Serafim Batzoglou

	2009
32		Serafim Batzoglou: Research in Computational Molecular Biology, 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings Springer 2009
31		Marc A. Schaub, Irene M. Kaplow, Marina Sirota, Chuong B. Do, Atul J. Butte, Serafim Batzoglou: A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics 25(12): (2009)
	2008
30		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		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		Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou: Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. RECOMB 2008: 423
	2007
27		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		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		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		Samuel S. Gross, Olga Russakovsky, Chuong B. Do, Serafim Batzoglou: Training Conditional Random Fields for Maximum Labelwise Accuracy. NIPS 2006: 529-536
23		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		Chuong B. Do, Samuel S. Gross, Serafim Batzoglou: CONTRAlign: Discriminative Training for Protein Sequence Alignment. RECOMB 2006: 160-174
21		Eugene Davydov, Serafim Batzoglou: A computational model for RNA multiple structural alignment. Theor. Comput. Sci. 368(3): 205-216 (2006)
	2005
20		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		Eugene Davydov, Serafim Batzoglou: A Computational Model for RNA Multiple Structural Alignment.. CPM 2004: 254-269
16		Mukund Sundararajan, Michael Brudno, Kerrin Small, Arend Sidow, Serafim Batzoglou: Chaining Algorithms for Alignment of Draft Sequence. WABI 2004: 326-337
15		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		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		Su-In Lee, Serafim Batzoglou: ICA-based Clustering of Genes from Microarray Expression Data. NIPS 2003
11		Serafim Batzoglou, Lior Pachter: Gene Regulation - Session Introduction. Pacific Symposium on Biocomputing 2003: 3-4
10		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		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		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		Serafim Batzoglou, Sorin Istrail: Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem. CPM 1999: 66-77
5		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		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	Atul J. Butte	[31]
10	Michael Chapman	[10]
11	Olivier Couronne	[13] [15]
12	Vlado Dancík	[1] [2] [3]
13	Eugene Davydov	[17] [21]
14	Scott E. Decatur	[1] [2] [3]
15	Chuong B. Do	[13] [18] [22] [24] [25] [28] [29] [30] [31]
16	Inna Dubchak	[13] [15]
17	Martin Farach-Colton (Martin Farach)	[1] [2] [3]
18	Jason Flannick	[23] [27] [29]
19	Chuan-Sheng Foo	[30]
20	Eugene Fratkin	[26] [28]
21	Saurabh Garg	[9]
22	Berthold Göttgens	[10]
23	Samuel S. Gross	[22] [24]
24	Bernd Hamann	[15]
25	Sridhar Hannenhalli	[1] [2] [3]
26	Sorin Istrail	[6]
27	Irene M. Kaplow	[31]
28	Daniel J. Kleitman	[4] [5]
29	Eric S. Lander	[4] [5] [7] [8]
30	Su-In Lee	[12]
31	Jun S. Liu	[14]
32	X. Shirley Liu	[14]
33	Yueyi Liu	[14]
34	Sanket Malde	[13]
35	Aswath Manohar	[20]
36	Harley H. McAdams	[23]
37	Jill P. Mesirov	[7] [8]
38	Burkhard Morgenstern	[9] [10]
39	S. Muthukrishnan (S. Muthu Muthukrishnan)	[1] [3]
40	Brian T. Naughton	[26]
41	Antal F. Novak	[23] [27] [29]
42	Lior Pachter	[4] [5] [7] [11]
43	Len A. Pennacchio	[15]
44	Alexander Poliakov	[13]
45	Oliver Rinner	[9]
46	Edward M. Rubin	[15]
47	Olga Russakovsky	[24]
48	Marc A. Schaub	[31]
49	Alexander Sczyrba	[9]
50	Nameeta Shah	[15]
51	Nigam H. Shah (Nigam Shah, N. H. Shah)	[27]
52	Arend Sidow	[16]
53	Marina Sirota	[31]
54	Steven Skiena	[1] [2] [3]
55	Kerrin Small	[16]
56	Valentin I. Spitkovsky	[4] [5]
57	Balaji S. Srinivasan	[23] [27] [29]
58	Mukund Sundararajan	[16]
59	Andreas Sundquist	[28]
60	Leila Taher	[9]
61	Liping Wei	[14]
62	Daniel A. Woods	[25]

Colors in the list of coauthors