Bonnie Berger

Bonnie Berger

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Emerging technologies towards enhancing privacy in genomic data sharing.

Genome Biol 2019 07 2;20(1):128. Epub 2019 Jul 2.

Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.1186/s13059-019-1741-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604426PMC
July 2019

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.

Nat Biotechnol 2019 06 6;37(6):685-691. Epub 2019 May 6.

Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41587-019-0113-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551256PMC
June 2019

Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape.

Cell Syst 2019 Jun 5;8(6):483-493.e7. Epub 2019 Jun 5.

Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA; Department of Mathematics, MIT, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597305PMC
June 2019

Metagenomic binning through low-density hashing.

Bioinformatics 2019 01;35(2):219-226

Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330020PMC
January 2019

Protecting Genomic Data Privacy with Probabilistic Modeling.

Pac Symp Biocomput 2019 ;24:403-414

Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447070PMC
January 2019

Joker de Bruijn: Covering k-Mers Using Joker Characters.

J Comput Biol 2018 11 17;25(11):1171-1178. Epub 2018 Aug 17.

2 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts.

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http://dx.doi.org/10.1089/cmb.2018.0032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247992PMC
November 2018

Realizing private and practical pharmacological collaboration.

Science 2018 10;362(6412):347-350

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/science.aat4807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6519716PMC
October 2018

Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks.

Cell Syst 2018 08 20;7(2):185-191.e4. Epub 2018 Jun 20.

Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.05.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469860PMC
August 2018

Statistical Binning for Barcoded Reads Improves Downstream Analyses.

Cell Syst 2018 08;7(2):219-226.e5

Computer Science and AI Lab, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214366PMC
August 2018

Secure genome-wide association analysis using multiparty computation.

Nat Biotechnol 2018 07 7;36(6):547-551. Epub 2018 May 7.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://www.nature.com/doifinder/10.1038/nbt.4108
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http://dx.doi.org/10.1038/nbt.4108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990440PMC
July 2018

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs.

Res Comput Mol Biol 2018 Apr;10812:245-247

Computational and Systems Biology, MIT, Cambridge, MA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5917602PMC
April 2018

Generalizable visualization of mega-scale single-cell data.

Res Comput Mol Biol 2018 Apr;10812:251-253

Department of Computer Science, UIUC, Urbana, IL 61801, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5917073PMC
April 2018

Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses.

Res Comput Mol Biol 2018 Apr;10812:280-282

Computer Science and AI Lab, MIT, Cambridge, MA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989713PMC
April 2018

Squeakr: an exact and approximate k-mer counting system.

Bioinformatics 2018 02;34(4):568-575

Department of Computer Science, Stony Brook University, Stony Brook, NY 11790, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx636DOI Listing
February 2018

Finding RNA structure in the unstructured RBPome.

BMC Genomics 2018 02 20;19(1):154. Epub 2018 Feb 20.

Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1186/s12864-018-4540-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819699PMC
February 2018

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks.

Cell Syst 2018 Jan 20;6(1):65-74.e3. Epub 2017 Dec 20.

Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.11.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808454PMC
January 2018

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.

Bioinformatics 2017 09;33(18):2968

International Society for Computational Biology, Inc. (ISCB), 9650 Rockville Pike Bethesda, Maryland 20814, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870847PMC
September 2017

Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping.

Cell Syst 2017 09;5(3):230-236.e5

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5661997PMC
September 2017

Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner.

Bioinformatics 2017 07;33(14):2245-2246

Department of Mathematics, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx289DOI Listing
July 2017

Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter.

Bioinformatics 2017 07;33(14):2249-2250

Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx291DOI Listing
July 2017

Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock.

Bioinformatics 2017 07;33(14):2247-2248

Department of Mathematics, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx290DOI Listing
July 2017

Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev.

Bioinformatics 2017 07;33(14):2243-2244

Department of Mathematics, MIT, Cambridge, MA, USA.

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https://academic.oup.com/bioinformatics/article/33/14/2243/3
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http://dx.doi.org/10.1093/bioinformatics/btx288DOI Listing
July 2017

Identification of protein complexes by integrating multiple alignment of protein interaction networks.

Bioinformatics 2017 Jun;33(11):1681-1688

Department of Industrial Engineering and Engineering Management, National Tsing Hua University, Hsinchu, Taiwan.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btx043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860626PMC
June 2017

2017 Outstanding Contributions to ISCB Award: Fran Lewitter.

PLoS Comput Biol 2017 Jun 30;13(6):e1005560. Epub 2017 Jun 30.

Department of Mathematics, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493284PMC
June 2017

2017 ISCB Innovator Award: Aviv Regev.

PLoS Comput Biol 2017 06 30;13(6):e1005558. Epub 2017 Jun 30.

Department of Mathematics, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1005558
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http://dx.doi.org/10.1371/journal.pcbi.1005558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493285PMC
June 2017

2017 ISCB Overton Prize awarded to Christoph Bock.

PLoS Comput Biol 2017 06 30;13(6):e1005559. Epub 2017 Jun 30.

Department of Mathematics, MIT, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493286PMC
June 2017

2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner.

PLoS Comput Biol 2017 Jun 30;13(6):e1005561. Epub 2017 Jun 30.

Department of Mathematics, MIT, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493287PMC
June 2017

2017 Outstanding Contributions to ISCB Award: Fran Lewitter.

F1000Res 2017 26;6. Epub 2017 Jun 26.

Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.12688/f1000research.11587.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490472PMC
June 2017

2017 ISCB Overton Prize: Christoph Bock.

F1000Res 2017 26;6. Epub 2017 Jun 26.

Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.12688/f1000research.11586.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490473PMC
June 2017

2017 ISCB Innovator Award: Aviv Regev.

F1000Res 2017 26;6. Epub 2017 Jun 26.

Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

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https://f1000research.com/articles/6-998/v1
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http://dx.doi.org/10.12688/f1000research.11585.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490476PMC
June 2017

2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner.

F1000Res 2017 26;6. Epub 2017 Jun 26.

Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.12688/f1000research.11588.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490481PMC
June 2017

Joker de Bruijn: Sequence Libraries to Cover All -mers Using Joker Characters.

Res Comput Mol Biol 2017 May;10229:389-390

Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1007/978-3-319-56970-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5917071PMC
May 2017

An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.

Proc Data Compress Conf 2016 Mar-Apr;2016:221-230. Epub 2016 Dec 19.

Massachusetts Institute of Technology CSAIL & Mathematics. Cambridge, MA.

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http://dx.doi.org/10.1109/DCC.2016.39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568552PMC
December 2016

Compact Integration of Multi-Network Topology for Functional Analysis of Genes.

Cell Syst 2016 Dec 23;3(6):540-548.e5. Epub 2016 Nov 23.

Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA; Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.10.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225290PMC
December 2016

Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities.

Genome Biol 2016 11 14;17(1):228. Epub 2016 Nov 14.

Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck Street, Boston, 02115, MA, USA.

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http://dx.doi.org/10.1186/s13059-016-1084-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5108086PMC
November 2016

Fast genotyping of known SNPs through approximate k-mer matching.

Bioinformatics 2016 09;32(17):i538-i544

Computer Science and AI Lab Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013917PMC
September 2016

Structured States of Disordered Proteins from Genomic Sequences.

Cell 2016 Sep;167(1):158-170.e12

Department of Systems Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451116PMC
September 2016

Reconstructing Causal Biological Networks through Active Learning.

PLoS One 2016 1;11(3):e0150611. Epub 2016 Mar 1.

Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150611PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773135PMC
August 2016

Computational Biology in the 21st Century: Scaling with Compressive Algorithms.

Commun ACM 2016 Aug;59(8):72-80

Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA.

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http://dx.doi.org/10.1145/2957324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5615407PMC
August 2016

Enabling Privacy-Preserving GWASs in Heterogeneous Human Populations.

Cell Syst 2016 07 21;3(1):54-61. Epub 2016 Jul 21.

Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.04.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4994706PMC
July 2016

RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.

Bioinformatics 2016 06;32(12):i351-i359

Computer Science and Artificial Intelligence Laboratory Math Department, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908343PMC
June 2016

Realizing privacy preserving genome-wide association studies.

Bioinformatics 2016 05 14;32(9):1293-300. Epub 2016 Jan 14.

Department of Mathematics and CSAIL, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848404PMC
May 2016

Compressive mapping for next-generation sequencing.

Nat Biotechnol 2016 Apr;34(4):374-6

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080835PMC
http://dx.doi.org/10.1038/nbt.3511DOI Listing
April 2016

Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning.

Res Comput Mol Biol 2016 Apr;9649:255-257

Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5260810PMC
April 2016

Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers.

J Comput Biol 2016 Feb 29;23(2):67-79. Epub 2015 Dec 29.

1 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , Cambridge, MA.

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http://dx.doi.org/10.1089/cmb.2015.0179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752187PMC
February 2016

Two-Variance-Component Model Improves Genetic Prediction in Family Datasets.

Am J Hum Genet 2015 Nov;97(5):677-90

Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667134PMC
November 2015

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes.

PLoS Genet 2015 Nov 12;11(11):e1005550. Epub 2015 Nov 12.

Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642934PMC
November 2015

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals.

PLoS Genet 2015 Nov 20;11(11):e1005652. Epub 2015 Nov 20.

Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654475PMC
November 2015

Reply to "Do genome-scale models need exact solvers or clearer standards?".

Mol Syst Biol 2015 Oct 14;11(10):830. Epub 2015 Oct 14.

Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631201PMC
http://dx.doi.org/10.15252/msb.20156548DOI Listing
October 2015

Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.

J Comput Biol 2015 Aug 22;22(8):715-28. Epub 2015 Jun 22.

1 Department of Mathematics, Massachusetts Institute of Technology , Cambridge, Massachusetts.

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http://dx.doi.org/10.1089/cmb.2015.0085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523039PMC
August 2015

Entropy-scaling search of massive biological data.

Cell Syst 2015 Aug;1(2):130-140

Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 ; Computer Science and AI Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.

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http://dx.doi.org/10.1016/j.cels.2015.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4591002PMC
August 2015

One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data.

Proc IEEE Symp Secur Priv Workshops 2015 20;2015:41-49. Epub 2015 Jul 20.

Department of Mathematics and CSAIL, Massachusetts Institute of Technology.

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http://dx.doi.org/10.1109/SPW.2015.25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708597PMC
July 2015

Exploiting ontology graph for predicting sparsely annotated gene function.

Bioinformatics 2015 Jun;31(12):i357-64

Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA and Department of Mathematics, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542782PMC
June 2015

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.

F1000Res 2015 15;4:12. Epub 2015 Jan 15.

International Society for Computational Biology, La Jolla, CA, USA ; Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA.

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http://dx.doi.org/10.12688/f1000research.6038.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457108PMC
June 2015

Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks.

Res Comput Mol Biol 2015 Apr 26;9029:62-64. Epub 2015 Mar 26.

Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-3-319-16706-0_9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524124PMC
April 2015

HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data.

Res Comput Mol Biol 2015 26;9029:28-29. Epub 2015 Mar 26.

Department of Mathematics, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-3-319-16706-0_4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558598PMC
March 2015

Efficient Bayesian mixed-model analysis increases association power in large cohorts.

Nat Genet 2015 Mar 2;47(3):284-90. Epub 2015 Feb 2.

1] Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [3] Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.3190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342297PMC
March 2015

Quality score compression improves genotyping accuracy.

Nat Biotechnol 2015 Mar;33(3):240-3

1] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4439189PMC
March 2015

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.

Bioinformatics 2015 Feb 2;31(4):616-7. Epub 2015 Feb 2.

International Society for Computational Biology, La Jolla, CA, USA, SRI International, Menlo Park, CA, USA, Department of Mathematics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA, Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbruecken, Germany, Hebrew University & Institute of Advanced Studies, Jerusalem, Israel, Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA, Department of Immunology and Infectious Disease, Harvard School of Public Health, Cambridge, MA, USA, Broad Institute of Harvard and MIT, Cambridge, MA, USA, Sheffield Institute for Translational Neuroscience, Harvard School of Public Health, Boston, MA, USA, Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany and Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA International Society for Computational Biology, La Jolla, CA, USA, SRI International, Menlo Park, CA, USA, Department of Mathematics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA, Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbruecken, Germany, Hebrew University & Institute of Advanced Studies, Jerusalem, Israel, Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA, Department of Immunology and Infectious Disease, Harvard School of Public Health, Cambridge, MA, USA, Broad Institute of Harvard and MIT, Cambridge, MA, USA, Sheffield Institute for Translational Neuroscience, Harvard School of Public Health, Boston, MA, USA, Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany and Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA International Society for Computational Biology, La Jolla, CA, USA, SRI International, Menlo Park, CA, USA, Department o

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http://dx.doi.org/10.1093/bioinformatics/btv019DOI Listing
February 2015

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models.

Nat Commun 2014 Oct 7;5:4893. Epub 2014 Oct 7.

1] Mathematics Department, Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA [2] Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/ncomms5893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205847PMC
October 2014

Ancient human genomes suggest three ancestral populations for present-day Europeans.

Authors:
Iosif Lazaridis Nick Patterson Alissa Mittnik Gabriel Renaud Swapan Mallick Karola Kirsanow Peter H Sudmant Joshua G Schraiber Sergi Castellano Mark Lipson Bonnie Berger Christos Economou Ruth Bollongino Qiaomei Fu Kirsten I Bos Susanne Nordenfelt Heng Li Cesare de Filippo Kay Prüfer Susanna Sawyer Cosimo Posth Wolfgang Haak Fredrik Hallgren Elin Fornander Nadin Rohland Dominique Delsate Michael Francken Jean-Michel Guinet Joachim Wahl George Ayodo Hamza A Babiker Graciela Bailliet Elena Balanovska Oleg Balanovsky Ramiro Barrantes Gabriel Bedoya Haim Ben-Ami Judit Bene Fouad Berrada Claudio M Bravi Francesca Brisighelli George B J Busby Francesco Cali Mikhail Churnosov David E C Cole Daniel Corach Larissa Damba George van Driem Stanislav Dryomov Jean-Michel Dugoujon Sardana A Fedorova Irene Gallego Romero Marina Gubina Michael Hammer Brenna M Henn Tor Hervig Ugur Hodoglugil Aashish R Jha Sena Karachanak-Yankova Rita Khusainova Elza Khusnutdinova Rick Kittles Toomas Kivisild William Klitz Vaidutis Kučinskas Alena Kushniarevich Leila Laredj Sergey Litvinov Theologos Loukidis Robert W Mahley Béla Melegh Ene Metspalu Julio Molina Joanna Mountain Klemetti Näkkäläjärvi Desislava Nesheva Thomas Nyambo Ludmila Osipova Jüri Parik Fedor Platonov Olga Posukh Valentino Romano Francisco Rothhammer Igor Rudan Ruslan Ruizbakiev Hovhannes Sahakyan Antti Sajantila Antonio Salas Elena B Starikovskaya Ayele Tarekegn Draga Toncheva Shahlo Turdikulova Ingrida Uktveryte Olga Utevska René Vasquez Mercedes Villena Mikhail Voevoda Cheryl A Winkler Levon Yepiskoposyan Pierre Zalloua Tatijana Zemunik Alan Cooper Cristian Capelli Mark G Thomas Andres Ruiz-Linares Sarah A Tishkoff Lalji Singh Kumarasamy Thangaraj Richard Villems David Comas Rem Sukernik Mait Metspalu Matthias Meyer Evan E Eichler Joachim Burger Montgomery Slatkin Svante Pääbo Janet Kelso David Reich Johannes Krause

Nature 2014 Sep;513(7518):409-13

1] Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany. [2] Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany. [3] Max Planck Institut für Geschichte und Naturwissenschaften, Jena 07745, Germany.

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September 2014

Reconstructing Austronesian population history in Island Southeast Asia.

Nat Commun 2014 Aug 19;5:4689. Epub 2014 Aug 19.

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ncomms5689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143916PMC
August 2014

Simultaneous alignment and folding of protein sequences.

J Comput Biol 2014 Jul 25;21(7):477-91. Epub 2014 Apr 25.

1 School of Computer Science, McGill University , Montreal, Canada .

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http://dx.doi.org/10.1089/cmb.2013.0163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082353PMC
July 2014

Improving the power of GWAS and avoiding confounding from population stratification with PC-Select.

Genetics 2014 Jul 29;197(3):1045-9. Epub 2014 Apr 29.

*Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139

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http://dx.doi.org/10.1534/genetics.114.164285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096359PMC
July 2014

A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.

Cell 2014 Jul;158(2):434-448

Whitehead Institute for Biomedical Research, Cambridge, MA 02114, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.05.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104544PMC
July 2014

Traversing the -mer Landscape of NGS Read Datasets for Quality Score Sparsification.

Res Comput Mol Biol 2014 Apr;8394:385-399

Massachusetts Institute of Technology, Cambridge MA 02139, USA http://people.csail.mit.edu/bab/.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558603PMC
April 2014

HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data.

PLoS Comput Biol 2014 Mar 27;10(3):e1003502. Epub 2014 Mar 27.

Department of Mathematics, MIT, Cambridge, Massachusetts, United States of America; Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967924PMC
March 2014

Ancient west Eurasian ancestry in southern and eastern Africa.

Proc Natl Acad Sci U S A 2014 Feb 3;111(7):2632-7. Epub 2014 Feb 3.

Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932865PMC
February 2014

Optimizing a global alignment of protein interaction networks.

Bioinformatics 2013 Nov 17;29(21):2765-73. Epub 2013 Sep 17.

Computer Science and Artificial Intelligence Laboratory and Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Computer Science and Department of Industrial Engineering and Engineering Management, National Tsing Hua University, Hsinchu 30013, Taiwan.

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http://dx.doi.org/10.1093/bioinformatics/btt486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799479PMC
November 2013

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis.

BMC Bioinformatics 2013 Oct 4;14:299. Epub 2013 Oct 4.

Mathematics Department and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.1186/1471-2105-14-299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851523PMC
October 2013

Reconstruction of phyletic trees by global alignment of multiple metabolic networks.

BMC Bioinformatics 2013 21;14 Suppl 2:S12. Epub 2013 Jan 21.

Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549807PMC
September 2013

Genetic evidence for recent population mixture in India.

Am J Hum Genet 2013 Sep 8;93(3):422-38. Epub 2013 Aug 8.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.ajhg.2013.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769933PMC
September 2013

Efficient moment-based inference of admixture parameters and sources of gene flow.

Mol Biol Evol 2013 Aug 24;30(8):1788-802. Epub 2013 May 24.

Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology.

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http://dx.doi.org/10.1093/molbev/mst099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708505PMC
August 2013

Compressive genomics for protein databases.

Bioinformatics 2013 Jul;29(13):i283-90

Department of Computer Science, Tufts University, Medford, MA 02451, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851851PMC
July 2013

Structure-based whole-genome realignment reveals many novel noncoding RNAs.

Genome Res 2013 Jun 7;23(6):1018-27. Epub 2013 Jan 7.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.137091.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668356PMC
June 2013

Computational solutions for omics data.

Nat Rev Genet 2013 May;14(5):333-46

Department of Mathematics and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nrg3433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966295PMC
May 2013

Inferring admixture histories of human populations using linkage disequilibrium.

Genetics 2013 Apr 14;193(4):1233-54. Epub 2013 Feb 14.

Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1534/genetics.112.147330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606100PMC
April 2013

Computational analysis of noncoding RNAs.

Wiley Interdiscip Rev RNA 2012 Nov-Dec;3(6):759-78. Epub 2012 Sep 18.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1002/wrna.1134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472101PMC
February 2013

A global sampling approach to designing and reengineering RNA secondary structures.

Nucleic Acids Res 2012 Nov 31;40(20):10041-52. Epub 2012 Aug 31.

Computer Science and Artificial Intelligence Laboratory, Department of Mathematics, MIT, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/nar/gks768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488226PMC
November 2012

Compressive genomics.

Nat Biotechnol 2012 Jul 10;30(7):627-30. Epub 2012 Jul 10.

Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.2241DOI Listing
July 2012

Making sense out of massive data by going beyond differential expression.

Proc Natl Acad Sci U S A 2012 Apr 23;109(15):5594-9. Epub 2012 Mar 23.

Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.1118792109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326474PMC
April 2012

Assessing statistical significance in causal graphs.

BMC Bioinformatics 2012 Feb 20;13:35. Epub 2012 Feb 20.

Computational Sciences Center of Emphasis, Pfizer Worldwide Research & Development, Cambridge, MA, USA.

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http://dx.doi.org/10.1186/1471-2105-13-35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307026PMC
February 2012