Pierre Baldi, PhD - Publications

Affiliations: 
University of California, Irvine, Irvine, CA 
Website:
http://www.igb.uci.edu/~pfbaldi/

150 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Urban G, Torrisi M, Magnan CN, Pollastri G, Baldi P. Protein profiles: Biases and protocols. Computational and Structural Biotechnology Journal. 18: 2281-2289. PMID 32994887 DOI: 10.1016/J.Csbj.2020.08.015  0.336
2020 Ott J, Linstead E, LaHaye N, Baldi P. Learning in the machine: To share or not to share? Neural Networks : the Official Journal of the International Neural Network Society. 126: 235-249. PMID 32259763 DOI: 10.1016/J.Neunet.2020.03.016  0.661
2020 Ott J, Pritchard M, Best N, Linstead E, Curcic M, Baldi P. A Fortran-Keras Deep Learning Bridge for Scientific Computing Scientific Programming. 2020: 1-13. DOI: 10.1155/2020/8888811  0.677
2019 Chen YH, Su CC, Deng W, Lock LF, Donovan PJ, Kayala MA, Baldi P, Lee HC, Chen Y, Wang PH. Mitochondrial Akt Signaling Modulated Reprogramming of Somatic Cells. Scientific Reports. 9: 9919. PMID 31289326 DOI: 10.1038/S41598-019-46359-6  0.735
2019 Patterson K, Shavarebi F, Magnan C, Chang I, Qi X, Baldi P, Bilanchone V, Sandmeyer SB. Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites. Genome Research. PMID 31249062 DOI: 10.1101/Gr.240861.118  0.577
2017 Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, et al. Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of Biological Rhythms. 748730417728663. PMID 29098954 DOI: 10.1177/0748730417728663  0.318
2017 Eng CH, Backman TWH, Bailey CB, Magnan C, García Martín H, Katz L, Baldi P, Keasling JD. ClusterCAD: a computational platform for type I modular polyketide synthase design. Nucleic Acids Research. PMID 29040649 DOI: 10.1093/Nar/Gkx893  0.311
2016 Magnan C, Yu J, Chang I, Jahn E, Kanomata Y, Wu J, Zeller M, Oakes M, Baldi P, Sandmeyer S. Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity. Plos One. 11: e0162363. PMID 27603307 DOI: 10.1371/Journal.Pone.0162363  0.773
2016 Borrego SL, Fahrmann J, Datta R, Stringari C, Grapov D, Zeller M, Chen Y, Wang P, Baldi P, Gratton E, Fiehn O, Kaiser P. Metabolic changes associated with methionine stress sensitivity in MDA-MB-468 breast cancer cells. Cancer & Metabolism. 4: 9. PMID 27141305 DOI: 10.1186/S40170-016-0148-6  0.715
2016 Galiez C, Magnan C, Coste F, Baldi P. VIRALpro: a tool to identify viral capsid and tail sequences. Bioinformatics (Oxford, England). PMID 26733451 DOI: 10.1093/Bioinformatics/Btv727  0.316
2015 Lusci A, Browning M, Fooshee D, Swamidass J, Baldi P. Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. Journal of Cheminformatics. 7: 63. PMID 26719774 DOI: 10.1186/S13321-015-0110-6  0.321
2015 Patel VR, Ceglia N, Zeller M, Eckel-Mahan K, Sassone-Corsi P, Baldi P. The Pervasiveness and Plasticity of Circadian Oscillations: the Coupled Circadian-Oscillators Framework. Bioinformatics (Oxford, England). PMID 26049162 DOI: 10.1093/Bioinformatics/Btv353  0.723
2014 Zeller M, Magnan CN, Patel VR, Rigor P, Sender L, Baldi P. A Genomic Analysis Pipeline and Its Application to Pediatric Cancers. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 11: 826-39. PMID 26356856 DOI: 10.1109/Tcbb.2014.2330616  0.757
2014 Magnan CN, Baldi P. SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. Bioinformatics (Oxford, England). 30: 2592-7. PMID 24860169 DOI: 10.1093/Bioinformatics/Btu352  0.359
2014 Nagata K, Randall A, Baldi P. Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures. Bioinformatics (Oxford, England). 30: 1681-9. PMID 24574112 DOI: 10.1093/Bioinformatics/Btu106  0.689
2013 Sadowski P, Baldi P. Small-molecule 3D structure prediction using open crystallography data. Journal of Chemical Information and Modeling. 53: 3127-30. PMID 24261562 DOI: 10.1021/Ci4005282  0.334
2013 Gordon EA, Whisenant TC, Zeller M, Kaake RM, Gordon WM, Krotee P, Patel V, Huang L, Baldi P, Bardwell L. Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate. Cellular Signalling. 25: 2518-29. PMID 23981301 DOI: 10.1016/J.Cellsig.2013.08.004  0.738
2013 Feher VA, Randall A, Baldi P, Bush RM, de la Maza LM, Amaro RE. A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins. Plos One. 8: e68934. PMID 23935908 DOI: 10.1371/Journal.Pone.0068934  0.561
2013 Lusci A, Pollastri G, Baldi P. Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules. Journal of Chemical Information and Modeling. 53: 1563-75. PMID 23795551 DOI: 10.1021/Ci400187Y  0.316
2013 Bellet MM, Deriu E, Liu JZ, Grimaldi B, Blaschitz C, Zeller M, Edwards RA, Sahar S, Dandekar S, Baldi P, George MD, Raffatellu M, Sassone-Corsi P. Circadian clock regulates the host response to Salmonella. Proceedings of the National Academy of Sciences of the United States of America. 110: 9897-902. PMID 23716692 DOI: 10.1073/Pnas.1120636110  0.73
2013 Chang I, Baldi P. A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions. Bioinformatics (Oxford, England). 29: 1299-307. PMID 23613486 DOI: 10.1093/Bioinformatics/Btt140  0.59
2013 Vogel-Ciernia A, Matheos DP, Barrett RM, Kramár EA, Azzawi S, Chen Y, Magnan CN, Zeller M, Sylvain A, Haettig J, Jia Y, Tran A, Dang R, Post RJ, Chabrier M, ... ... Baldi P, et al. The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. Nature Neuroscience. 16: 552-61. PMID 23525042 DOI: 10.1038/Nn.3359  0.722
2012 Ren D, Dalmau M, Randall A, Shindel MM, Baldi P, Wang SW. Biomimetic Design of Protein Nanomaterials for Hydrophobic Molecular Transport. Advanced Functional Materials. 22: 3170-3180. PMID 23526705 DOI: 10.1002/Adfm.201200052  0.559
2012 Kayala MA, Baldi P. ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning. Journal of Chemical Information and Modeling. 52: 2526-40. PMID 22978639 DOI: 10.1021/Ci3003039  0.751
2012 Lee SH, Hoshino Y, Randall A, Zeng Z, Baldi P, Doong RA, Shea KJ. Engineered synthetic polymer nanoparticles as IgG affinity ligands. Journal of the American Chemical Society. 134: 15765-72. PMID 22924890 DOI: 10.1021/Ja303612D  0.466
2012 Di Lena P, Nagata K, Baldi P. Deep architectures for protein contact map prediction. Bioinformatics (Oxford, England). 28: 2449-57. PMID 22847931 DOI: 10.1093/Bioinformatics/Bts475  0.582
2012 Hopkin AS, Gordon W, Klein RH, Espitia F, Daily K, Zeller M, Baldi P, Andersen B. GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program. Plos Genetics. 8: e1002829. PMID 22829784 DOI: 10.1371/Journal.Pgen.1002829  0.757
2012 Hoverter NP, Ting JH, Sundaresh S, Baldi P, Waterman ML. A WNT/p21 circuit directed by the C-clamp, a sequence-specific DNA binding domain in TCFs. Molecular and Cellular Biology. 32: 3648-62. PMID 22778133 DOI: 10.1128/Mcb.06769-11  0.713
2012 Kayala MA, Baldi P. Cyber-T web server: differential analysis of high-throughput data. Nucleic Acids Research. 40: W553-9. PMID 22600740 DOI: 10.1093/Nar/Gks420  0.758
2012 Fooshee DR, Nguyen TB, Nizkorodov SA, Laskin J, Laskin A, Baldi P. COBRA: a computational brewing application for predicting the molecular composition of organic aerosols. Environmental Science & Technology. 46: 6048-55. PMID 22568707 DOI: 10.1021/Es3003734  0.303
2012 Kao A, Randall A, Yang Y, Patel VR, Kandur W, Guan S, Rychnovsky SD, Baldi P, Huang L. Mapping the structural topology of the yeast 19S proteasomal regulatory particle using chemical cross-linking and probabilistic modeling. Molecular & Cellular Proteomics : McP. 11: 1566-77. PMID 22550050 DOI: 10.1074/Mcp.M112.018374  0.567
2012 Fang L, Kaake RM, Patel VR, Yang Y, Baldi P, Huang L. Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy. Molecular & Cellular Proteomics : McP. 11: 138-47. PMID 22474085 DOI: 10.1074/Mcp.M111.016352  0.303
2012 Nasr R, Vernica R, Li C, Baldi P. Speeding up chemical searches using the inverted index: the convergence of chemoinformatics and text search methods. Journal of Chemical Information and Modeling. 52: 891-900. PMID 22462644 DOI: 10.1021/Ci200552R  0.789
2012 Qi X, Daily K, Nguyen K, Wang H, Mayhew D, Rigor P, Forouzan S, Johnston M, Mitra RD, Baldi P, Sandmeyer S. Retrotransposon profiling of RNA polymerase III initiation sites. Genome Research. 22: 681-92. PMID 22287102 DOI: 10.1101/Gr.131219.111  0.638
2012 Srikrishnan S, Randall A, Baldi P, Da Silva NA. Rationally selected single-site mutants of the Thermoascus aurantiacus endoglucanase increase hydrolytic activity on cellulosic substrates. Biotechnology and Bioengineering. 109: 1595-9. PMID 22180009 DOI: 10.1002/Bit.24414  0.519
2012 Nagata K, Randall A, Baldi P. SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations. Proteins. 80: 142-53. PMID 22072531 DOI: 10.1002/Prot.23170  0.698
2012 Di Lena P, Nagata K, Baldi P. Deep spatio-temporal architectures and learning for protein structure prediction Advances in Neural Information Processing Systems. 1: 512-520.  0.5
2011 Nasr R, Kristensen T, Baldi P. Tree and Hashing Data Structures to Speed up Chemical Searches: Analysis and Experiments. Molecular Informatics. 30: 791-800. PMID 27467411 DOI: 10.1002/Minf.201100089  0.792
2011 Daily K, Patel VR, Rigor P, Xie X, Baldi P. MotifMap: integrative genome-wide maps of regulatory motif sites for model species. Bmc Bioinformatics. 12: 495. PMID 22208852 DOI: 10.1186/1471-2105-12-495  0.651
2011 Baldi P. Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre. Journal of Chemical Information and Modeling. 51: 3029. PMID 22107601 DOI: 10.1021/Ci200460Z  0.309
2011 Chang I, Heiske M, Letellier T, Wallace D, Baldi P. Modeling of mitochondria bioenergetics using a composable chemiosmotic energy transduction rate law: theory and experimental validation. Plos One. 6: e14820. PMID 21931590 DOI: 10.1371/Journal.Pone.0014820  0.574
2011 Barry AE, Trieu A, Fowkes FJ, Pablo J, Kalantari-Dehaghi M, Jasinskas A, Tan X, Kayala MA, Tavul L, Siba PM, Day KP, Baldi P, Felgner PL, Doolan DL. The stability and complexity of antibody responses to the major surface antigen of Plasmodium falciparum are associated with age in a malaria endemic area. Molecular & Cellular Proteomics : McP. 10: M111.008326. PMID 21825279 DOI: 10.1074/Mcp.M111.008326  0.748
2011 Kayala MA, Azencott CA, Chen JH, Baldi P. Learning to predict chemical reactions. Journal of Chemical Information and Modeling. 51: 2209-22. PMID 21819139 DOI: 10.1021/Ci200207Y  0.778
2011 Trieu A, Kayala MA, Burk C, Molina DM, Freilich DA, Richie TL, Baldi P, Felgner PL, Doolan DL. Sterile protective immunity to malaria is associated with a panel of novel P. falciparum antigens. Molecular & Cellular Proteomics : McP. 10: M111.007948. PMID 21628511 DOI: 10.1074/Mcp.M111.007948  0.749
2011 Andronico A, Randall A, Benz RW, Baldi P. Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. Journal of Chemical Information and Modeling. 51: 760-76. PMID 21417267 DOI: 10.1021/Ci100223T  0.564
2011 Clemens K, Larsen L, Zhang M, Kuznetsov Y, Bilanchone V, Randall A, Harned A, Dasilva R, Nagashima K, McPherson A, Baldi P, Sandmeyer S. The TY3 Gag3 spacer controls intracellular condensation and uncoating. Journal of Virology. 85: 3055-66. PMID 21270167 DOI: 10.1128/Jvi.01055-10  0.508
2011 Cruz-Fisher MI, Cheng C, Sun G, Pal S, Teng A, Molina DM, Kayala MA, Vigil A, Baldi P, Felgner PL, Liang X, de la Maza LM. Identification of immunodominant antigens by probing a whole Chlamydia trachomatis open reading frame proteome microarray using sera from immunized mice. Infection and Immunity. 79: 246-57. PMID 20956570 DOI: 10.1128/Iai.00626-10  0.757
2011 Kao A, Chiu CL, Vellucci D, Yang Y, Patel VR, Guan S, Randall A, Baldi P, Rychnovsky SD, Huang L. Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Molecular & Cellular Proteomics : McP. 10: M110.002212. PMID 20736410 DOI: 10.1074/Mcp.M110.002212  0.54
2011 Baldi P, Azencott C, Swamidass SJ. Bridging the gap between neural network and kernel methods: Applications to drug discovery Frontiers in Artificial Intelligence and Applications. 226: 3-13. DOI: 10.3233/978-1-60750-692-8-3  0.749
2011 Nasr R, Kristensen T, Baldi P. Tree and hashing data structures to speed up chemical searches: Analysis and experiments Molecular Informatics. 30: 791-800. DOI: 10.1002/minf.201100089  0.773
2011 Kayala MA, Baldi P. A machine learning approach to predict chemical reactions Advances in Neural Information Processing Systems 24: 25th Annual Conference On Neural Information Processing Systems 2011, Nips 2011 0.728
2010 Daily K, Rigor P, Christley S, Xie X, Baldi P. Data structures and compression algorithms for high-throughput sequencing technologies. Bmc Bioinformatics. 11: 514. PMID 20946637 DOI: 10.1186/1471-2105-11-514  0.647
2010 Magnan CN, Zeller M, Kayala MA, Vigil A, Randall A, Felgner PL, Baldi P. High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics (Oxford, England). 26: 2936-43. PMID 20934990 DOI: 10.1093/Bioinformatics/Btq551  0.788
2010 Compani B, Su T, Chang I, Cheng J, Shah KH, Whisenant T, Dou Y, Bergmann A, Cheong R, Wold B, Bardwell L, Levchenko A, Baldi P, Mjolsness E. A scalable and integrative system for pathway bioinformatics and systems biology. Advances in Experimental Medicine and Biology. 680: 523-34. PMID 20865537 DOI: 10.1007/978-1-4419-5913-3_58  0.678
2010 Nasr R, Hirschberg DS, Baldi P. Hashing algorithms and data structures for rapid searches of fingerprint vectors. Journal of Chemical Information and Modeling. 50: 1358-68. PMID 20681581 DOI: 10.1021/Ci100132G  0.786
2010 Baldi P, Nasr R. When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme values. Journal of Chemical Information and Modeling. 50: 1205-22. PMID 20540577 DOI: 10.1021/Ci100010V  0.778
2010 Liang L, Leng D, Burk C, Nakajima-Sasaki R, Kayala MA, Atluri VL, Pablo J, Unal B, Ficht TA, Gotuzzo E, Saito M, Morrow WJ, Liang X, Baldi P, Gilman RH, et al. Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens. Plos Neglected Tropical Diseases. 4: e673. PMID 20454614 DOI: 10.1371/Journal.Pntd.0000673  0.75
2010 Swamidass SJ, Azencott CA, Daily K, Baldi P. A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinformatics (Oxford, England). 26: 1348-56. PMID 20378557 DOI: 10.1093/Bioinformatics/Btq140  0.774
2010 Mochon AB, Jin Y, Ye J, Kayala MA, Wingard JR, Clancy CJ, Nguyen MH, Felgner P, Baldi P, Liu H. Serological profiling of a Candida albicans protein microarray reveals permanent host-pathogen interplay and stage-specific responses during candidemia. Plos Pathogens. 6: e1000827. PMID 20361054 DOI: 10.1371/Journal.Ppat.1000827  0.747
2010 Crompton PD, Kayala MA, Traore B, Kayentao K, Ongoiba A, Weiss GE, Molina DM, Burk CR, Waisberg M, Jasinskas A, Tan X, Doumbo S, Doumtabe D, Kone Y, Narum DL, ... ... Baldi P, et al. A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proceedings of the National Academy of Sciences of the United States of America. 107: 6958-63. PMID 20351286 DOI: 10.1073/Pnas.1001323107  0.752
2010 Guzmán DL, Randall A, Baldi P, Guan Z. Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability. Proceedings of the National Academy of Sciences of the United States of America. 107: 1989-94. PMID 20080695 DOI: 10.1073/Pnas.0905796107  0.542
2010 Baldi P, Itti L. Of bits and wows: A Bayesian theory of surprise with applications to attention. Neural Networks : the Official Journal of the International Neural Network Society. 23: 649-66. PMID 20080025 DOI: 10.1016/J.Neunet.2009.12.007  0.311
2010 Molina DM, Pal S, Kayala MA, Teng A, Kim PJ, Baldi P, Felgner PL, Liang X, de la Maza LM. Identification of immunodominant antigens of Chlamydia trachomatis using proteome microarrays. Vaccine. 28: 3014-24. PMID 20044059 DOI: 10.1016/J.Vaccine.2009.12.020  0.753
2010 Mochon AB, Jin Y, Kayala MA, Wingard JR, Clancy CJ, Nguyen MH, Felgner P, Baldi P, Liu H. Correction: Serological Profiling of a Candida albicans Protein Microarray Reveals Permanent Host-Pathogen Interplay and Stage-Specific Responses during Candidemia Plos Pathogens. 6. DOI: 10.1371/Annotation/Eff399E1-51E0-43B1-Bdf4-1A11E9Ada9Bd  0.743
2010 Chen JH, Kayala MA, Baldi P. Reaction explorer:towards a knowledge map of organic chemistry to support dynamic assessment and personalized instruction Acs Symposium Series. 1060: 191-209. DOI: 10.1021/bk-2010-1060.ch011  0.742
2010 Chang I, Letellier T, Wallace D, Baldi P. 127 A new generalized energy transduction rate law for modeling of OXPHOS systems and pathologies Mitochondrion. 10: 235-236. DOI: 10.1016/J.Mito.2009.12.118  0.54
2010 Randall A, Baldi P. Transmembrane beta-barrel protein structure prediction Structural Bioinformatics of Membrane Proteins. 83-102. DOI: 10.1007/978-3-7091-0045-5_5  0.488
2010 Linstead E, Hughes L, Lopes C, Baldi P. Information-theoretic metrics for project-level scattering and tangling Seke 2010 - Proceedings of the 22nd International Conference On Software Engineering and Knowledge Engineering. 141-146.  0.607
2009 Nasr RJ, Swamidass SJ, Baldi PF. Large scale study of multiple-molecule queries. Journal of Cheminformatics. 1: 7. PMID 20298525 DOI: 10.1186/1758-2946-1-7  0.782
2009 Chen JH, Baldi P. No electron left behind: a rule-based expert system to predict chemical reactions and reaction mechanisms. Journal of Chemical Information and Modeling. 49: 2034-43. PMID 19719121 DOI: 10.1021/Ci900157K  0.458
2009 Felgner PL, Kayala MA, Vigil A, Burk C, Nakajima-Sasaki R, Pablo J, Molina DM, Hirst S, Chew JS, Wang D, Tan G, Duffield M, Yang R, Neel J, Chantratita N, ... ... Baldi P, et al. A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Proceedings of the National Academy of Sciences of the United States of America. 106: 13499-504. PMID 19666533 DOI: 10.1073/Pnas.0812080106  0.76
2009 Magnan CN, Randall A, Baldi P. SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics (Oxford, England). 25: 2200-7. PMID 19549632 DOI: 10.1093/Bioinformatics/Btp386  0.596
2009 Brandon MC, Wallace DC, Baldi P. Data structures and compression algorithms for genomic sequence data. Bioinformatics (Oxford, England). 25: 1731-8. PMID 19447783 DOI: 10.1093/Bioinformatics/Btp319  0.776
2009 Swamidass SJ, Azencott CA, Lin TW, Gramajo H, Tsai SC, Baldi P. Influence relevance voting: an accurate and interpretable virtual high throughput screening method. Journal of Chemical Information and Modeling. 49: 756-66. PMID 19391629 DOI: 10.1021/Ci8004379  0.787
2009 Sweredoski MJ, Baldi P. COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Engineering, Design & Selection : Peds. 22: 113-20. PMID 19074155 DOI: 10.1093/Protein/Gzn075  0.634
2009 Chang L, Sundaresh S, Elliott J, Anton PA, Baldi P, Licudine A, Mayer M, Vuong T, Hirano M, Naliboff BD, Ameen VZ, Mayer EA. Dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis in irritable bowel syndrome. Neurogastroenterology and Motility : the Official Journal of the European Gastrointestinal Motility Society. 21: 149-59. PMID 18684212 DOI: 10.1111/J.1365-2982.2008.01171.X  0.698
2009 Brandon MC, Ruiz-Pesini E, Mishmar D, Procaccio V, Lott MT, Nguyen KC, Spolim S, Patil U, Baldi P, Wallace DC. MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences. Human Mutation. 30: 1-6. PMID 18566966 DOI: 10.1002/Humu.20801  0.771
2009 Linstead E, Hughes L, Lopes C, Baldi P. Exploring Java software vocabulary: A search and mining perspective Proceedings - International Conference On Software Engineering. 29-32. DOI: 10.1109/SUITE.2009.5070017  0.628
2009 Ossher J, Bajracharya S, Linstead E, Baldi P, Lopes C. SourcererDB: An aggregated repository of statically analyzed and cross-linked open source java projects Proceedings of the 2009 6th Ieee International Working Conference On Mining Software Repositories, Msr 2009. 183-186. DOI: 10.1109/MSR.2009.5069501  0.609
2009 Linstead E, Baldi P. Mining the coherence of GNOME bug reports with statistical topic models Proceedings of the 2009 6th Ieee International Working Conference On Mining Software Repositories, Msr 2009. 99-102. DOI: 10.1109/MSR.2009.5069486  0.622
2009 Linstead E, Hughes L, Lopes C, Baldi P. Capturing java naming conventions with first-order markov models Ieee International Conference On Program Comprehension. 313-314. DOI: 10.1109/ICPC.2009.5090074  0.618
2009 Linstead E, Bajracharya S, Ngo T, Rigor P, Lopes C, Baldi P. Sourcerer: Mining and searching internet-scale software repositories Data Mining and Knowledge Discovery. 18: 300-336. DOI: 10.1007/S10618-008-0118-X  0.689
2009 Linstead E, Rigor P, Bajracharya S, Lopes C, Baldi P. Mining Internet-scale software repositories Advances in Neural Information Processing Systems 20 - Proceedings of the 2007 Conference 0.618
2008 Cheng J, Tegge AN, Baldi P. Machine learning methods for protein structure prediction. Ieee Reviews in Biomedical Engineering. 1: 41-9. PMID 22274898 DOI: 10.1109/Rbme.2008.2008239  0.317
2008 Randall A, Baldi P. SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. Bmc Structural Biology. 8: 52. PMID 19055744 DOI: 10.1186/1472-6807-8-52  0.582
2008 Doolan DL, Mu Y, Unal B, Sundaresh S, Hirst S, Valdez C, Randall A, Molina D, Liang X, Freilich DA, Oloo JA, Blair PL, Aguiar JC, Baldi P, Davies DH, et al. Profiling humoral immune responses to P. falciparum infection with protein microarrays. Proteomics. 8: 4680-94. PMID 18937256 DOI: 10.1002/Pmic.200800194  0.777
2008 Baldi P, Hirschberg DS, Nasr RJ. Speeding up chemical database searches using a proximity filter based on the logical exclusive or. Journal of Chemical Information and Modeling. 48: 1367-78. PMID 18593143 DOI: 10.1021/Ci800076S  0.787
2008 Benz RW, Swamidass SJ, Baldi P. Discovery of power-laws in chemical space. Journal of Chemical Information and Modeling. 48: 1138-51. PMID 18522387 DOI: 10.1021/Ci700353M  0.599
2008 Barbour AG, Jasinskas A, Kayala MA, Davies DH, Steere AC, Baldi P, Felgner PL. A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi. Infection and Immunity. 76: 3374-89. PMID 18474646 DOI: 10.1128/Iai.00048-08  0.761
2008 Sweredoski MJ, Baldi P. PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics (Oxford, England). 24: 1459-60. PMID 18443018 DOI: 10.1093/Bioinformatics/Btn199  0.631
2008 Wu L, Baldi P. Learning to play Go using recursive neural networks. Neural Networks : the Official Journal of the International Neural Network Society. 21: 1392-400. PMID 18420381 DOI: 10.1016/J.Neunet.2008.02.002  0.402
2008 Randall A, Cheng J, Sweredoski M, Baldi P. TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. Bioinformatics (Oxford, England). 24: 513-20. PMID 18006547 DOI: 10.1093/Bioinformatics/Btm548  0.716
2008 Baldi PF, Lopes CV, Linstead EJ, Bajracharya SK. A theory of aspects as latent topics Proceedings of the Conference On Object-Oriented Programming Systems, Languages, and Applications, Oopsla. 543-562. DOI: 10.1145/1449764.1449807  0.597
2008 Linstead E, Lopes C, Baldi P. An application of Latent Dirichlet Allocation to analyzing software evolution Proceedings - 7th International Conference On Machine Learning and Applications, Icmla 2008. 813-818. DOI: 10.1109/ICMLA.2008.47  0.643
2008 Chen JH, Baldi P. Synthesis explorer: A chemical reaction tutorial system for organic synthesis design and mechanism prediction Journal of Chemical Education. 85: 1699-1703. DOI: 10.1021/Ed085P1699  0.469
2007 Baldi P, Benz RW, Hirschberg DS, Swamidass SJ. Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrieval. Journal of Chemical Information and Modeling. 47: 2098-109. PMID 17967006 DOI: 10.1021/Ci700200N  0.625
2007 Sweredoski MJ, Donovan KJ, Nguyen BD, Shaka AJ, Baldi P. Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling. Bioinformatics (Oxford, England). 23: 2829-35. PMID 17895278 DOI: 10.1093/Bioinformatics/Btm406  0.629
2007 Sundaresh S, Randall A, Unal B, Petersen JM, Belisle JT, Hartley MG, Duffield M, Titball RW, Davies DH, Felgner PL, Baldi P. From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. Bioinformatics (Oxford, England). 23: i508-18. PMID 17646338 DOI: 10.1093/bioinformatics/btm207  0.779
2007 Chen JH, Linstead E, Swamidass SJ, Wang D, Baldi P. ChemDB update--full-text search and virtual chemical space. Bioinformatics (Oxford, England). 23: 2348-51. PMID 17599932 DOI: 10.1093/Bioinformatics/Btm341  0.789
2007 Komarova NL, Wu L, Baldi P. The fixed-size Luria-Delbruck model with a nonzero death rate. Mathematical Biosciences. 210: 253-90. PMID 17583754 DOI: 10.1016/J.Mbs.2007.04.007  0.374
2007 Eyles JE, Unal B, Hartley MG, Newstead SL, Flick-Smith H, Prior JL, Oyston PC, Randall A, Mu Y, Hirst S, Molina DM, Davies DH, Milne T, Griffin KF, Baldi P, et al. Immunodominant Francisella tularensis antigens identified using proteome microarray. Proteomics. 7: 2172-83. PMID 17533643 DOI: 10.1002/Pmic.200600985  0.557
2007 Swamidass SJ, Baldi P. Mathematical correction for fingerprint similarity measures to improve chemical retrieval. Journal of Chemical Information and Modeling. 47: 952-64. PMID 17444629 DOI: 10.1021/Ci600526A  0.624
2007 Cheng J, Baldi P. Improved residue contact prediction using support vector machines and a large feature set. Bmc Bioinformatics. 8: 113. PMID 17407573 DOI: 10.1186/1471-2105-8-113  0.312
2007 Azencott CA, Ksikes A, Swamidass SJ, Chen JH, Ralaivola L, Baldi P. One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties. Journal of Chemical Information and Modeling. 47: 965-74. PMID 17338509 DOI: 10.1021/Ci600397P  0.787
2007 Swamidass SJ, Baldi P. Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time. Journal of Chemical Information and Modeling. 47: 302-17. PMID 17326616 DOI: 10.1021/Ci600358F  0.632
2007 Ruiz-Pesini E, Lott MT, Procaccio V, Poole JC, Brandon MC, Mishmar D, Yi C, Kreuziger J, Baldi P, Wallace DC. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Research. 35: D823-8. PMID 17178747 DOI: 10.1093/Nar/Gkl927  0.761
2007 Linstead E, Rigor P, Bajracharya S, Lopes C, Baldi P. Mining concepts from code with probabilistic topic models Ase'07 - 2007 Acm/Ieee International Conference On Automated Software Engineering. 461-464. DOI: 10.1145/1321631.1321709  0.642
2007 Jurdak R, Baldi P, Lopes CV. Adaptive low power listening for wireless sensor networks Ieee Transactions On Mobile Computing. 6: 988-1004. DOI: 10.1109/Tmc.2007.1037  0.629
2007 Linstead E, Rigor P, Bajracharya S, Lopes C, Baldi P. Mining eclipse developer contributions via author-topic models Proceedings - Icse 2007 Workshops: Fourth International Workshop On Mining Software Repositories, Msr 2007. DOI: 10.1109/MSR.2007.20  0.645
2006 Dou Y, Fox-Walsh KL, Baldi PF, Hertel KJ. Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site. Rna (New York, N.Y.). 12: 2047-56. PMID 17053087 DOI: 10.1261/Rna.151106  0.441
2006 Danziger SA, Swamidass SJ, Zeng J, Dearth LR, Lu Q, Chen JH, Cheng J, Hoang VP, Saigo H, Luo R, Baldi P, Brachmann RK, Lathrop RH. Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 3: 114-25. PMID 17048398 DOI: 10.1109/Tcbb.2006.22  0.662
2006 Brandon M, Baldi P, Wallace DC. Mitochondrial mutations in cancer. Oncogene. 25: 4647-62. PMID 16892079 DOI: 10.1038/Sj.Onc.1209607  0.754
2006 Pollastri G, Vullo A, Frasconi P, Baldi P. Modular DAG-RNN architectures for assembling coarse protein structures. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 631-50. PMID 16706716 DOI: 10.1089/Cmb.2006.13.631  0.337
2006 Sundaresh S, Doolan DL, Hirst S, Mu Y, Unal B, Davies DH, Felgner PL, Baldi P. Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics (Oxford, England). 22: 1760-6. PMID 16644788 DOI: 10.1093/Bioinformatics/Btl162  0.736
2006 Cheng J, Baldi P. A machine learning information retrieval approach to protein fold recognition. Bioinformatics (Oxford, England). 22: 1456-63. PMID 16547073 DOI: 10.1093/Bioinformatics/Btl102  0.348
2006 Lin TW, Melgar MM, Kurth D, Swamidass SJ, Purdon J, Tseng T, Gago G, Baldi P, Gramajo H, Tsai SC. Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America. 103: 3072-7. PMID 16492739 DOI: 10.1073/Pnas.0510580103  0.603
2006 Tagwerker C, Flick K, Cui M, Guerrero C, Dou Y, Auer B, Baldi P, Huang L, Kaiser P. A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking. Molecular & Cellular Proteomics : McP. 5: 737-48. PMID 16432255 DOI: 10.1074/Mcp.M500368-Mcp200  0.519
2006 Cheng J, Randall A, Baldi P. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins. 62: 1125-32. PMID 16372356 DOI: 10.1002/Prot.20810  0.58
2006 Cheng J, Saigo H, Baldi P. Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins. 62: 617-29. PMID 16320312 DOI: 10.1002/Prot.20787  0.342
2006 Bajracharya S, Ngo T, Linstead E, Dou Y, Rigor P, Baldi P, Lopes C. Sourcerer: A search engine for open source code supporting structure-based search Proceedings of the Conference On Object-Oriented Programming Systems, Languages, and Applications, Oopsla. 2006: 681-682. DOI: 10.1145/1176617.1176671  0.709
2006 Cheng J, Sweredoski MJ, Baldi P. DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks Data Mining and Knowledge Discovery. 13: 1-10. DOI: 10.1007/S10618-005-0023-5  0.632
2005 Sundaresh S, Hung SP, Hatfield GW, Baldi P. How noisy and replicable are DNA microarry data? International Journal of Bioinformatics Research and Applications. 1: 31-50. PMID 18048120 DOI: 10.1504/Ijbra.2005.006901  0.709
2005 Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF, Hertel KJ. The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proceedings of the National Academy of Sciences of the United States of America. 102: 16176-81. PMID 16260721 DOI: 10.1073/Pnas.0508489102  0.435
2005 Chen J, Swamidass SJ, Dou Y, Bruand J, Baldi P. ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics (Oxford, England). 21: 4133-9. PMID 16174682 DOI: 10.1093/Bioinformatics/Bti683  0.747
2005 Ralaivola L, Swamidass SJ, Saigo H, Baldi P. Graph kernels for chemical informatics. Neural Networks : the Official Journal of the International Neural Network Society. 18: 1093-110. PMID 16157471 DOI: 10.1016/J.Neunet.2005.07.009  0.633
2005 Chung DM, Dou Y, Baldi P, Nowick JS. The absence of favorable aromatic interactions between beta-sheet peptides. Journal of the American Chemical Society. 127: 9998-9. PMID 16011353 DOI: 10.1021/Ja052351P  0.487
2005 Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Research. 33: W72-6. PMID 15980571 DOI: 10.1093/Nar/Gki396  0.717
2005 Swamidass SJ, Chen J, Bruand J, Phung P, Ralaivola L, Baldi P. Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics (Oxford, England). 21: i359-68. PMID 15961479 DOI: 10.1093/Bioinformatics/Bti1055  0.691
2005 Irwin B, Aye M, Baldi P, Beliakova-Bethell N, Cheng H, Dou Y, Liou W, Sandmeyer S. Retroviruses and yeast retrotransposons use overlapping sets of host genes. Genome Research. 15: 641-54. PMID 15837808 DOI: 10.1101/Gr.3739005  0.512
2005 Davies DH, Liang X, Hernandez JE, Randall A, Hirst S, Mu Y, Romero KM, Nguyen TT, Kalantari-Dehaghi M, Crotty S, Baldi P, Villarreal LP, Felgner PL. Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proceedings of the National Academy of Sciences of the United States of America. 102: 547-52. PMID 15647345 DOI: 10.1073/Pnas.0408782102  0.576
2005 Brandon MC, Lott MT, Nguyen KC, Spolim S, Navathe SB, Baldi P, Wallace DC. MITOMAP: a human mitochondrial genome database--2004 update. Nucleic Acids Research. 33: D611-3. PMID 15608272 DOI: 10.1093/Nar/Gki079  0.768
2005 Cheng J, Sweredoski MJ, Baldi P. Accurate prediction of protein disordered regions by mining protein structure data Data Mining and Knowledge Discovery. 11: 213-222. DOI: 10.1007/S10618-005-0001-Y  0.642
2005 Jurdak R, Baldi P, Lopes CV. U-MAC: A proactive and adaptive UWB medium access control protocol Wireless Communications and Mobile Computing. 5: 551-566. DOI: 10.1002/Wcm.312  0.63
2004 Randall AZ, Baldi P, Villarreal LP. Structural proteomics of the poxvirus family. Artificial Intelligence in Medicine. 31: 105-15. PMID 15219289 DOI: 10.1016/J.Artmed.2004.01.006  0.583
2004 Dou Y, Baisnée PF, Pollastri G, Pécout Y, Nowick J, Baldi P. ICBS: a database of interactions between protein chains mediated by beta-sheet formation. Bioinformatics (Oxford, England). 20: 2767-77. PMID 15166020 DOI: 10.1093/Bioinformatics/Bth326  0.764
2004 Baldi P, Pollastri G. The principled design of large-scale recursive neural network architectures-DAG-RNNs and the protein structure prediction problem Journal of Machine Learning Research. 4: 575-602. DOI: 10.1162/153244304773936054  0.328
2004 Jurdak R, Lopes CV, Baldi P. A survey, classification and comparative analysis of medium access control protocols for ad hoc networks Ieee Communications Surveys & Tutorials. 6: 2-16. DOI: 10.1109/Comst.2004.5342231  0.627
2004 Guermeur Y, Pollastri G, Elisseeff A, Zelus D, Paugam-Moisy H, Baldi P. Combining protein secondary structure prediction models with ensemble methods of optimal complexity Neurocomputing. 56: 305-327. DOI: 10.1016/J.Neucom.2003.10.004  0.329
2002 Baisnée PF, Hampson S, Baldi P. Why are complementary DNA strands symmetric? Bioinformatics (Oxford, England). 18: 1021-33. PMID 12176825 DOI: 10.1093/Bioinformatics/18.8.1021  0.774
2002 Hung SP, Baldi P, Hatfield GW. Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. The Journal of Biological Chemistry. 277: 40309-23. PMID 12130640 DOI: 10.1074/Jbc.M204044200  0.3
2002 Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins. 47: 228-35. PMID 11933069 DOI: 10.1002/Prot.10082  0.326
2002 Pollastri G, Baldi P, Fariselli P, Casadio R. Prediction of coordination number and relative solvent accessibility in proteins. Proteins. 47: 142-53. PMID 11933061 DOI: 10.1002/Prot.10069  0.351
2002 Baldi P, Pollastri G. A machine learning strategy for protein analysis Ieee Intelligent Systems and Their Applications. 17: 28-35. DOI: 10.1109/5254.999217  0.308
2001 Pollastri G, Baldi P, Fariselli P, Casadio R. Improved prediction of the number of residue contacts in proteins by recurrent neural networks. Bioinformatics (Oxford, England). 17: S234-42. PMID 11473014 DOI: 10.1093/Bioinformatics/17.Suppl_1.S234  0.326
2001 Baisnée PF, Baldi P, Brunak S, Pedersen AG. Flexibility of the genetic code with respect to DNA structure. Bioinformatics (Oxford, England). 17: 237-48. PMID 11294789 DOI: 10.1093/Bioinformatics/17.3.237  0.768
2000 Baldi P, Baisnée PF. Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics (Oxford, England). 16: 865-89. PMID 11120677 DOI: 10.1093/Bioinformatics/16.10.865  0.782
2000 Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (Oxford, England). 16: 412-24. PMID 10871264 DOI: 10.1093/Bioinformatics/16.5.412  0.306
1996 Baldi P, Brunak S, Chauvin Y, Krogh A. Naturally occurring nucleosome positioning signals in human exons and introns Journal of Molecular Biology. 263: 503-510. PMID 8918932 DOI: 10.1006/Jmbi.1996.0592  0.302
1996 Baldi P. Substitution matrices and hidden Markov models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 2: 487-91. PMID 8521277 DOI: 10.1089/Cmb.1995.2.487  0.304
1987 Aschbacher M, Baldi P, Baum EB, Wilson RM. Embeddings of Ultrametric Spaces in Finite Dimensional Structures Siam Journal On Algebraic Discrete Methods. 8: 564-577. DOI: 10.1137/0608046  0.331
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