Serafim Batzoglou

2008
30	EE	Chuong B. Do, Chuan-Sheng Foo, Serafim Batzoglou: A max-margin model for efficient simultaneous alignment and folding of RNA sequences. ISMB 2008: 68-76
29	EE	Jason Flannick, Antal F. Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou: Automatic Parameter Learning for Multiple Network Alignment. RECOMB 2008: 214-231
28	EE	Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou: Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. RECOMB 2008: 423
2007
27	EE	Balaji S. Srinivasan, Nigam H. Shah, Jason Flannick, Eduardo Abeliuk, Antal F. Novak, Serafim Batzoglou: Current progress in network research: toward reference networks for key model organisms. Briefings in Bioinformatics 8(5): 318-332 (2007)
2006
26	EE	Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, Serafim Batzoglou: MotifCut: regulatory motifs finding with maximum density subgraphs. ISMB (Supplement of Bioinformatics) 2006: 156-157
25	EE	Chuong B. Do, Daniel A. Woods, Serafim Batzoglou: CONTRAfold: RNA secondary structure prediction without physics-based models. ISMB (Supplement of Bioinformatics) 2006: 90-98
24	EE	Samuel S. Gross, Olga Russakovsky, Chuong B. Do, Serafim Batzoglou: Training Conditional Random Fields for Maximum Labelwise Accuracy. NIPS 2006: 529-536
23	EE	Balaji S. Srinivasan, Antal F. Novak, Jason Flannick, Serafim Batzoglou, Harley H. McAdams: Integrated Protein Interaction Networks for 11 Microbes. RECOMB 2006: 1-14
22	EE	Chuong B. Do, Samuel S. Gross, Serafim Batzoglou: CONTRAlign: Discriminative Training for Protein Sequence Alignment. RECOMB 2006: 160-174
21	EE	Eugene Davydov, Serafim Batzoglou: A computational model for RNA multiple structural alignment. Theor. Comput. Sci. 368(3): 205-216 (2006)
2005
20	EE	Aswath Manohar, Serafim Batzoglou: TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree. CSB 2005: 111-119
19		Serafim Batzoglou: The many faces of sequence alignment. Briefings in Bioinformatics 6(1): 6-22 (2005)
2004
18		Chuong B. Do, Michael Brudno, Serafim Batzoglou: PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. AAAI 2004: 703-708
17	EE	Eugene Davydov, Serafim Batzoglou: A Computational Model for RNA Multiple Structural Alignment.. CPM 2004: 254-269
16	EE	Mukund Sundararajan, Michael Brudno, Kerrin Small, Arend Sidow, Serafim Batzoglou: Chaining Algorithms for Alignment of Draft Sequence. WABI 2004: 326-337
15	EE	Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak: Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics 20(5): 636-643 (2004)
14		Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, X. Shirley Liu: A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Research 32(Web-Server-Issue): 204-207 (2004)
2003
13	EE	Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou: Glocal alignment: finding rearrangements during alignment. ISMB (Supplement of Bioinformatics) 2003: 54-62
12	EE	Su-In Lee, Serafim Batzoglou: ICA-based Clustering of Genes from Microarray Expression Data. NIPS 2003
11	EE	Serafim Batzoglou, Lior Pachter: Gene Regulation - Session Introduction. Pacific Symposium on Biocomputing 2003: 3-4
10	EE	Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern: Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics 4: 66 (2003)
9		Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern: AGenDA: homology-based gene prediction. Bioinformatics 19(12): 1575-1577 (2003)
2000
8	EE	Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander: Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). RECOMB 2000: 45
7	EE	Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander: Human and mouse gene structure: comparative analysis and application to exon prediction. RECOMB 2000: 46-53
1999
6	EE	Serafim Batzoglou, Sorin Istrail: Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem. CPM 1999: 66-77
5	EE	Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman: A dictionary based approach for gene annotation. RECOMB 1999: 285-294
4		Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, E. Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger: A Dictionary-Based Approach for Gene Annotation. Journal of Computational Biology 6(3/4): (1999)
1997
3	EE	Richa Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan, Steven Skiena: Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. RECOMB 1997: 1-2
2		Richa Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, Steven Skiena: Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. SODA 1997: 390-399
1		Richa Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Sridhar Hannenhalli, Martin Farach, S. Muthukrishnan, Steven Skiena: Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. Journal of Computational Biology 4(3): 275-296 (1997)

Coauthor Index

1	Eduardo Abeliuk	[27]
2	Richa Agarwala	[1] [2] [3]
3	E. Banks	[4]
4	William S. Beebee	[5]
5	Bonnie Berger	[4] [5] [7] [8]
6	E. Wes Bethel (Wes Bethel)	[15]
7	Michael Brudno	[9] [10] [13] [15] [16] [18]
8	Douglas L. Brutlag	[14] [26]
9	Michael Chapman	[10]
10	Olivier Couronne	[13] [15]
11	Vlado Dancík	[1] [2] [3]
12	Eugene Davydov	[17] [21]
13	Scott E. Decatur	[1] [2] [3]
14	Chuong B. Do	[13] [18] [22] [24] [25] [28] [29] [30]
15	Inna Dubchak	[13] [15]
16	Martin Farach-Colton (Martin Farach)	[1] [2] [3]
17	Jason Flannick	[23] [27] [29]
18	Chuan-Sheng Foo	[30]
19	Eugene Fratkin	[26] [28]
20	Saurabh Garg	[9]
21	Berthold Göttgens	[10]
22	Samuel S. Gross	[22] [24]
23	Bernd Hamann	[15]
24	Sridhar Hannenhalli	[1] [2] [3]
25	Sorin Istrail	[6]
26	Daniel J. Kleitman	[4] [5]
27	Eric S. Lander	[4] [5] [7] [8]
28	Su-In Lee	[12]
29	Jun S. Liu	[14]
30	X. Shirley Liu	[14]
31	Yueyi Liu	[14]
32	Sanket Malde	[13]
33	Aswath Manohar	[20]
34	Harley H. McAdams	[23]
35	Jill P. Mesirov	[7] [8]
36	Burkhard Morgenstern	[9] [10]
37	S. Muthukrishnan (S. Muthu Muthukrishnan)	[1] [3]
38	Brian T. Naughton	[26]
39	Antal F. Novak	[23] [27] [29]
40	Lior Pachter	[4] [5] [7] [11]
41	Len A. Pennacchio	[15]
42	Alexander Poliakov	[13]
43	Oliver Rinner	[9]
44	Edward M. Rubin	[15]
45	Olga Russakovsky	[24]
46	Alexander Sczyrba	[9]
47	Nameeta Shah	[15]
48	Nigam H. Shah	[27]
49	Arend Sidow	[16]
50	Steven Skiena	[1] [2] [3]
51	Kerrin Small	[16]
52	Valentin I. Spitkovsky	[4] [5]
53	Balaji S. Srinivasan	[23] [27] [29]
54	Mukund Sundararajan	[16]
55	Andreas Sundquist	[28]
56	Leila Taher	[9]
57	Liping Wei	[14]
58	Daniel A. Woods	[25]

Colors in the list of coauthors