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1

What is the expectation maximization algorithm?

Do, Chuong B, Batzoglou, Serafim

Journal:

Nature Biotechnology

Year:

2008

Language:

english

File:

PDF, 856 KB

english, 2008

2

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

Kuleshov, Volodymyr, Jiang, Chao, Zhou, Wenyu, Jahanbani, Fereshteh, Batzoglou, Serafim, Snyder, Michael

Journal:

Nature Biotechnology

Year:

2015

Language:

english

File:

PDF, 1.19 MB

english, 2015

3

High-quality genome sequences of uncultured microbes by assembly of read clouds

Bishara, Alex, Moss, Eli L, Kolmogorov, Mikhail, Parada, Alma E, Weng, Ziming, Sidow, Arend, Dekas, Anne E, Batzoglou, Serafim, Bhatt, Ami S

Journal:

Nature Biotechnology

Year:

2018

Language:

english

File:

PDF, 5.27 MB

english, 2018

4

A computational model for RNA multiple structural alignment

Eugene Davydov, Serafim Batzoglou

Journal:

Theoretical Computer Science

Year:

2006

Language:

english

File:

PDF, 468 KB

english, 2006

5

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

Valouev, Anton, Johnson, David S, Sundquist, Andreas, Medina, Catherine, Anton, Elizabeth, Batzoglou, Serafim, Myers, Richard M, Sidow, Arend

Journal:

Year:

2008

Language:

english

File:

PDF, 349 KB

english, 2008

6

Multiple sequence alignment

Robert C Edgar, Serafim Batzoglou

Journal:

Current Opinion in Structural Biology

Year:

2006

Language:

english

File:

PDF, 102 KB

english, 2006

7

A serial founder effect model for human settlement out of Africa

Deshpande, O., Batzoglou, S., Feldman, M. W, Luca Cavalli-Sforza, L

Journal:

Proceedings Biological Sciences

Year:

2009

Language:

english

File:

PDF, 158 KB

english, 2009

8

CONTRAfold: RNA secondary structure prediction without physics-based models

Do, C. B., Woods, D. A., Batzoglou, S.

Journal:

Year:

2006

Language:

english

File:

PDF, 648 KB

english, 2006

9

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

Davydov, Eugene V., Goode, David L., Sirota, Marina, Cooper, Gregory M., Sidow, Arend, Batzoglou, Serafim, Wasserman, Wyeth W.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.39 MB

english, 2010

10

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

Wang, Bo, Zhu, Junjie, Pierson, Emma, Ramazzotti, Daniele, Batzoglou, Serafim

Journal:

Year:

2017

Language:

english

File:

PDF, 4.40 MB

english, 2017

11

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

Galagan, James E., Calvo, Sarah E., Cuomo, Christina, Ma, Li-Jun, Wortman, Jennifer R., Batzoglou, Serafim, Lee, Su-In, Baştürkmen, Meray, Spevak, Christina C., Clutterbuck, John

Journal:

Year:

2005

Language:

english

File:

PDF, 1.29 MB

english, 2005

12

Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies

Sundquist, Andreas, Ronaghi, Mostafa, Tang, Haixu, Pevzner, Pavel, Batzoglou, Serafim, Christoffels, Alan

Journal:

Year:

2007

Language:

english

File:

PDF, 697 KB

english, 2007

13

Fast and sensitive multiple alignment of large genomic sequences

Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern

Journal:

BMC Bioinformatics

Year:

2003

Language:

english

File:

PDF, 436 KB

english, 2003

14

Bacterial flora-typing with targeted, chip-based Pyrosequencing

Andreas Sundquist, Saharnaz Bigdeli, Roxana Jalili, Maurice L Druzin, Sarah Waller, Kristin M Pullen, Yasser Y El-Sayed, M Mark Taslimi, Serafim Batzoglou, Mostafa Ronaghi

Journal:

BMC Microbiology

Year:

2007

Language:

english

File:

PDF, 2.38 MB

english, 2007

15

Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans

Xiao Liu, Fuhui Long, Hanchuan Peng, Sarah J. Aerni, Min Jiang, Adolfo Sánchez-Blanco, John I. Murray, Elicia Preston, Barbara Mericle, Serafim Batzoglou, Eugene W. Myers, Stuart K. Kim

Journal:

Year:

2009

Language:

english

File:

PDF, 1.28 MB

english, 2009

16

Eprosartan effect on fibrinolytic/hemostatic variables in arterial hypertension: a comparative study to losartan

Thomas K. Makris, Panagiota G. Krespi, Antonios N. Hatzizacharias, Dimetrios Papadopoulos, Evangelos Batzoglou, Maria Kouli, Perseas Gioldasis, Vassilios V. Votteas

Journal:

American Journal of Hypertension

Year:

2003

Language:

english

File:

PDF, 32 KB

english, 2003

17

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 5541 || How Many Bootstrap Replicates Are Necessary?

Batzoglou, Serafim

Year:

2009

Language:

english

File:

PDF, 355 KB

english, 2009

18

CONTRAST: a discriminative, phylogeny-free approach to multiple informantde novogene prediction

Samuel S Gross, Chuong B Do, Marina Sirota, Serafim Batzoglou

Journal:

Year:

2007

Language:

english

File:

PDF, 1.01 MB

english, 2007

19

Evidence for intelligent (algorithm) design

Balaji S Srinivasan, Chuong B Do, Serafim Batzoglou

Journal:

Year:

2006

Language:

english

File:

PDF, 53 KB

english, 2006

20

Application of independent component analysis to microarrays

Su-In Lee, Serafim Batzoglou

Journal:

Year:

2003

Language:

english

File:

PDF, 771 KB

english, 2003

21

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 5541 || The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory

Batzoglou, Serafim

Year:

2009

Language:

english

File:

PDF, 281 KB

english, 2009

22

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 5541 || Spatial Clustering of Multivariate Genomic and Epigenomic Information

Batzoglou, Serafim

Year:

2009

Language:

english

File:

PDF, 1.06 MB

english, 2009

23

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 5541 || A Statistical Framework for the Functional Analysis of Metagenomes

Batzoglou, Serafim

Year:

2009

Language:

english

File:

PDF, 927 KB

english, 2009

24

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 5541 ||

Batzoglou, Serafim

Year:

2009

Language:

english

File:

PDF, 24.74 MB

english, 2009

25

Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model

AGARWALA, RICHA, BATZOGLOU, SERAFIM, DANČÍK, VLADO, DECATUR, SCOTT E., HANNENHALLI, SRIDHAR, FARACH, MARTIN, MUTHUKRISHNAN, S., SKIENA, STEVEN

Journal:

Journal of Computational Biology

Year:

1997

Language:

english

File:

PDF, 8.91 MB

english, 1997

26

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

Kundaje, A., Kyriazopoulou-Panagiotopoulou, S., Libbrecht, M., Smith, C. L., Raha, D., Winters, E. E., Johnson, S. M., Snyder, M., Batzoglou, S., Sidow, A.

Journal:

Genome Research

Year:

2012

Language:

english

File:

PDF, 2.53 MB

english, 2012

27

[IEEE 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05) - Stanford, CA, USA (2005.08.11-2005.08.11)] 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05) - TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree

Manohar, A., Batzoglou, S.

Year:

2005

Language:

english

File:

PDF, 259 KB

english, 2005

28

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., Chen, Y., DeSalvo, G., Epstein, C., Fisher-Aylor, K. I., E

Journal:

Genome Research

Year:

2012

Language:

english

File:

PDF, 2.58 MB

english, 2012

29

A Dictionary-Based Approach for Gene Annotation

Pachter, Lior, Batzoglou, Serafim, Spitkovsky, Valentin I., Banks, Eric, Lander, Eric S., Kleitman, Daniel J., Berger, Bonnie

Journal:

Journal of Computational Biology

Year:

1999

Language:

english

File:

PDF, 360 KB

english, 1999

30

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

Salari, Raheleh, Saleh, Syed Shayon, Kashef-Haghighi, Dorna, Khavari, David, Newburger, Daniel E., West, Robert B., Sidow, Arend, Batzoglou, Serafim

Journal:

Journal of Computational Biology

Year:

2013

Language:

english

File:

PDF, 363 KB

english, 2013

31

Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models

Rodriguez, Jesse M., Bercovici, Sivan, Elmore, Megan, Batzoglou, Serafim

Journal:

Journal of Computational Biology

Year:

2013

Language:

english

File:

PDF, 422 KB

english, 2013

32

Genome evolution during progression to breast cancer

Newburger, D. E., Kashef-Haghighi, D., Weng, Z., Salari, R., Sweeney, R. T., Brunner, A. L., Zhu, S. X., Guo, X., Varma, S., Troxell, M. L., West, R. B., Batzoglou, S., Sidow, A.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.25 MB

english, 2013

33

The many faces of sequence alignment

Journal:

Briefings in Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1001 KB

english, 2005

34

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments

Shah, N., Couronne, O., Pennacchio, L. A., Brudno, M., Batzoglou, S., Bethel, E. W., Rubin, E. M., Hamann, B., Dubchak, I.

Journal:

Year:

2004

Language:

english

File:

PDF, 355 KB

english, 2004

35

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome

Newburger, D. E., Natsoulis, G., Grimes, S., Bell, J. M., Davis, R. W., Batzoglou, S., Ji, H. P.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.46 MB

english, 2012

36

Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction

Journal:

Genome Research

Year:

2000

Language:

english

File:

PDF, 2.61 MB

english, 2000

37

Current progress in network research: toward reference networks for key model organisms

Srinivasan, B. S., Shah, N. H., Flannick, J. A., Abeliuk, E., Novak, A. F., Batzoglou, S.

Journal:

Briefings in Bioinformatics

Year:

2007

Language:

english

File:

PDF, 803 KB

english, 2007

38

ARACHNE: A Whole-Genome Shotgun Assembler

Journal:

Genome Research

Year:

2002

Language:

english

File:

PDF, 674 KB

english, 2002

39

Glocal alignment: finding rearrangements during alignment

Brudno, M., Malde, S., Poliakov, A., Do, C. B., Couronne, O., Dubchak, I., Batzoglou, S.

Journal:

Year:

2003

Language:

english

File:

PDF, 137 KB

english, 2003

40

Sequencing a Genome by Walking with Clone-End Sequences: A Mathematical Analysis

Journal:

Genome Research

Year:

1999

Language:

english

File:

PDF, 869 KB

english, 1999

41

Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans

Aerni, S. J., Liu, X., Do, C. B., Gross, S. S., Nguyen, A., Guo, S. D., Long, F., Peng, H., Kim, S. S., Batzoglou, S.

Journal:

Year:

2013

Language:

english

File:

PDF, 394 KB

english, 2013

42

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

Goode, D. L., Cooper, G. M., Schmutz, J., Dickson, M., Gonzales, E., Tsai, M., Karra, K., Davydov, E., Batzoglou, S., Myers, R. M., Sidow, A.

Journal:

Genome Research

Year:

2010

Language:

english

File:

PDF, 568 KB

english, 2010

43

Editorial

Batzoglou, S., Schwartz, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 49 KB

english, 2014

44

Genetic and Computational Identification of a Conserved Bacterial Metabolic Module

Boutte, Cara C., Srinivasan, Balaji S., Flannick, Jason A., Novak, Antal F., Martens, Andrew T., Batzoglou, Serafim, Viollier, Patrick H., Crosson, Sean, Laub, Michael T.

Journal:

Year:

2008

Language:

english

File:

PDF, 1.44 MB

english, 2008

45

Autoimmune Disease Classification by Inverse Association with SNP Alleles

Sirota, Marina, Schaub, Marc A., Batzoglou, Serafim, Robinson, William H., Butte, Atul J., Allison, David B.

Journal:

Year:

2009

Language:

english

File:

PDF, 410 KB

english, 2009

46

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

Do, C. B., Foo, C.-S., Batzoglou, S.

Journal:

Year:

2008

Language:

english

File:

PDF, 248 KB

english, 2008

47

Short read alignment with populations of genomes

Huang, L., Popic, V., Batzoglou, S.

Journal:

Year:

2013

Language:

english

File:

PDF, 729 KB

english, 2013

48

A Classifier-based approach to identify genetic similarities between diseases

Schaub, M. A., Kaplow, I. M., Sirota, M., Do, C. B., Butte, A. J., Batzoglou, S.

Journal:

Year:

2009

Language:

english

File:

PDF, 272 KB

english, 2009

49

Reconstruction of genealogical relationships with applications to Phase III of HapMap

Kyriazopoulou-Panagiotopoulou, S., Kashef Haghighi, D., Aerni, S. J., Sundquist, A., Bercovici, S., Batzoglou, S.

Journal:

Year:

2011

Language:

english

File:

PDF, 327 KB

english, 2011

50

[ACM Press the fourth annual international conference - Tokyo, Japan (2000..-..)] Proceedings of the fourth annual international conference on Computational molecular biology - RECOMB '00 - Sequencing a genome by walking with clone-end sequences (abstract)

Batzoglou, Serafim, Berger, Bonnie, Mesirov, Jill, Lander, Eric S.

Year:

2000

Language:

english

File:

PDF, 43 KB

english, 2000

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