Publications

2020

Caravagna, G., Heide, T., Williams, M.J., Zapata, L., Nichol, D., Chkhaidze, K., ...Acar, A. (2020). Subclonal reconstruction of tumors by using machine learning and population genetics.. Nat Genet, 52 (9), 898-907. doi:10.1038/s41588-020-0675-5
Fedorec, A.J.H., Robinson, C.M., Wen, K.Y., Barnes, C.P. (2020). FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data.. ACS Synth Biol, doi:10.1021/acssynbio.0c00296
Karkaria, B.D., Treloar, N.J., Barnes, C.P., Fedorec, A.J.H. (2020). From Microbial Communities to Distributed Computing Systems. Frontiers in Bioengineering and Biotechnology, 8 doi:10.3389/fbioe.2020.00834
Lakatos, E., Williams, M.J., Schenck, R.O., Cross, W.C.H., Househam, J., Zapata, L., ...Barnes, C.P. (2020). Evolutionary dynamics of neoantigens in growing tumors.. Nat Genet, doi:10.1038/s41588-020-0687-1
Robinson, C., Fedorec, A., Yan Wen, K., Barnes, C. (2020). FlopR: An open source software package for calibration and normalization of plate reader and flow cytometry data. .
Treloar, N.J., Fedorec, A.J.H., Ingalls, B., Barnes, C.P. (2020). Deep reinforcement learning for the control of microbial co-cultures in bioreactors.. PLoS Comput Biol, 16 (4), e1007783. doi:10.1371/journal.pcbi.1007783
Werner, B., Case, J., Williams, M.J., Chkhaidze, K., Temko, D., Fernández-Mateos, J., ...Spiteri, I. (2020). Measuring single cell divisions in human tissues from multi-region sequencing data. Nature Communications, 11 (1), 1035. doi:10.1038/s41467-020-14844-6
Williams, M.J., Zapata, L., Werner, B., Barnes, C.P., Sottoriva, A., Graham, T.A. (2020). Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios. eLife, 9 doi:10.7554/eLife.48714

2019

Baker, A.-.M., Gabbutt, C., Williams, M.J., Cereser, B., Jawad, N., Rodriguez-Justo, M., ...McDonald, S.A. (2019). Crypt fusion as a homeostatic mechanism in the human colon. Gut, doi:10.1136/gutjnl-2018-317540
Fedorec, A.J.H., Karkaria, B., Sulu, M., Barnes, C. (2019). Single strain control of microbial consortia. .
Fedorec, A.J.H., Ozdemir, T., Doshi, A., Ho, Y.-.K., Rosa, L., Rutter, J., ...Barnes, C.P. (2019). Two New Plasmid Post-segregational Killing Mechanisms for the Implementation of Synthetic Gene Networks in Escherichia coli.. iScience, doi:10.1016/j.isci.2019.03.019
Lakatos, E., Williams, M., Schenck, R., Cross, W., Househam, J., Werner, B., ...Anderson, A. (2019). Evolutionary dynamics of neoantigens in growing tumours. .
Russell-Buckland, J., Barnes, C.P., Tachtsidis, I. (2019). A Bayesian framework for the analysis of systems biology models of the brain.. PLoS Comput Biol, 15 (4), e1006631. doi:10.1371/journal.pcbi.1006631
Rutter, J.W., Ozdemir, T., Galimov, E.R., Quintaneiro, L.M., Rosa, L., Thomas, G.M., ...Barnes, C.P. (2019). Detecting Changes in the Caenorhabditis elegans Intestinal Environment Using an Engineered Bacterial Biosensor.. ACS Synth Biol, doi:10.1021/acssynbio.9b00166
Shaw, L., Bassam, H., Barnes, C.P., Walker, A., Klein, N., Balloux, F. (2019). Modelling microbiome recovery after antibiotics using a stability landscape framework. ISME Journal, doi:10.1038/s41396-019-0392-1
Wen, K.Y., Rutter, J.W., Barnes, C.P., Dekker, L. (2019). Fundamental Building Blocks of Whole-Cell Biosensor Design. In Thouand, G. (Ed.), Handbook of Cell Biosensors. (pp. 1-23). Springer International Publishing.

2018

Barnes, C.P., Fedorec, A.J.H. (2018). Five amazing ways redesigning biological cells could help us fight cancer. [Digital scholarly resource]. Retrieved from: https://theconversation.com/five-amazing-ways-redesigning-biological-cells-could-help-us-fight-cancer-95256
Boeing, P., Leon, M., Nesbeth, D.N., Finkelstein, A., Barnes, C. (2018). Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology. Processes, 6 (9), doi:10.3390/pr6090167
Dalchau, N., Szép, G., Hernansaiz-Ballesteros, R., Barnes, C.P., Cardelli, L., Phillips, A., Csikász-Nagy, A. (2018). Computing with biological switches and clocks. Natural Computing, 1-19. doi:10.1007/s11047-018-9686-x
Heide, T., Zapata, L., Williams, M.J., Werner, B., Caravagna, G., Barnes, C.P., ...Sottoriva, A. (2018). Reply to 'Neutral tumor evolution?'. Nat Genet, doi:10.1038/s41588-018-0256-z
Ozdemir, T., Fedorec, A.J.H., Danino, T., Barnes, C.P. (2018). Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity. Cell systems, 7 (1), 5-16. doi:10.1016/j.cels.2018.06.008
Perez-Carrasco, R., Barnes, C.P., Schaerli, Y., Isalan, M., Briscoe, J., Page, K.M. (2018). Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors.. Cell systems, doi:10.1016/j.cels.2018.02.008
Treloar, N., Fedorec, A.J.H., Ingalls, B., Barnes, C. (2018). Deep reinforcement learning for the control of microbial co-cultures in bioreactors. .
Werner, B., Williams, M.J., Barnes, C.P., Graham, T.A., Sottoriva, A. (2018). Reply to 'Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution'.. Nat Genet, doi:10.1038/s41588-018-0235-4
Williams, M.J., Werner, B., Barnes, C.P., Graham, T.A., Sottoriva, A. (2018). Reply: Is the evolution of tumors Darwinian or non-Darwinian?. National Science Review, 5 (1), 17-19. doi:10.1093/nsr/nwx131
Williams, M.J., Werner, B., Heide, T., Barnes, C.P., Graham, T.A., Sottoriva, A. (2018). Reply to 'Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data'. Nature Genetics, 50 (12), 1628-1630. doi:10.1038/s41588-018-0210-0
Williams, M.J., Werner, B., Heide, T., Curtis, C., Barnes, C.P., Sottoriva, A., Graham, T.A. (2018). Quantification of subclonal selection in cancer from bulk sequencing data. NATURE GENETICS, 50 (6), 895-+. doi:10.1038/s41588-018-0128-6

2017

Sottoriva, A., Barnes, C.P., Graham, T.A. (2017). Catch my drift? Making sense of genomic intra-tumour heterogeneity.. Biochim Biophys Acta, doi:10.1016/j.bbcan.2016.12.003
Williams, M.J., Werner, B., Barnes, C.P., Graham, T.A., Sottoriva, A. (2017). Reply: Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures. Nature Genetics, 49 (9), 1289-1291. doi:10.1038/ng.3877

2016

Baier, G., Barnes, C., Crowe, D., Gilmore, S., Grimm, U., Lewis, P., ...Shepherd, A. (2016). SysMIC: A Blueprint for interdisciplinary online training in the life sciences. [Digital scholarly resource]. Retrieved from: https://doi.org/10.7287/peerj.preprints.2523v1
Boeing, P., Ozdemir, T., Barnes, C.P. (2016). Design Tools for Synthetic Biology. In Synthetic Biology Handbook. CRC Press.
Cohen, M., Page, K.M., Perez-Carrasco, R., Barnes, C.P., Briscoe, J. (2016). Mathematical models help explain experimental data. Response to 'Transcriptional interpretation of Shh morphogen signaling: computational modeling validates empirically established models'. DEVELOPMENT, 143 (10), 1640-1643. doi:10.1242/dev.138461
Fedorec, A.J.H., Ozdemir, T., Barnes, C.P. (2016). Determining the efficacy of post-segregational killing systems in commensal Escherichia coli.
Filippi, S., Barnes, C.P., Kirk, P.D.W., Kudo, T., Kunida, K., McMahon, S.S., ...Stumpf, M.P.H. (2016). Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling. Cell Reports, doi:10.1016/j.celrep.2016.05.024
Gonzales, D.T., ozdemir, T., Thomas, G.M., barnes, C. (2016). An acetoacetate-inducible bacterial sensor. [Digital scholarly resource]. Retrieved from: http://dx.doi.org/10.1101/035972
Leon, M., Woods, M.L., Fedorec, A.J., Barnes, C.P. (2016). A computational method for the investigation of multistable systems and its application to genetic switches.. BMC Systems Biology, 10 (1), 130. doi:10.1186/s12918-016-0375-z
Ozdemir, T., Fedorec, A., Barnes, C. (2016). Toxin-Antitoxin stabilised biosensors in the commensal Escherichia coli nissle 1917 for the detection of dysbiotic changes in the intestinal microbiota.
Williams, M.J., Werner, B., Barnes, C.P., Graham, T.A., Sottoriva, A. (2016). Identification of neutral tumor evolution across cancer types. Nature Genetics, 48 238-244. doi:10.1038/ng.3489
Woods, M.L., Barnes, C.P. (2016). Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair. PLoS Computational Biology, 12 (10), doi:10.1371/journal.pcbi.1005131
Woods, M., Leon, M., Perez-Carrasco, R., Barnes, C.P. (2016). A statistical approach reveals designs for the most robust stochastic gene oscillators. ACS Synthetic Biology,

2015

Cohen, M., Kicheva, A., Ribeiro, A., Blassberg, R., Page, K.M., Barnes, C.P., Briscoe, J. (2015). Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms.. NATURE COMMUNICATIONS, 6 doi:10.1038/ncomms7709

2014

Boeing, P., Nesbeth, D.N., Finkelstein, A., Barnes, C. (2014). An Aspect Oriented Design and Modelling Framework for Synthetic Biology..
Cohen, M., Page, K.M., Perez-Carrasco, R., Barnes, C.P., Briscoe, J. (2014). A theoretical framework for the regulation of Shh morphogen-controlled gene expression.. DEVELOPMENT, 141 (20), 3868-3878. doi:10.1242/dev.112573
Liepe, J., Kirk, P., Filippi, S., Toni, T., Barnes, C.P., Stumpf, M.P.H. (2014). A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation.. NATURE PROTOCOLS, 9 (2), 439-456. doi:10.1038/nprot.2014.025
Matzke, W., Barnes, C.P., Jentzsch, E., Mascher, T., Stumpf, M.P.H. (2014). On Industrial Strength Bio-design Automation. In Ermolayev, V., Mayr, H.C., Nikitchenko, M., Spivakovsky, A., Zholtkevych, G. (Eds.), Information and Communication Technologies in Education, Research, and Industrial Applications.. (pp. 277-299). Springer International Publishing.
Mulle, J.G., Pulver, A.E., McGrath, J.A., Wolyniec, P.S., Dodd, A.F., Cutler, D.J., ...Conrad, D.F. (2014). Reciprocal duplication of the williams-beuren syndrome deletion on chromosome 7q11.23 is associated with schizophrenia. BIOLOGICAL PSYCHIATRY, 75 (5), 371-377. doi:10.1016/j.biopsych.2013.05.040
Silk, D., Kirk, P.D.W., Barnes, C.P., Toni, T., Stumpf, M.P.H. (2014). Model selection in systems biology depends on experimental design.. PLOS COMPUTATIONAL BIOLOGY, 10 (6), doi:10.1371/journal.pcbi.1003650
Woods, M.L., Carmona-Fontaine, C., Barnes, C.P., Couzin, I.D., Mayor, R., Page, K.M. (2014). Directional collective cell migration emerges as a property of cell interactions.. PLOS ONE, 9 (9), doi:10.1371/journal.pone.0104969

2013

Chaidos, A., Barnes, C.P., Cowan, G., May, P.C., Melo, V., Hatjiharissi, E., ...Terpos, E. (2013). Clinical drug resistance linked to interconvertible phenotypic and functional states of tumor-propagating cells in multiple myeloma.. BLOOD, 121 (2), 318-328. doi:10.1182/blood-2012-06-436220
Grozeva, D., Kirov, G., Conrad, D.F., Barnes, C.P., Hurles, M., Owen, M.J., ...Craddock, N. (2013). Reduced burden of very large and rare CNVs in bipolar affective disorder. BIPOLAR DISORDERS, 15 (8), 893-898. doi:10.1111/bdi.12125

2012

Barnes, C.P., Filippi, S., Stumpf, M.P.H., Thorne, T. (2012). Considerate approaches to constructing summary statistics for ABC model selection. Statistics and Computing, 1-17.
Barnes, C.P., Huvet, M., Harmston, N., Stumpf, M.P.H. (2012). Mathematical models for systems biology and how to construct them. In Robertson, B.D., Wren, B.W. (Eds.), Systems Microbiology: Current Topics and Applications. .
Blauw, H.M., Barnes, C.P., Van Vught, P.W.J., Van Rheenen, W., Verheul, M., Cuppen, E., ...Van Den Berg, L.H. (2012). SMN1 gene duplications are associated with sporadic ALS. NEUROLOGY, 78 (11), 776-780. doi:10.1212/WNL.0b013e318249f697
Filippi, S., Barnes, C.P., Cornebise, J., Stumpf, M.P.H. (2012). On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo. Statistical Applications in Genetics and Molecular Biology, 12 (1), doi:10.1515/sagmb-2012-0069
Grozeva, D., Conrad, D.F., Barnes, C.P., Hurles, M., Owen, M.J., O'Donovan, M.C., ...Kirov, G. (2012). Independent estimation of the frequency of rare CNVs in the UK population confirms their role in schizophrenia. SCHIZOPHRENIA RESEARCH, 135 (1-3), 1-7. doi:10.1016/j.schres.2011.11.004
Kristiansson, K., Perola, M., Tikkanen, E., Kettunen, J., Surakka, I., Havulinna, A.S., ...Kajantie, E. (2012). Genome-wide screen for metabolic syndrome susceptibility loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits. CIRCULATION-CARDIOVASCULAR GENETICS, 5 (2), 242-249. doi:10.1161/CIRCGENETICS.111.961482
Liepe, J., Taylor, H., Barnes, C.P., Huvet, M., Bugeon, L., Thorne, T., ...Stumpf, M.P.H. (2012). Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation.. INTEGRATIVE BIOLOGY, 4 (3), 335-345. doi:10.1039/c2ib00175f

2011

Barnes, C.P., Silk, D., Sheng, X., Stumpf, M.P.H. (2011). Bayesian design of synthetic biological systems.. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108 (37), 15190-15195. doi:10.1073/pnas.1017972108
Barnes, C.P., Silk, D., Stumpf, M.P.H. (2011). Bayesian design strategies for synthetic biology. INTERFACE FOCUS, 1 (6), 895-908. doi:10.1098/rsfs.2011.0056
MacDonald, J.T., Barnes, C., Kitney, R.I., Freemont, P.S., Stan, G.-.B.V. (2011). Computational design approaches and tools for synthetic biology.. INTEGRATIVE BIOLOGY, 3 (2), 97-108. doi:10.1039/c0ib00077a
Silk, D., Kirk, P.D.W., Barnes, C.P., Toni, T., Rose, A., Moon, S., ...Stumpf, M.P.H. (2011). Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes.. NATURE COMMUNICATIONS, 2 doi:10.1038/ncomms1496
Zhou, Y., Liepe, J., Sheng, X., Stumpf, M.P.H., Barnes, C. (2011). GPU accelerated biochemical network simulation.. BIOINFORMATICS, 27 (6), 874-876. doi:10.1093/bioinformatics/btr015

2010

Altshuler, D.M., Gibbs, R.A., Peltonen, L., Schaffner, S.F., Yu, F., Dermitzakis, E., ...Gabriel, S.B. (2010). Integrating common and rare genetic variation in diverse human populations. NATURE, 467 (7311), 52-58. doi:10.1038/nature09298
Conrad, D.F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., ...Campbell, P. (2010). Origins and functional impact of copy number variation in the human genome.. NATURE, 464 (7289), 704-712. doi:10.1038/nature08516
Craddock, N., Hurles, M.E., Cardin, N., Pearson, R.D., Plagnol, V., Robson, S., ...Giannoulatou, E. (2010). Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. NATURE, 464 (7289), 713-U86. doi:10.1038/nature08979
Liepe, J., Barnes, C., Cule, E., Erguler, K., Kirk, P., Toni, T., Stumpf, M.P.H. (2010). ABC-SysBio--approximate Bayesian computation in Python with GPU support.. BIOINFORMATICS, 26 (14), 1797-1799. doi:10.1093/bioinformatics/btq278
Surakka, I., Kristiansson, K., Anttila, V., Inouye, M., Barnes, C., Moutsianas, L., ...Peltonen, L. (2010). Founder population-specific HapMap panel increases power in GWA studies through improved imputation accuracy and CNV tagging. GENOME RESEARCH, 20 (10), 1344-1351. doi:10.1101/gr.106534.110

2009

Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2009). Search for particles decaying into a Z boson and a photon in collisions p (p)over-bar at root s = 1.96 TeV (vol 641, pg 415, 2006). PHYSICS LETTERS B, 670 (4-5), 455-458. doi:10.1016/j.physletb.2008.11.032
Takeuchi, F., McGinnis, R., Bourgeois, S., Barnes, C., Eriksson, N., Soranzo, N., ...McLaren, W. (2009). A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose.. PLOS GENETICS, 5 (3), doi:10.1371/journal.pgen.1000433

2008

Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2008). Measurement of sigma(p(p)over-bar -> Z)center dot Br(Z ->tau tau) at root s=1.96 TeV (vol 71, art no. 072004, 2005). PHYSICAL REVIEW D, 77 (3), doi:10.1103/PhysRevD.77.039901
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2008). Measurement of inclusive differential cross sections for Gamma(1S) production in p(p)over-bar collisions at root s = 1.96 TeV (vol 94, art no 232001, 2005). PHYSICAL REVIEW LETTERS, 100 (4), doi:10.1103/PhysRevLett.100.049902
Alves, A.A., Andrade Filho, L.M., Barbosa, A.F., Bediaga, I., Cernicchiaro, G., Guerrer, G., ...Marujo, F. (2008). The LHCb Detector at the LHC. JOURNAL OF INSTRUMENTATION, 3 doi:10.1088/1748-0221/3/08/S08005
Barnes, C., Plagnol, V., Fitzgerald, T., Redon, R., Marchini, J., Clayton, D., Hurles, M. (2008). A robust statistical method for case-control association testing with copy number variation.. Nature genetics, 40 (10), 1245-1252.
Collaboration, D., Abazov, V. (2008). Measurement of the ratios of the Z/G* + >= n jet production cross sections to the total inclusive Z/G* cross section in ppbar collisions at sqrt(s) = 1.96 TeV. PHYSICS LETTERS B, 658 (4), 112-119. doi:10.1016/j.physletb.2007.10.046

2007

Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Alexeev, G.D. (2007). Lifetime difference and CP-violating phase in the B-s(0) system. PHYSICAL REVIEW LETTERS, 98 (12), doi:10.1103/PhysRevLett.98.121801
Collaboration, D., Abazov, V. (2007). Multivariate searches for single top quark production with the D0 detector. PHYSICAL REVIEW D, 75 (9), doi:10.1103/PhysRevD.75.092007
Collaboration, D., Abazov, V. (2007). Experimental discrimination between charge 2e/3 top quark and charge 4e/3 exotic quark production scenarios. PHYSICAL REVIEW LETTERS, 98 (4), doi:10.1103/PhysRevLett.98.041801
Collaboration, D., Abazov, V. (2007). Measurement of the ppbar to ttbar production cross section at sqrt(s)=1.96 TeV in the fully hadronic decay channel. PHYSICAL REVIEW D, 76 (7), doi:10.1103/PhysRevD.76.072007
Collaboration, D., Abazov, V. (2007). Search for techniparticles in e +jets events at D0. PHYSICAL REVIEW LETTERS, 98 (22), doi:10.1103/PhysRevLett.98.221801
Collaboration, D., Abazov, V. (2007). Search for single production of scalar leptoquarks in p\bar{p} collisions decaying into muons and quarks with the D0 detector. PHYSICS LETTERS B, 647 (2-3), 74-81. doi:10.1016/j.physletb.2007.01.064
Collaboration, D., Abazov, V. (2007). Measurement of the charge asymmetry in semileptonic Bs decays. PHYSICAL REVIEW LETTERS, 98 (15), doi:10.1103/PhysRevLett.98.151801
Collaboration, D., Abazov, V. (2007). Search for production of single top quarks via flavor-changing neutral currents at the Tevatron. Phys.Rev.Lett., 99 (19), doi:10.1103/PhysRevLett.99.191802
Collaboration, D., Abazov, V.M. (2007). Measurement of the W boson helicity in top quark decay at D0. PHYSICAL REVIEW D, 75 (3), doi:10.1103/PhysRevD.75.031102
Collaboration, D., Abazov, V.M. (2007). Search for the pair production of scalar top quarks in the acoplanar charm jet topology in p pbar collisions at sqrt(s)=1.96 TeV. PHYSICS LETTERS B, 645 (2-3), 119-127. doi:10.1016/j.physletb.2006.12.024
Collaboration, D., Abazov, V.M. (2007). Evidence for production of single top quarks and first direct measurement of |Vtb|. PHYSICAL REVIEW LETTERS, 98 (18), doi:10.1103/PhysRevLett.98.181802
Collaboration, D., Abazov, V.M. (2007). Combined D0 Measurements Constraining the CP-violating Phase and Width Difference in the $B_s^0$ System. PHYSICAL REVIEW D, 76 (5), doi:10.1103/PhysRevD.76.057101
Collaboration, D., al, V.A.E. (2007). Measurement of the top quark mass in the dilepton channel. PHYSICS LETTERS B, 655 (1-2), 7-14. doi:10.1016/j.physletb.2007.08.074

2006

Aaltonen, T., Adelman, J., Álvarez González, B., Amerio, S., Amidei, D., Anastassov, A., ...Apresyan, A. (2006). Search for the production of scalar bottom quarks in pp̄ collisions at √s=1.96TeV. PHYSICAL REVIEW LETTERS, 97 (17), doi:10.1103/PhysRevLett.97.171806
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, D.L., Adams, M., ...Ahmed, S.N. (2006). The upgraded DO detector. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT, 565 (2), 463-537. doi:10.1016/j.nima.2006.05.248
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2006). Measurement of the isolated photon cross section in p(p)over-bar collisions at root s=1.96 TeV. PHYSICS LETTERS B, 639 (3-4), 151-158. doi:10.1016/j.physletb.2006.04.048
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2006). Search for the Higgs boson in H -> WW(*) decays in p(p)over-bar collisions at root(s)=1.96 TeV. PHYSICAL REVIEW LETTERS, 96 (1), doi:10.1103/PhysRevLett.96.011801
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2006). Search for associated Higgs boson production WH→WWW *→l±νl′±ν′+X in pp̄ collisions at s=1.96TeV. Physical Review Letters, 97 (15), doi:10.1103/PhysRevLett.97.151804
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2006). Search for squarks and gluinos in events with jets and missing transverse energy in p over(p, ̄) collisions at sqrt(s) = 1.96  TeV. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics, 638 (2-3), 119-127. doi:10.1016/j.physletb.2006.05.030
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2006). Search for pair production of second generation scalar leptoquarks in p(p)over-bar collisions at root s-=1.96 TeV. PHYSICS LETTERS B, 636 (3-4), 183-190. doi:10.1016/j.physletb.2006.03.056
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2006). Search for squarks and gluinos in events with jets and missing transverse energy in p(p)over-bar collisions at root s-=1.96 TeV. PHYSICS LETTERS B, 638 (2-3), 119-127. doi:10.1016/j.physletb.2006.05.030
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2006). Search for associated Higgs boson production WH -> WWW*-> l(+/-)nu l('+/-)nu(')+X in p(p)over-bar collisions at root S=1.96 TeV. PHYSICAL REVIEW LETTERS, 97 (15), doi:10.1103/PhysRevLett.97.151804
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2006). Measurement of the B-s(0) lifetime using semileptonic decays. PHYSICAL REVIEW LETTERS, 97 (24), doi:10.1103/PhysRevLett.97.241801
Collaboration, D. (2006). Measurement of B(t->Wb)/B(t->Wq) at sqrt(s) = 1.96 TeV. PHYSICS LETTERS B, 639 (6), 616-622. doi:10.1016/j.physletb.2006.07.019
Collaboration, D., Abazov, V. (2006). Search for the Rare Decay B0_s -> phi mu^+ mu- with the D0 Detector. PHYSICAL REVIEW D, 74 (3), doi:10.1103/PhysRevD.74.031107
Collaboration, D., Abazov, V. (2006). Direct Limits on the Bs Oscillation Frequency. PHYSICAL REVIEW LETTERS, 97 (2), doi:10.1103/PhysRevLett.97.021802
Collaboration, D., Abazov, V. (2006). Search for resonant second generation slepton production at the Tevatron. PHYSICAL REVIEW LETTERS, 97 (11), doi:10.1103/PhysRevLett.97.111801
Collaboration, D., Abazov, V. (2006). Search for particles decaying into a Z boson and a photon in p\bar{p} collisions at \sqrt{s} = 1.96 TeV. PHYSICS LETTERS B, 641 (6), 415-422. doi:10.1016/j.physletb.2006.08.079
Collaboration, D., Abazov, V. (2006). Search for the Standard Model Higgs Boson in the ZH --> neutrino-neutrino-b-b channel. PHYSICAL REVIEW LETTERS, 97 (16), doi:10.1103/PhysRevLett.97.161803
Collaboration, D., Abazov, V. (2006). Search for Neutral, Long-lived Particles Decaying into Two Muons in p-pbar Collisions at sqrt(s) = 1.96 TeV. PHYSICAL REVIEW LETTERS, 97 (16), doi:10.1103/PhysRevLett.97.161802
Collaboration, D., Abazov, V. (2006). Search for W' boson production in the W'->tb decay channel. PHYSICS LETTERS B, 641 (6), 423-431. doi:10.1016/j.physletb.2006.09.021
Collaboration, D., Abazov, V. (2006). Limits on anomalous trilinear gauge couplings from WW->e+e-, WW->emu, and WW->mu+mu- events from p-pbar collisions at sqrt(s)=1.96 TeV. PHYSICAL REVIEW D, 74 (5), doi:10.1103/PhysRevD.74.057101
Collaboration, D., Abazov, V. (2006). Measurement of the CP-violation parameter of B^0 mixing and decay with pp(bar) -> mu mu X data. PHYSICAL REVIEW D, 74 (9), doi:10.1103/PhysRevD.74.092001
Collaboration, D., Abazov, V. (2006). Measurement of the top quark mass in the lepton+jets final state with the matrix element method. PHYSICAL REVIEW D, 74 (9), doi:10.1103/PhysRevD.74.092005
Collaboration, D., Abazov, V. (2006). Measurement of the ttbar production cross section in pbarp collisions at sqrt(s) = 1.96 TeV using secondary vertex b tagging. PHYSICAL REVIEW D, 74 (11), doi:10.1103/PhysRevD.74.112004
Collaboration, D., Abazov, V.M. (2006). Search for R-parity violating supersymmetry via the LLE couplings lambda_{121}, lambda_{122} or lambda_{133} in ppbar collisions at sqrt(s)=1.96 TeV. PHYSICS LETTERS B, 638 (5-6), 441-449. doi:10.1016/j.physletb.2006.05.077
Collaboration, D., Abazov, V.M. (2006). Search for a heavy resonance decaying into a Z+jet final state in p-pbar collisions at sqrt(s) = 1.96 TeV using the D0 detector. PHYSICAL REVIEW D, 74 (1), doi:10.1103/PhysRevD.74.011104
Collaboration, D., Abazov, V.M. (2006). Search for scalar leptoquarks in the acoplanar jet topology in ppbar collisions at sqrt(s)=1.96 TeV. PHYSICS LETTERS B, 640 (5-6), 230-237. doi:10.1016/j.physletb.2006.08.020
Collaboration, D., Abazov, V.M. (2006). Measurement of Bd mixing using opposite-side flavor tagging. PHYSICAL REVIEW D, 74 (11), doi:10.1103/PhysRevD.74.112002
Lancaster, M., Nurse, E., Waters, D.C.D.F.C. (2006). Measurement of the ttBar production cross section in ppBar collisions at sqrt[s] =1.96 TeV in the all hadronic decay mode. Physical Review D, 74 072005-.
Lancaster, M., Waters, D.C.D.F.C. (2006). Search for a Neutral Higgs Boson Decaying to a W Boson Pair in pp? Collisions at sqrt[s]=1.96??TeV. Physical Review Letters, 97 081802-.

2005

Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, D.L., Adams, M., ...Ahmed, S.N. (2005). Measurement of dijet azimuthal decorrelations at central rapidities in p(p)over-bar collisions at root s=1.96 TeV. PHYSICAL REVIEW LETTERS, 94 (22), doi:10.1103/PhysRevLett.94.221801
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, D.L., Adams, M., ...Ahmed, S.N. (2005). Search for supersymmetry with gauge-mediated breaking in diphoton events at D0. PHYSICAL REVIEW LETTERS, 94 (4), doi:10.1103/PhysRevLett.94.041801
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, D.L., Adams, M., ...Ahmed, S.N. (2005). Measurement of the B-s(0) lifetime in the exclusive decay channel B-s(0)-> J/psi phi. PHYSICAL REVIEW LETTERS, 94 (4), doi:10.1103/PhysRevLett.94.042001
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Production of WZ events in pp collisions at square root(s) = 1.96 TeV and limits on anomalous WWZ couplings.. Physical review letters, 95 (14), 141802-. doi:10.1103/physrevlett.95.141802
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of the t(t)over-bar production cross section in p(p)over-bar collisions at root s=1.96 TeV using lepton plus jets events with lifetime b-tagging. PHYSICS LETTERS B, 626 35-44. doi:10.1016/j.physletb.2005.08.103
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of the t(t)over-bar production cross section in p(p)over-bar collisions at root s=1.96 TeV using kinematic characteristics of lepton plus jets events. PHYSICS LETTERS B, 626 45-54. doi:10.1016/j.physletb.2005.08.104
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of the t(t)over-bar production cross section in p(p)over-bar collisions at root s=1.96 TeV in dilepton final states. PHYSICS LETTERS B, 626 55-64. doi:10.1016/j.physletb.2005.08.105
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for large extra spatial dimensions in dimuon production with the D0 detector. PHYSICAL REVIEW LETTERS, 95 (16), doi:10.1103/PhysRevLett.95.161602
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of the lifetime difference in the B-s(0) system. PHYSICAL REVIEW LETTERS, 95 (17), doi:10.1103/PhysRevLett.95.171801
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of semileptonic branching fractions of B mesons to narrow D-** states - art. no. 1711803. PHYSICAL REVIEW LETTERS, 95 (17), doi:10.1103/PhysRevLett.95.171803
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for neutral supersymmetric Higgs bosons in multijet events at root s=1.96 TeV. PHYSICAL REVIEW LETTERS, 95 (15), doi:10.1103/PhysRevLett.95.151801
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for supersymmetry via associated production of charginos and neutralinos in final states with three leptons. PHYSICAL REVIEW LETTERS, 95 (15), doi:10.1103/PhysRevLett.95.151805
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Production of WZ events in pp(-) collisions at root s=1.96 TeV and limits on anomalous WWZ couplings. PHYSICAL REVIEW LETTERS, 95 (14), doi:10.1103/PhysRevLett.95.141802
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for single top quark production in pp collisions at root s=1.96 TeV. PHYSICS LETTERS B, 622 (3-4), 265-276. doi:10.1016/j.physletb.2005.07.027
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for randall-sundrum gravitons in dilepton and diphoton final states. PHYSICAL REVIEW LETTERS, 95 (9), doi:10.1103/PhysRevLett.95.091801
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Study Z gamma events and limits on anomalous ZZ gamma and Z gamma gamma couplings in pp(-) collisions at root s=1.96 Tev. PHYSICAL REVIEW LETTERS, 95 (5), doi:10.1103/PhysRevLett.95.051802
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for right-handed W bosons in top quark decay. PHYSICAL REVIEW D, 72 (1), doi:10.1103/PhysRevD.72.011104
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of inclusive differential cross sections for Upsilon(1S) production in p(p)over-bar collisions at root s=1.96 TeV. PHYSICAL REVIEW LETTERS, 94 (23), doi:10.1103/PhysRevLett.94.232001
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of the pp(-)-> W gamma plus X cross section at root s=1.96 TeV and WW gamma anomalous coupling limits. PHYSICAL REVIEW D, 71 (9), doi:10.1103/PhysRevD.71.091108
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of the ratio of B+ and B-0 meson lifetimes. PHYSICAL REVIEW LETTERS, 94 (18), doi:10.1103/PhysRevLett.94.182001
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of the ratio of inclusive cross sections sigma(p(p)over-bar -> Z plus b jet)/sigma(p(p)over-bar -> Z plus jet) at root s=1.96 TeV. PHYSICAL REVIEW LETTERS, 94 (16), doi:10.1103/PhysRevLett.94.161801
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for first-generation scalar leptoquarks in p(p)over-bar collisions at root s=1.96 TeV. PHYSICAL REVIEW D, 71 (7), doi:10.1103/PhysRevD.71.071104
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of sigma(p(p)over-bar -> Z)center dot Br(Z ->tau tau) at root s=1.96 TeV. PHYSICAL REVIEW D, 71 (7), doi:10.1103/PhysRevD.71.072004
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of the WW production cross section in p(p)over-bar collisions at root(s)over-bar=1.96 TeV. PHYSICAL REVIEW LETTERS, 94 (15), doi:10.1103/PhysRevLett.94.151801
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for anomalous heavy-flavor quark production in association with W bosons. PHYSICAL REVIEW LETTERS, 94 (15), doi:10.1103/PhysRevLett.94.152002
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Measurement of the Lambda(0)(b) lifetime in the decay Lambda(0)(b)-> J/psi Lambda(0) with the D0 detector. PHYSICAL REVIEW LETTERS, 94 (10), doi:10.1103/PhysRevLett.94.102001
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for Wbb(-) and WH production in pp(-) collisions at root s=1.96 TeV. PHYSICAL REVIEW LETTERS, 94 (9), doi:10.1103/PhysRevLett.94.091802
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, M., Adams, T., ...Ahsan, M. (2005). Search for the flavour-changing neutral current B-s(0)->mu+mu- in p(p)over-bar collisions at root s=1.96 TeV with the D0 dectector. PHYSICAL REVIEW LETTERS, 94 (7), doi:10.1103/PhysRevLett.94.071802
Abazov, V.M., Abbott, B., Abolins, M., Nurse, E.L. (2005). Study of Z gamma events and limits on anomalous Z Z gamma and Z gamma gamma couplings in p anti-p collisions at s** (1/2) = 1.96-TeV. Physical Review Letters, 95 051802-. doi:10.1103/PhysRevLett.95.051802
Lancaster, M., Waters, D.C.D.F.C. (2005). Measurement of the tt-bar Production Cross Section in p-bar p Collisions at sqrt s = 1.96 TeV using Kinematic Fitting of b-tagged Lepton + Jet Events. Physical Review D, 71 072005-.
Lancaster, M., Waters, D.C.D.F.C. (2005). Measurement of the tt-bar Production Cross Section in pp-bar Collisions at s**(1/2) = 1.96 TeV Using Lepton + Jets Events with Secondary Vertex b-Tagging. Physical Review D, 71 052003-.

2004

Abazov, V.M., Abbott, B., Abdesselam, A., Abolins, M., Abramov, V., Acharya, B.S., ...Affolder, T. (2004). Combination of CDF and D0 results on the W boson mass and width. PHYSICAL REVIEW D, 70 (9), doi:10.1103/PhysRevD.70.092008
Abazov, V.M., Abbott, B., Abdesselam, A., Abolins, M., Abramov, V., Acharya, B.S., ...Alexeev, G.D. (2004). Search for pair production of light scalar top quarks in p(p)over-bar collisions at root s=1.8 TeV. PHYSICAL REVIEW LETTERS, 93 (1), doi:10.1103/PhysRevLett.93.011801
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, D.L., Adams, M., ...Ahmed, S.N. (2004). Observation and properties of the X(3872) decaying to J/psi pi(+)pi(-) in p(p)over-bar collisions at root s=1.96 TeV. PHYSICAL REVIEW LETTERS, 93 (16), doi:10.1103/PhysRevLett.93.162002
Abazov, V.M., Abbott, B., Abolins, M., Acharya, B.S., Adams, D.L., Adams, M., ...Ahmed, S.N. (2004). Search for doubly charged Higgs boson pair production in the decay to mu(+)mu(+)mu(-)mu(-) in p(p)over-bar collisions at root s=1.96 TeV. PHYSICAL REVIEW LETTERS, 93 (14), doi:10.1103/PhysRevLett.93.141801
Acosta, D., Affolder, T., Akimoto, T., Albrow, M.G., Ambrose, D., Amerio, S., ...Annovi, A. (2004). Measurement of the t(t)over-bar production cross section in p(p)over-bar collisions at root s=1.96 TeV using dilepton events. PHYSICAL REVIEW LETTERS, 93 (14), doi:10.1103/PhysRevLett.93.142001

2002

Lancaster, M., Waters, D.C.D.F.C. (2002). Search for Single-Top-Quark Production in p anti-p Collisions at s**(1/2) = 1.8 TeV. Physical Review D, 65 091120-.

2001

Toumi, R., Syroka, J., Barnes, C., Lewis, P. (2001). Robust non-Gaussian statistics and long-range correlation of total ozone. Atmospheric Science Letters, 2 (1-4), 94-103. doi:10.1006/asle.2001.0042