change and Membrane Deformation of Influenza Hemagglutinin Fusion Peptides
J Li, P Das, R Zhou
The Journal of Physical Chemistry B, 6459--6464, ACS Publications, 2010

Patient-Centric Privacy: Envisioning Collaboration Between Payers, Providers & Patients With The Patient At The Core
Tyrone W A Grandison
the 6th International Conference on Collaborative Computing: Networking, Applications and Worksharing, pp. 1--5, IEEE, 2010

Simulating Collaboration From Multiple, Potentially Non-Collaborative Healthcare Systems To Create A Single View of a Patient
Tyrone W A Grandison, Varun Bhgwan, Daniel Gruhl
the 6th International Conference on Collaborative Computing: Networking, Applications and Worksharing, IEEE, 2010

Antiretroviral Therapy Optimisation without Genotype Resistance
M. CF Prosperi, M. Rosen-Zvi, A. Altmann, M. Zazzi, S. Di Giambenedetto, R. Kaiser, E. Schulter, D. Struck, P. Sloot, D. A. van de Vijver, A. Vandamme, A. Sonnerborg
PLoS ONE 5(10), e13753, Public Library of Science San Francisco, USA, 2010

Medical Content-Based Retrieval for Clinical Decision Support
Tanveer Syeda-Mahmood, James Duncan, Fei Wang, Jayashree Kalpathy-Cramer
Springer-Verlag Berlin Heidelberg, 2010

Cardiac disease detection from echocardiogram using edge filtered scale-invariant motion features
Ritwik Kumar, Fei Wang, David Beymer, Tanveer Syeda-Mahmood
Computer Vision and Pattern Recognition Workshops (CVPRW), 2010 IEEE Computer Society Conference on, pp. 162--169

AALIM: A Cardiac Clinical Decision Support System Powered By Advanced Multi-modal Analytics
D Gruhl, A Amir, D Beymer, G Julia, H Greenspan, A Hobbs, K Pohl, T Syeda-Mahmood, J Terdiman, F Wang
International Medical Informatics Conference (MedInfo), 2010

Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls
J A Morrone, R Zhou, BJ Berne
Journal of Chemical Theory and Computation, 1465, ACS Publications, 2010

Unlocking Medical Archives with Multi-Modal Content to Deliver Enhanced Analytics
K Brannon, S Doraiswamy, T Grandison
13th World Congress on Medical and Health Informatics (MEDINFO), 2010

Regulatory Compliance and the Correlation to Privacy Protection in Healthcare
Bhatti R T Grandison
International Journal of Computational Models and Algorithms in Medicine, IGI Global, 2010

Improving Security Policy Coverage in Healthcare
Grandison T R Bhatti
Certification and Security in Health-Related Web applications: Concepts and Solutions, IGI Global, 2010

Enabling Next-Gen Healthcare Services through Evidence-based Medical Integration and Analytics
Gruhl D V Bhagwan T Grandison
19th Annual Frontiers in Service Conference, Citeseer, 2010

WISE Healthcare: Enabling Medical Collaboration in a Web 2.0 World
Grandison T, E Kandogan, V Bhagwan
13th World Congress on Medical and Health Informatics (MEDINFO), Citeseer, 2010

Enabling the Health Internet - Market-Friendly Information Extraction of Online Healthcare Sources
C Grant, T Grandison, A Alba
13th World Congress on Medical and Health Informatics (MEDINFO), Citeseer, 2010

Healthcare Chains - Enabling Application and Data Privacy Controls for Healthcare Information System
E Omran, T Grandison, S A Almaati
13th World Congress on Medical and Health Informatics (MEDINFO), Citeseer, 2010

Privacy for Healthcare Social Networks
E M Maximilien, T Grandison
13th World Congress on Medical and Health Informatics (MEDINFO), Citeseer, 2010

Different sets of QTLs influence fitness variation in yeast
G H Romano, Y Gurvich, O Lavi, I Ulitsky, R Shamir, M Kupiec
Molecular Systems Biology 6(1), Nature Publishing Group, 2010

Towards a rigorous assessment of systems biology models: The DREAM3 challenges
R J Prill, D Marbach, J Saez-Rodriguez, P K Sorger, L G Alexopoulos, X Xue, N D Clarke, G Altan-Bonnet, G Stolovitzky
PLoS ONE 5(2), e9202, Public Library of Science, 2010

Revealing strengths and weaknesses of methods for gene network inference
D Marbach, R J Prill, T Schaffter, C Mattiussi, D Floreano, G Stolovitzky
Proc Natl Acad Sci U S A 107(14), 6286, 2010

Temporal Graphical Models for Cross-Species Gene Regulatory Network Discovery
Y Liu, A Niculescu-Mizil, A Lozano, Y Lu
International conference on Computational Systems Bioinformatics (CSB), 2010

Towards a rigorous assessment of systems biology models: the DREAM3 challenges.
Robert J Prill, Daniel Marbach, Julio Saez-Rodriguez, Peter K Sorger, Leonidas G Alexopoulos, Xiaowei Xue, Neil D Clarke, Gregoire Altan-Bonnet, Gustavo Stolovitzky
PLoS One 5(2), e9202, 2010

Revealing strengths and weaknesses of methods for gene network inference.
Daniel Marbach, Robert J Prill, Thomas Schaffter, Claudio Mattiussi, Dario Floreano, Gustavo Stolovitzky
Proc Natl Acad Sci U S A 107(14), 6286--6291, 2010


Delimiting subterritories of the human subthalamic nucleus by means of microelectrode recordings and a Hidden Markov Model
A Zaidel, A Spivak, L Shpigelman, H Bergman, Z Israel
Movement Disorders 24(12), 1785--1793, John Wiley \& Sons, 2009

A Cluster Overlap Measure for Comparison of Activations in fMRI Studies
G Cecchi, R Garg, A Rao
Medical Image Computing and Computer-Assisted Intervention--MICCAI 2009, pp. 1018--1025, Springer

An optimization approach to understanding structure-function relationships in the visual cortex
A R Rao, G A Cecchi
Proceedings of the 2009 international joint conference on Neural Networks, pp. 1152--1159

The challenges of systems biology. Preface.
G Stolovitzky, P Kahlem, A Califano
Annals of the New York Academy of Sciences 1158(Annals of the New York Academy o), 2009

Distal Tumors Elicit Distinctive Gene Expression Changes in Mouse Brain Different from Those Induced by Arthritis
M.J. Alvarez, M.C. Salibe, G. Stolovitzky, M. Rubinstein, F.J.Pitossi and O.L. Podhajcer
The Open Neuroscience Journal3, 13-25, 2009

Recognition Mechanism of siRNA by Viral p19 Suppressor of RNA Silencing: A Molecular Dynamics Study
Z Xia, Z Zhu, J Zhu, R Zhou
Biophysical journal 96(5), 1761--1769, Elsevier, 2009

Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus
Z Xia, G Jin, J Zhu, R Zhou
Bioinformatics 25(18), 2309, Oxford Univ Press, 2009

Development and Utilization of a Spatial and Temporal Modeling System to Investigate Disease Outbreaks in Vermont
Hulse, C. L., Conant, J. L., Kaufman, J. H., Edlund, S. B., Ford, D. A.
PHIN 2009, CDC

Temporal and spatial effects of lunar calendar holidays on influenza A transmission in Israel
Kaufman J, Edlund S, Bromberg M, Chodick G, Lessler J, Mesika Yossi, Ram R, Douglas J, Kaufman Z, Levanthal A, Marom R, Shalev V.
Second International Conference on Infectious Diseases Dynamics, Elsevier, 2009

Infectious disease modeling: creating a community to respond to biological threats
Kaufman J, Edlund S, Douglas J.
Statistical Communications in Infectious Diseases 1(1), 1, The Berkeley Electronic Press, 2009

A spatiotemporal model for influenza
Edlund S, Bromberg M, Chodick G, Douglas J, Ford D, Kaufman Z, Lessler J, Marom R, Mesika Y, Ram R, Shalev V, Kaufman J.
HIC 2009, Frontiers of Health Informatics, HIC

Analysis of clinical uncertainties by health professionals and patients: an example from mental health
K Lloyd, M Cella, M Tanenblatt, A Coden
BMC Medical Informatics and Decision Making 9(1), 34, BioMed Central Ltd, 2009

Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions …

Method and apparatus for protein structure analysis
P Athma, AK Royyuru, BD Silverman, R Zhou, P …

Method and apparatus for protein structure analysis
P Athma, A K Royyuru, B D Silverman, R Zhou
US Patent 7,499,805, 2009 - Google Patents, Google Patents
US Patent 7,499,805

Statistical Indices for Computational and Data Driven Class Discovery in Microarray Data
R Giancarlo, D Scaturro, F Utro
Biological Data Mining, pp. 295, Chapman & Hall, 2009

Minimizing recombinations in consensus networks for phylogeographic studies
L Parida, A Javed, M Mel{'e}, F Calafell, J Bertranpetit, others
BMC bioinformatics 10(Suppl 1), S72, BioMed Central Ltd, 2009

Infectious disease modeling: Creating a community to respond to biological threats
J Kaufman, S Edlund, J Douglas
Statistical Communications in Infectious Diseases 1(1), 1, bepress, 2009

Geographical Structure of the Y-chromosomal Genetic Landscape of the Levant: A coastal-inland contrast
M El-Sibai, D E Platt, M Haber, Y Xue, S C Youhanna, R S Wells, H Izaabel, M F Sanyoura, H Harmanani, M A Bonab, others
Annals of human genetics 73(6), 568--581, John Wiley \& Sons, 2009

Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment
M C F Prosperi, A Altmann, M Rosen-Zvi, E Aharoni, G Borgulya, F Bazso, A S{`a}nnerborg, E Schulter, D Struck, G Ulivi, others
Antiviral therapy 14(3), 433--442, International Medical Press, 2009

Sorting cancer karyotypes by elementary operations
M Ozery-Flato, R Shamir
Journal of Computational Biology 16(10), 1445--1460, Mary Ann Liebert, Inc., 2009

Glucose regulates transcription in yeast through a network of signaling pathways
S Zaman, S I Lippman, L Schneper, Noam Slonim, J R Broach
Molecular Systems Biology 5(1), Nature Publishing Group, 2009

Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity
P Das, J Li, A K Royyuru, R Zhou
Journal of Computational Chemistry 30(11), 1654--1663, Wiley Online Library, 2009

Textual data compression in computational biology: a synopsis
R Giancarlo, D Scaturro, F Utro
Bioinformatics 25(13), 1575, Oxford Univ Press, 2009

Grouped graphical Granger modeling for gene expression regulatory networks discovery
A C Lozano, N Abe, Y Liu, S Rosset
Bioinformatics 25(12), i110, Oxford Univ Press, 2009

Dewetting and Hydrophobic Interaction in Physical and Biological Systems
B J Berne, J D Weeks, R Zhou
Annual review of physical chemistry60, 85--103, Annual Reviews, 2009

Lessons from the DREAM2 Challenges
G Stolovitzky, R J Prill, A Califano
Annals of the New York Academy of Sciences 1158(1), 159--195, Wiley Online Library, 2009

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes
A A Margolin, T Palomero, P Sumazin, A Califano, A Ferrando, G A Stolovitzky
Proc Natl Acad Sci U S A. 6(106), 244-9 , BioMed Central Ltd, 2009

Lessons from the DREAM2 Challenges.
Gustavo Stolovitzky, Robert J Prill, Andrea Califano
Ann N Y Acad Sci1158, 159--195, 2009


Stability Analysis of Mixtures of Mutagenetic Trees
Jasmina Bogojeska, Thomas Lengauer, J\"org Rahnenf\"uhrer
BMC Bioinformatics, 2008

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
Jasmina Bogojeska, Adrian Alexa, Andr\'e Altmann, Thomas Lengauer, J\"org Rahnenf\"uhrer
Bioinformatics 24(20), 2391--2392, Oxford Univ Press, 2008

Maximum-Likelihood Estimation of Site-Specific Mutation Rates in Human Mitochondrial DNA …
DF Soria
Hernanz, C Tyler-Smith, AK Royyuru … - Genetics, 2008 -

Y-chromosomal diversity in Lebanon is structured by recent historical events
P A Zalloua, Y Xue, J Khalife, N Makhoul, L Debiane, D E Platt, A K Royyuru, R J Herrera, D F S Hernanz, J Blue-Smith, others
The American Journal of Human Genetics 82(4), 873--882, Elsevier, 2008

Massively parallel molecular dynamics simulations of lysozyme unfolding
R Zhou, M Eleftheriou, C C Hon, RS Germain, AK Royyuru, BJ Berne
IBM Journal of Research and Development 52(1.2), 19--30, IBM, 2008


The Genographic Project public participation mitochondrial DNA database
DM Behar, S Rosset, J Blue
Smith, O … - PLoS Genet, 2007 -

Dead-end elimination for multistate protein design
Chen Yanover, Menachem Fromer, Julia M Shifman
Journal of computational chemistry 28(13), 2122--2129, Wiley Online Library, 2007

Nanopore in metal-dielectric sandwich for DNA position control
S Polonsky, S Rossnagel, G Stolovitzky
Applied Physics Letters 91(15), 153103, 2007

Dialogue on Reverse-Engineering Assessment and Methods: The DREAM of High-Throughput Pathway Inference
G Stolovitzky, D Monroe, A Califano
Annals of the New York Academy of Sciences 1115(1), 1--22, Wiley Online Library, 2007

Destruction of long-range interactions by a single mutation in lysozyme
R Zhou, M Eleftheriou, A K Royyuru, B J Berne
Proceedings of the National Academy of Sciences 104(14), 5824, National Acad Sciences, 2007


Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins
R. Zhou, A. Royyuru, P. Athma, F. Suits
Int J Bioinform Res Appl 2(2), 161--176, 2006

Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields
M Eleftheriou, R S Germain, A K Royyuru, R Zhou
Journal of the American Chemical Society 128(41), 13388--13395, ACS Publications, 2006

Inferring Common Origins from mtDNA
A Royyuru, G Alexe, D Platt, R Vijaya-Satya, L Parida, S Rosset, G Bhanot
Research in Computational Molecular Biology, pp. 246--247, 2006

Deep computing in biology: challenges and progress
A Royyuru
Proceedings of the 15th international conference on …, 2006 -


Reconstructing biological networks using conditional correlation analysis
J. J. Rice, Y. Tu, G. Stolovitzky
Bioinformatics 21(6), 765--773, 2005

Screening and Refinement of Protein Structures from Fold Recognition
R. Zhou, BD Silverman, G. Dent, A. Royyuru, A. Curioni, A. Logen

Dynamic properties of network motifs contribute to biological network organization.
Robert J Prill, Pablo A Iglesias, Andre Levchenko
PLoS Biol 3(11), e343, 2005


RECOMB2004Currents in Computational Molecular Biology
R Zhou, G Dent, A Royyuru, P Atham
2004 - A. Gramada and PE Bourne, Eds


Spatial profiling of protein hydrophobicity: Native vs. decoy structures
R Zhou, B D Silverman, A K Royyuru, P Athma
Proteins: Structure, Function, and Bioinformatics 52(4), 561--572, John Wiley \& Sons, 2003

Hydrophobicity of protein domains: spatially profiling their distribution
R Zhou, A Royyuru, P Athma, BD Silverman
… and Theoretical Computer Science (DIMACS) Workshop …, 2003


Principles of mucin architecture: structural studies on synthetic glycopeptides bearing …
DM Coltart, AK Royyuru, LJ Williams, PW …
J. Am. Chem. Soc, 2002 -

Principles of Mucin Architecture: Structural Studies on Synthetic Glycopeptides Bearing Clustered Mono-, Di-, Tri-, an
DM Coltart, AK Royyuru, LJ Williams, P W Glunz, D Sames, SD Kuduk, JB Schwarz, X
T Chen, SJ Danishefsky, and DH Live, 2002


Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells
U. Klein, Y. Tu, G. Stolovitzky, M. Mattioli, G. Cattoretti, H. Husson, A. Freedman, G. Inghirami, L. Cro, L. Baldini, A. Neri, A. Califano and R. Dalla Favera,
Journal of Experimental Medicine 194(11), 1625, 2001

Blue Gene: a vision for protein science using a petaflop supercomputer
Frances Allen, G Almasi, Wanda Andreoni, D Beece, Bruce J. Berne, A Bright, Jose Brunheroto, Calin Cascaval, J Castanos, Paul Coteus
IBM Systems Journal 40(2), 310-327, IBM, 2001


Insights into glycoproteins: A structural motif for mucins from a glycopeptide
DH Live, RA Kumar, L Williams, D Sames
Peptides for the New Millennium: Proceedings of the …, 2000 -

Systematic and fully automated identification of protein sequence patterns
R K Hart, A K Royyuru, G Stolovitzky, A Califano
Journal of Computational Biology 7(3-4), 585--600, 2000

Systematic and automated discovery of patterns in PROSITE families
R Hart, A K Royyuru, G Stolovitzky, A Califano
Proceedings of the fourth annual international conference on Computational molecular biology, pp. 147--154, 2000

Systematic and fully automatic discovery of protein sequence patterns
RK Hart, G Stolovitzky, AK Royyuru, A …
J Comput Biol, 2000