Pierre Baldi, PhD - Publications

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

410 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
2021 Lashgari E, Ott J, Connelly A, Baldi P, Maoz U. An end-to-end CNN with attentional mechanism applied to raw EEG in a BCI classification task. Journal of Neural Engineering. PMID 34352734 DOI: 10.1088/1741-2552/ac1ade  1
2021 Alhassen S, Chen S, Alhassen L, Phan A, Khoudari M, De Silva A, Barhoosh H, Wang Z, Parrocha C, Shapiro E, Henrich C, Wang Z, Mutesa L, Baldi P, Abbott GW, et al. Intergenerational trauma transmission is associated with brain metabotranscriptome remodeling and mitochondrial dysfunction. Communications Biology. 4: 783. PMID 34168265 DOI: 10.1038/s42003-021-02255-2  0.04
2021 Campbell RR, Chen S, Beardwood JH, López AJ, Pham LV, Keiser AM, Childs JE, Matheos DP, Swarup V, Baldi P, Wood MA. Cocaine induces paradigm-specific changes to the transcriptome within the ventral tegmental area. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. PMID 34155331 DOI: 10.1038/s41386-021-01031-4  1
2021 Beucler T, Pritchard M, Rasp S, Ott J, Baldi P, Gentine P. Enforcing Analytic Constraints in Neural Networks Emulating Physical Systems. Physical Review Letters. 126: 098302. PMID 33750168 DOI: 10.1103/PhysRevLett.126.098302  1
2021 Tavakoli M, Agostinelli F, Baldi P. SPLASH: Learnable activation functions for improving accuracy and adversarial robustness. Neural Networks : the Official Journal of the International Neural Network Society. 140: 1-12. PMID 33743319 DOI: 10.1016/j.neunet.2021.02.023  0.01
2021 Kadish D, Mood AD, Tavakoli M, Gutman ES, Baldi P, Van Vranken DL. Methyl Cation Affinities of Canonical Organic Functional Groups. The Journal of Organic Chemistry. PMID 33596071 DOI: 10.1021/acs.joc.0c02327  0.01
2021 Alhassen W, Chen S, Vawter M, Robbins BK, Nguyen H, Myint TN, Saito Y, Schulmann A, Nauli SM, Civelli O, Baldi P, Alachkar A. Patterns of cilia gene dysregulations in major psychiatric disorders. Progress in Neuro-Psychopharmacology & Biological Psychiatry. 110255. PMID 33508383 DOI: 10.1016/j.pnpbp.2021.110255  0.01
2021 Lee CK, Samad M, Hofer I, Cannesson M, Baldi P. Development and validation of an interpretable neural network for prediction of postoperative in-hospital mortality. Npj Digital Medicine. 4: 8. PMID 33420341 DOI: 10.1038/s41746-020-00377-1  0.01
2020 Greco CM, Cervantes M, Fustin JM, Ito K, Ceglia N, Samad M, Shi J, Koronowski KB, Forne I, Ranjit S, Gaucher J, Kinouchi K, Kojima R, Gratton E, Li W, ... Baldi P, et al. S-adenosyl-l-homocysteine hydrolase links methionine metabolism to the circadian clock and chromatin remodeling. Science Advances. 6. PMID 33328229 DOI: 10.1126/sciadv.abc5629  1
2020 Umerani MJ, Pratakshya P, Chatterjee A, Cerna Sanchez JA, Kim HS, Ilc G, Kovačič M, Magnan C, Marmiroli B, Sartori B, Kwansa AL, Orins H, Bartlett AW, Leung EM, Feng Z, ... ... Baldi P, et al. Structure, self-assembly, and properties of a truncated reflectin variant. Proceedings of the National Academy of Sciences of the United States of America. PMID 33323484 DOI: 10.1073/pnas.2009044117  1
2020 Tognini P, Samad M, Kinouchi K, Liu Y, Helbling JC, Moisan MP, Eckel-Mahan KL, Baldi P, Sassone-Corsi P. Reshaping circadian metabolism in the suprachiasmatic nucleus and prefrontal cortex by nutritional challenge. Proceedings of the National Academy of Sciences of the United States of America. PMID 33172990 DOI: 10.1073/pnas.2016589117  1
2020 Thrift WJ, Ronaghi S, Samad M, Wei H, Nguyen DG, Cabuslay AS, Groome CE, Santiago PJ, Baldi P, Hochbaum AI, Ragan R. Deep Learning Analysis of Vibrational Spectra of Bacterial Lysate for Rapid Antimicrobial Susceptibility Testing. Acs Nano. PMID 33095005 DOI: 10.1021/acsnano.0c05693  0.04
2020 Baldi P, Shahbaba B. Bayesian Causality. The American Statistician. 74: 249-257. PMID 33041343 DOI: 10.1080/00031305.2019.1647876  0.01
2020 Napoli D, Lupori L, Mazziotti R, Sagona G, Bagnoli S, Samad M, Sacramento EK, Kirkpartick J, Putignano E, Chen S, Terzibasi Tozzini E, Tognini P, Baldi P, Kwok JC, Cellerino A, et al. MiR-29 coordinates age-dependent plasticity brakes in the adult visual cortex. Embo Reports. e50431. PMID 33026181 DOI: 10.15252/embr.202050431  1
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  1
2020 Di Lena P, Baldi P. Fold recognition by scoring protein maps using the congruence coefficient. Bioinformatics (Oxford, England). PMID 32976564 DOI: 10.1093/bioinformatics/btaa833  1
2020 Urban G, Feil N, Csuka E, Hashemi K, Ekelem C, Choi F, Mesinkovska NA, Baldi P. Combining Deep Learning With Optical Coherence Tomography Imaging to Determine Scalp Hair and Follicle Counts. Lasers in Surgery and Medicine. PMID 32960994 DOI: 10.1002/lsm.23324  1
2020 Greco CM, Garetto S, Montellier E, Liu Y, Chen S, Baldi P, Sassone-Corsi P, Lucci J. A non-pharmacological therapeutic approach in the gut triggers distal metabolic rewiring capable of ameliorating diet-induced dysfunctions encompassed by metabolic syndrome. Scientific Reports. 10: 12915. PMID 32737396 DOI: 10.1038/S41598-020-69469-Y  1
2020 Chen S, Alhassen W, Yoshimura R, De Silva A, Abbott GW, Baldi P, Alachkar A. Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis. Communications Biology. 3: 409. PMID 32732995 DOI: 10.1038/s42003-020-01124-8  0.01
2020 Urban G, Porhemmat S, Stark M, Feeley B, Okada K, Baldi P. Classifying shoulder implants in X-ray images using deep learning. Computational and Structural Biotechnology Journal. 18: 967-972. PMID 32368331 DOI: 10.1016/J.Csbj.2020.04.005  1
2020 Hofer IS, Lee C, Gabel E, Baldi P, Cannesson M. Development and validation of a deep neural network model to predict postoperative mortality, acute kidney injury, and reintubation using a single feature set. Npj Digital Medicine. 3: 58. PMID 32352036 DOI: 10.1038/s41746-020-0248-0  0.01
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  1
2020 Ramadori G, Ioris RM, Villanyi Z, Firnkes R, Panasenko OO, Allen G, Konstantinidou G, Aras E, Brenachot X, Biscotti T, Charollais A, Luchetti M, Bezrukov F, Santinelli A, Samad M, ... Baldi P, et al. FKBP10 Regulates Protein Translation to Sustain Lung Cancer Growth. Cell Reports. 30: 3851-3863.e6. PMID 32187554 DOI: 10.1016/J.Celrep.2020.02.082  1
2020 Mood AD, Tavakoli M, Gutman ES, Kadish D, Baldi P, Van Vranken DL. Methyl Anion Affinities of the Canonical Organic Functional Groups. The Journal of Organic Chemistry. PMID 31995384 DOI: 10.1021/Acs.Joc.9B03187  0.01
2020 Ershoff BD, Lee CK, Wray CL, Agopian VG, Urban G, Baldi P, Cannesson M. Training and Validation of Deep Neural Networks for the Prediction of 90-Day Post-Liver Transplant Mortality Using UNOS Registry Data. Transplantation Proceedings. PMID 31926745 DOI: 10.1016/j.transproceed.2019.10.019  1
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  1
2020 Acero MA, Adamson P, Aliaga L, Alion T, Allakhverdian V, Anfimov N, Antoshkin A, Arrieta-Diaz E, Aurisano A, Back A, Backhouse C, Baird M, Balashov N, Baldi P, Bambah BA, et al. Measurement of neutrino-induced neutral-current coherent π0 production in the NOvA near detector Physical Review D. 102. DOI: 10.1103/Physrevd.102.012004  0.04
2020 Acero MA, Adamson P, Aliaga L, Alion T, Allakhverdian V, Anfimov N, Antoshkin A, Asquith L, Aurisano A, Back A, Backhouse C, Baird M, Balashov N, Baldi P, Bambah BA, et al. Search for multimessenger signals in NOvA coincident with LIGO/Virgo detections Physical Review D. 101: 112006. DOI: 10.1103/Physrevd.101.112006  0.12
2020 Li L, Nayak N, Bian J, Baldi P. Efficient neutrino oscillation parameter inference using Gaussian processes Physical Review D. 101. DOI: 10.1103/Physrevd.101.012001  0.2
2019 Li L, Pluta D, Shahbaba B, Fortin N, Ombao H, Baldi P. Modeling Dynamic Functional Connectivity with Latent Factor Gaussian Processes. Advances in Neural Information Processing Systems. 32: 8263-8273. PMID 33041607  0.12
2019 Cannesson M, Hofer I, Rinehart J, Lee C, Subramaniam K, Baldi P, Dubrawski A, Pinsky MR. Machine learning of physiological waveforms and electronic health record data to predict, diagnose and treat haemodynamic instability in surgical patients: protocol for a retrospective study. Bmj Open. 9: e031988. PMID 31796483 DOI: 10.1136/Bmjopen-2019-031988  0.01
2019 Gaucher J, Kinouchi K, Ceglia N, Montellier E, Peleg S, Greco CM, Schmidt A, Forne I, Masri S, Baldi P, Imhof A, Sassone-Corsi P. Distinct metabolic adaptation of liver circadian pathways to acute and chronic patterns of alcohol intake. Proceedings of the National Academy of Sciences of the United States of America. PMID 31757851 DOI: 10.1073/Pnas.1911189116  1
2019 Acero MA, Adamson P, Aliaga L, Alion T, Allakhverdian V, Altakarli S, Anfimov N, Antoshkin A, Aurisano A, Back A, Backhouse C, Baird M, Balashov N, Baldi P, Bambah BA, et al. First measurement of neutrino oscillation parameters using neutrinos and antineutrinos by NOvA. Physical Review Letters. 123: 151803. PMID 31702305 DOI: 10.1103/Physrevlett.123.151803  0.01
2019 Li L, Holbrook A, Shahbaba B, Baldi P. Neural network gradient Hamiltonian Monte Carlo. Computational Statistics. 34: 281-299. PMID 31695242 DOI: 10.1007/S00180-018-00861-Z  0.01
2019 Hill BL, Brown R, Gabel E, Rakocz N, Lee C, Cannesson M, Baldi P, Olde Loohuis L, Johnson R, Jew B, Maoz U, Mahajan A, Sankararaman S, Hofer I, Halperin E. An automated machine learning-based model predicts postoperative mortality using readily-extractable preoperative electronic health record data. British Journal of Anaesthesia. PMID 31627890 DOI: 10.1016/J.Bja.2019.07.030  0.01
2019 Karner HM, Webb CH, Carmona S, Liu Y, Lin B, Erhard M, Chan D, Baldi P, Spitale RC, Sun S. Functional Conservation of lncRNA JPX despite Sequence and Structural Divergence. Journal of Molecular Biology. PMID 31518612 DOI: 10.1016/J.Jmb.2019.09.002  0.01
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  1
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  1
2019 Koronowski KB, Kinouchi K, Welz PS, Smith JG, Zinna VM, Shi J, Samad M, Chen S, Magnan CN, Kinchen JM, Li W, Baldi P, Benitah SA, Sassone-Corsi P. Defining the Independence of the Liver Circadian Clock. Cell. 177: 1448-1462.e14. PMID 31150621 DOI: 10.1016/J.Cell.2019.04.025  1
2019 Baldi P, Vershynin R. The capacity of feedforward neural networks. Neural Networks : the Official Journal of the International Neural Network Society. 116: 288-311. PMID 31125915 DOI: 10.1016/J.Neunet.2019.04.009  0.01
2019 Aras E, Ramadori G, Kinouchi K, Liu Y, Ioris RM, Brenachot X, Ljubicic S, Veyrat-Durebex C, Mannucci S, Galié M, Baldi P, Sassone-Corsi P, Coppari R. Light Entrains Diurnal Changes in Insulin Sensitivity of Skeletal Muscle via Ventromedial Hypothalamic Neurons. Cell Reports. 27: 2385-2398.e3. PMID 31116983 DOI: 10.1016/J.Celrep.2019.04.093  1
2019 Sánchez A, Castro C, Flores DL, Gutiérrez E, Baldi P. Gap Junction Channels of Innexins and Connexins: Relations and Computational Perspectives. International Journal of Molecular Sciences. 20. PMID 31109150 DOI: 10.3390/Ijms20102476  0.08
2019 Sato S, Basse AL, Schönke M, Chen S, Samad M, Altıntaş A, Laker RC, Dalbram E, Barrès R, Baldi P, Treebak JT, Zierath JR, Sassone-Corsi P. Time of Exercise Specifies the Impact on Muscle Metabolic Pathways and Systemic Energy Homeostasis. Cell Metabolism. PMID 31006592 DOI: 10.1016/J.Cmet.2019.03.013  1
2019 Berchtold NC, Prieto GA, Phelan M, Gillen DL, Baldi P, Bennett DA, Buchman AS, Cotman CW. Hippocampal gene expression patterns linked to late-life physical activity oppose age and AD-related transcriptional decline. Neurobiology of Aging. 78: 142-154. PMID 30927700 DOI: 10.1016/J.Neurobiolaging.2019.02.012  0.01
2019 Li X, Zhao Q, Wei W, Lin Q, Magnan C, Emami MR, Wearick-Silva LE, Viola TW, Marshall PR, Yin J, Madugalle SU, Wang Z, Nainar S, Vågbø CB, Leighton LJ, ... ... Baldi PF, et al. The DNA modification N6-methyl-2'-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction. Nature Neuroscience. PMID 30778148 DOI: 10.1038/S41593-019-0339-X  1
2019 Westergaard D, Moseley P, Sørup FKH, Baldi P, Brunak S. Population-wide analysis of differences in disease progression patterns in men and women. Nature Communications. 10: 666. PMID 30737381 DOI: 10.1038/S41467-019-08475-9  1
2019 Acero MA, Adamson P, Aliaga L, Alion T, Allakhverdian V, Altakarli S, Anfimov N, Antoshkin A, Aurisano A, Back A, Backhouse C, Baird M, Balashov N, Baldi P, Bambah BA, et al. Observation of seasonal variation of atmospheric multiple-muon events in the NOvA Near Detector Physical Review D. 99: 122004. DOI: 10.1103/Physrevd.99.122004  0.01
2018 Kinouchi K, Magnan C, Ceglia N, Liu Y, Cervantes M, Pastore N, Huynh T, Ballabio A, Baldi P, Masri S, Sassone-Corsi P. Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle. Cell Reports. 25: 3299-3314.e6. PMID 30566858 DOI: 10.1016/J.Celrep.2018.11.077  1
2018 Liu S, Chen H, Ronquist S, Seaman L, Ceglia N, Meixner W, Chen PY, Higgins G, Baldi P, Smale S, Hero A, Muir LA, Rajapakse I. Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming. Iscience. 6: 232-246. PMID 30240614 DOI: 10.1016/J.Isci.2018.08.002  1
2018 Dyar KA, Lutter D, Artati A, Ceglia NJ, Liu Y, Armenta D, Jastroch M, Schneider S, de Mateo S, Cervantes M, Abbondante S, Tognini P, Orozco-Solis R, Kinouchi K, Wang C, ... ... Baldi P, et al. Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication between Clocks. Cell. 174: 1571-1585.e11. PMID 30193114 DOI: 10.1016/J.Cell.2018.08.042  1
2018 Kwapis JL, Alaghband Y, Kramár EA, López AJ, Vogel Ciernia A, White AO, Shu G, Rhee D, Michael CM, Montellier E, Liu Y, Magnan CN, Chen S, Sassone-Corsi P, Baldi P, et al. Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory. Nature Communications. 9: 3323. PMID 30127461 DOI: 10.1038/S41467-018-05868-0  1
2018 Urban G, Bache KM, Phan D, Sobrino A, Shmakov AK, Hachey SJ, Hughes C, Baldi P. Deep Learning for Drug Discovery and Cancer Research: Automated Analysis of Vascularization Images. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29993583 DOI: 10.1109/Tcbb.2018.2841396  1
2018 Urban G, Tripathi P, Alkayali T, Mittal M, Jalali F, Karnes W, Baldi P. Deep Learning Localizes and Identifies Polyps in Real Time with 96% Accuracy in Screening Colonoscopy. Gastroenterology. PMID 29928897 DOI: 10.1053/J.Gastro.2018.06.037  1
2018 Ceglia N, Liu Y, Chen S, Agostinelli F, Eckel-Mahan K, Sassone-Corsi P, Baldi P. CircadiOmics: circadian omic web portal. Nucleic Acids Research. PMID 29912458 DOI: 10.1093/Nar/Gky441  1
2018 Chang P, Grinband J, Weinberg BD, Bardis M, Khy M, Cadena G, Su MY, Cha S, Filippi CG, Bota D, Baldi P, Poisson LM, Jain R, Chow D. Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas. Ajnr. American Journal of Neuroradiology. PMID 29748206 DOI: 10.3174/Ajnr.A5667  1
2018 Baldi P, Sadowski P, Lu Z. Learning in the Machine: Random Backpropagation and the Deep Learning Channel. Artificial Intelligence. 260: 1-35. PMID 29731511 DOI: 10.1016/J.Artint.2018.03.003  1
2018 Lee CK, Hofer I, Gabel E, Baldi P, Cannesson M. Development and Validation of a Deep Neural Network Model for Prediction of Postoperative In-hospital Mortality. Anesthesiology. PMID 29664888 DOI: 10.1097/Aln.0000000000002186  0.01
2018 Nguyen CQ, Thrift WJ, Bhattacharjee A, Ranjbar S, Gallagher T, Darvishzadeh-Varcheie M, Sanderson RN, Capolino F, Whiteson K, Baldi P, Hochbaum AI, Ragan R. Longitudinal Monitoring of Biofilm Formation via Robust SERS Quantification of Pseudomonas aeruginosa-Produced Metabolite. Acs Applied Materials & Interfaces. PMID 29589446 DOI: 10.1021/Acsami.7B18592  0.01
2018 Urban G, Subrahmanya N, Baldi P. Inner and Outer Recursive Neural Networks for Chemoinformatics Applications. Journal of Chemical Information and Modeling. PMID 29320180 DOI: 10.1021/Acs.Jcim.7B00384  1
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  1
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  1
2017 Baldi P, Sadowski P, Lu Z. Learning in the machine: The symmetries of the deep learning channel. Neural Networks : the Official Journal of the International Neural Network Society. 95: 110-133. PMID 28938130 DOI: 10.1016/J.Neunet.2017.08.008  1
2017 Tognini P, Murakami M, Liu Y, Eckel-Mahan KL, Newman JC, Verdin E, Baldi P, Sassone-Corsi P. Distinct Circadian Signatures in Liver and Gut Clocks Revealed by Ketogenic Diet. Cell Metabolism. 26: 523-538.e5. PMID 28877456 DOI: 10.1016/J.Cmet.2017.08.015  1
2017 Mazziotti R, Baroncelli L, Ceglia N, Chelini G, Sala GD, Magnan C, Napoli D, Putignano E, Silingardi D, Tola J, Tognini P, Arthur JSC, Baldi P, Pizzorusso T. Mir-132/212 is required for maturation of binocular matching of orientation preference and depth perception. Nature Communications. 8: 15488. PMID 28534484 DOI: 10.1038/Ncomms15488  1
2017 Vogel Ciernia A, Kramár EA, Matheos DP, Havekes R, Hemstedt TJ, Magnan CN, Sakata K, Tran A, Azzawi S, Lopez A, Dang R, Wang W, Trieu B, Tong J, Barrett RM, ... ... Baldi P, et al. Mutation of neuron-specific chromatin remodeling subunit BAF53b: rescue of plasticity and memory by manipulating actin remodeling. Learning & Memory (Cold Spring Harbor, N.Y.). 24: 199-209. PMID 28416631 DOI: 10.1101/Lm.044602.116  1
2017 Wang J, Fang Z, Lang N, Yuan H, Su MY, Baldi P. A multi-resolution approach for spinal metastasis detection using deep Siamese neural networks. Computers in Biology and Medicine. 84: 137-146. PMID 28364643 DOI: 10.1016/J.Compbiomed.2017.03.024  1
2017 Liu Y, Sun S, Bredy T, Wood M, Spitale RC, Baldi P. MotifMap-RNA: a genome-wide map of RBP binding sites. Bioinformatics (Oxford, England). PMID 28334276 DOI: 10.1093/Bioinformatics/Btx087  0.08
2017 Ioris RM, Galié M, Ramadori G, Anderson JG, Charollais A, Konstantinidou G, Brenachot X, Aras E, Goga A, Ceglia N, Sebastián C, Martinvalet D, Mostoslavsky R, Baldi P, Coppari R. SIRT6 Suppresses Cancer Stem-like Capacity in Tumors with PI3K Activation Independently of Its Deacetylase Activity. Cell Reports. 18: 1858-1868. PMID 28228253 DOI: 10.1016/J.Celrep.2017.01.065  1
2017 Wang J, Ding H, Azamian F, Zhou B, Iribarren C, Molloi S, Baldi P. Detecting Cardiovascular Disease from Mammograms with Deep Learning. Ieee Transactions On Medical Imaging. PMID 28113340 DOI: 10.1109/Tmi.2017.2655486  1
2016 Sadowski P, Fooshee DR, Subrahmanya N, Baldi P. On the Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction. Journal of Chemical Information and Modeling. PMID 27749058 DOI: 10.1021/Acs.Jcim.6B00351  1
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  1
2016 Baldi P, Sadowski P. A theory of local learning, the learning channel, and the optimality of backpropagation. Neural Networks : the Official Journal of the International Neural Network Society. 83: 51-74. PMID 27584574 DOI: 10.1016/J.Neunet.2016.07.006  1
2016 Agostinelli F, Ceglia N, Shahbaba B, Sassone-Corsi P, Baldi P. What time is it? Deep learning approaches for circadian rhythms. Bioinformatics (Oxford, England). PMID 27542773 DOI: 10.1093/Bioinformatics/Btw504  1
2016 Murakami M, Tognini P, Liu Y, Eckel-Mahan KL, Baldi P, Sassone-Corsi P. Gut microbiota directs PPARγ-driven reprogramming of the liver circadian clock by nutritional challenge. Embo Reports. PMID 27418314 DOI: 10.15252/Embr.201642463  1
2016 Agostinelli F, Ceglia N, Shahbaba B, Sassone-Corsi P, Baldi P. What time is it? Deep learning approaches for circadian rhythms. Bioinformatics (Oxford, England). 32: i8-i17. PMID 27307647 DOI: 10.1093/Bioinformatics/Btw243  1
2016 Baldi P, Przytycka T. ISMB 2016 Proceedings. Bioinformatics (Oxford, England). 32: i1-i2. PMID 27307605 DOI: 10.1093/Bioinformatics/Btw326  0.01
2016 Masri S, Papagiannakopoulos T, Kinouchi K, Liu Y, Cervantes M, Baldi P, Jacks T, Sassone-Corsi P. Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis. Cell. 165: 896-909. PMID 27153497 DOI: 10.1016/J.Cell.2016.04.039  1
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  1
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  1
2016 Baldi P, Cranmer K, Faucett T, Sadowski P, Whiteson D. Parameterized neural networks for high-energy physics European Physical Journal C. 76. DOI: 10.1140/Epjc/S10052-016-4099-4  1
2016 Guest D, Collado J, Baldi P, Hsu S, Urban G, Whiteson D. Jet flavor classification in high-energy physics with deep neural networks Physical Review D. 94: 112002. DOI: 10.1103/Physrevd.94.112002  1
2016 Baldi P, Bauer K, Eng C, Sadowski P, Whiteson D. Jet substructure classification in high-energy physics with deep neural networks Physical Review D - Particles, Fields, Gravitation and Cosmology. 93. DOI: 10.1103/Physrevd.93.094034  1
2016 Baldi P, Terui K. Densification of FL chains via residuated frames Algebra Universalis. 1-27. DOI: 10.1007/s00012-016-0372-5  1
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  1
2015 Abbondante S, Eckel-Mahan KL, Ceglia NJ, Baldi P, Sassone-Corsi P. Comparative Circadian Metabolomics reveal Differential Effects of Nutritional Challenge in the Serum and Liver. The Journal of Biological Chemistry. PMID 26644470 DOI: 10.1074/Jbc.M115.681130  1
2015 Fooshee DR, Aiona PK, Laskin A, Laskin J, Nizkorodov SA, Baldi PF. Atmospheric Oxidation of Squalene: Molecular Study Using COBRA Modeling and High-Resolution Mass Spectrometry. Environmental Science & Technology. PMID 26492333 DOI: 10.1021/Acs.Est.5B03552  1
2015 Hielpos MS, Ferrero MC, Fernández AG, Bonetto J, Giambartolomei GH, Fossati CA, Baldi PC. CCL20 and Beta-Defensin 2 Production by Human Lung Epithelial Cells and Macrophages in Response to Brucella abortus Infection. Plos One. 10: e0140408. PMID 26448160 DOI: 10.1371/journal.pone.0140408  1
2015 Lane S, Di Lena P, Tormanen K, Baldi P, Liu H. Function and Regulation of Cph2 in Candida albicans. Eukaryotic Cell. 14: 1114-26. PMID 26342020 DOI: 10.1128/Ec.00102-15  1
2015 Mayer EA, Labus JS, Tillisch K, Cole SW, Baldi P. Towards a systems view of IBS. Nature Reviews. Gastroenterology & Hepatology. 12: 592-605. PMID 26303675 DOI: 10.1038/Nrgastro.2015.121  1
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  1
2015 Sequeira A, Rollins B, Magnan C, van Oven M, Baldi P, Myers RM, Barchas JD, Schatzberg AF, Watson SJ, Akil H, Bunney WE, Vawter MP. Mitochondrial mutations in subjects with psychiatric disorders. Plos One. 10: e0127280. PMID 26011537 DOI: 10.1371/Journal.Pone.0127280  1
2015 Baldi P, Sadowski P, Whiteson D. Enhanced Higgs boson to τ(+)τ(-) search with deep learning. Physical Review Letters. 114: 111801. PMID 25839260 DOI: 10.1103/Physrevlett.114.111801  1
2015 Pollak CN, Wanke MM, Estein SM, Delpino MV, Monachesi NE, Comercio EA, Fossati CA, Baldi PC. Immunization with Brucella VirB proteins reduces organ colonization in mice through a Th1-type immune response and elicits a similar immune response in dogs. Clinical and Vaccine Immunology : Cvi. 22: 274-81. PMID 25540276 DOI: 10.1128/CVI.00653-14  1
2015 La Porta N, Sablok G, Emilliani G, Hietala AM, Giovannelli A, Fontana P, Potenza E, Baldi P. Identification of low temperature stress regulated transcript sequences and gene families in Italian cypress. Molecular Biotechnology. 57: 407-18. PMID 25534982 DOI: 10.1007/s12033-014-9833-2  1
2015 Baldi P, Trapani S. Fourier coefficients of invariant random fields on homogeneous spaces of compact Lie groups Annales De L'Institut Henri Poincare (B) Probability and Statistics. 51: 648-671. DOI: 10.1214/14-AIHP600  1
2015 Baldi P, Ciabattoni A. Standard Completeness for Uninorm-Based Logics Proceedings of the International Symposium On Multiple-Valued Logic. 2015: 78-83. DOI: 10.1109/ISMVL.2015.20  1
2015 Baldi P, Sadowski P, Whiteson D. Enhanced Higgs boson to τ+τ- search with deep learning Physical Review Letters. 114. DOI: 10.1103/PhysRevLett.114.111801  1
2015 Shur VY, Neradovskiy MM, Dolbilov MA, Lobov AI, Zelenovskiy PS, Ushakov AD, Ushakova ES, Quillier E, Baldi P, De Micheli MP. Formation of broad domain boundary in congruent lithium niobate modified by proton exchange Ferroelectrics. 476: 146-155. DOI: 10.1080/00150193.2015.998946  1
2015 Neradovskiy MM, Shur VY, Naumova NA, Alikin DO, Lobov AI, Tronche H, Quiller E, Baldi P, De Micheli MP. Fabrication of SPE waveguides on PPLN: Formation of nanodomains and their impact on the SHG efficiency Ferroelectrics. 476: 127-133. DOI: 10.1080/00150193.2015.998919  1
2015 Baldi P, Ciabattoni A. Uniform proofs of standard completeness for extensions of first-order MTL Theoretical Computer Science. 603: 43-57. DOI: 10.1016/j.tcs.2015.07.014  1
2015 Baldi P, Blanke M, Castaldi P, Mimmo N, Simani S. Combined geometric and neural network approach to generic fault diagnosis in satellite reaction wheels Ifac Proceedings Volumes (Ifac-Papersonline). 48: 194-199. DOI: 10.1016/j.ifacol.2015.09.527  1
2015 Baldi P, Devoti R, Riguzzi F, Pietrantonio G. Satellite positioning and geophysics studies in Italy Rendiconti Lincei. 26: 33-41. DOI: 10.1007/s12210-015-0385-6  1
2015 Alazard T, Baldi P. Gravity Capillary Standing Water Waves Archive For Rational Mechanics and Analysis. 217: 741-830. DOI: 10.1007/s00205-015-0842-5  1
2015 Baldi P, Caramellino L, Rossi M. On sharp large deviations for the bridge of a general diffusion Lecture Notes in Mathematics. 2137: 427-441. DOI: 10.1007/978-3-319-18585-9_18  1
2015 Yarkony J, Beier T, Baldi P, Hamprecht FA. Parallel multicut segmentation via dual decomposition Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science). 8983: 56-68. DOI: 10.1007/978-3-319-17876-9_4  1
2015 Wolters PJ, Schouten HJ, Velasco R, Salvi S, Komjanc M, Si-Ammour A, Baldi P. Towards identification of the gene responsible for the columnar phenotype of 'McIntosh 'Wijcik" apple Acta Horticulturae. 1100: 55-62.  1
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  1
2014 Dyar KA, Ciciliot S, Wright LE, Biensø RS, Malagoli Tagliazucchi G, Patel VR, Forcato M, Peña-Paz MI, Gudiksen A, Solagna F, Albiero M, Moretti I, Eckel-Mahan KL, Baldi P, Sassone-Corsi P, et al. Erratum to "Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock" [Mol Metab 3 (2014) 29-41]. Molecular Metabolism. 3: 857. PMID 25503566 DOI: 10.1016/J.Molmet.2014.09.002  1
2014 Hoverter NP, Zeller MD, McQuade MM, Garibaldi A, Busch A, Selwan EM, Hertel KJ, Baldi P, Waterman ML. The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition. Nucleic Acids Research. 42: 13615-32. PMID 25414359 DOI: 10.1093/Nar/Gku1186  1
2014 Gordon WM, Zeller MD, Klein RH, Swindell WR, Ho H, Espetia F, Gudjonsson JE, Baldi PF, Andersen B. A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia. The Journal of Clinical Investigation. 124: 5205-18. PMID 25347468 DOI: 10.1172/Jci77138  1
2014 Masri S, Rigor P, Cervantes M, Ceglia N, Sebastian C, Xiao C, Roqueta-Rivera M, Deng C, Osborne TF, Mostoslavsky R, Baldi P, Sassone-Corsi P. Partitioning circadian transcription by SIRT6 leads to segregated control of cellular metabolism. Cell. 158: 659-72. PMID 25083875 DOI: 10.1016/J.Cell.2014.06.050  1
2014 Baldi P, Sadowski P, Whiteson D. Searching for exotic particles in high-energy physics with deep learning. Nature Communications. 5: 4308. PMID 24986233 DOI: 10.1038/Ncomms5308  1
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  1
2014 Patel VR, Eckel-Mahan K, Sassone-Corsi P, Baldi P. How pervasive are circadian oscillations? Trends in Cell Biology. 24: 329-31. PMID 24794425 DOI: 10.1016/J.Tcb.2014.04.005  1
2014 Baldi P, Sadowski P. The Dropout Learning Algorithm. Artificial Intelligence. 210: 78-122. PMID 24771879 DOI: 10.1016/J.Artint.2014.02.004  1
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  1
2014 Dyar KA, Ciciliot S, Wright LE, Biensø RS, Tagliazucchi GM, Patel VR, Forcato M, Paz MI, Gudiksen A, Solagna F, Albiero M, Moretti I, Eckel-Mahan KL, Baldi P, Sassone-Corsi P, et al. Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock. Molecular Metabolism. 3: 29-41. PMID 24567902 DOI: 10.1016/J.Molmet.2013.10.005  1
2014 Ferrero MC, Hielpos MS, Carvalho NB, Barrionuevo P, Corsetti PP, Giambartolomei GH, Oliveira SC, Baldi PC. Key role of Toll-like receptor 2 in the inflammatory response and major histocompatibility complex class ii downregulation in Brucella abortus-infected alveolar macrophages. Infection and Immunity. 82: 626-39. PMID 24478078 DOI: 10.1128/IAI.01237-13  1
2014 Sahar S, Masubuchi S, Eckel-Mahan K, Vollmer S, Galla L, Ceglia N, Masri S, Barth TK, Grimaldi B, Oluyemi O, Astarita G, Hallows WC, Piomelli D, Imhof A, Baldi P, et al. Circadian control of fatty acid elongation by SIRT1 protein-mediated deacetylation of acetyl-coenzyme A synthetase 1. The Journal of Biological Chemistry. 289: 6091-7. PMID 24425865 DOI: 10.1074/Jbc.M113.537191  1
2014 Chicco D, Sadowski P, Baldi P. Deep autoencoder neural networks for gene ontology annotation predictions Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 533-540. DOI: 10.1145/2649387.2649442  1
2014 Tyagi A, Gopi C, Baldi P, Kumar V, Islam A. CNFET-based 0.1 v to 0.6 v DC/DC converter 2014 Recent Advances in Engineering and Computational Sciences, Raecs 2014. DOI: 10.1109/RAECS.2014.6799605  1
2014 Stepanenko O, Quillier E, Tronche H, Baldi P, De Micheli M. Highly confining proton exchanged waveguides on Z-cut LiNbO3 with preserved nonlinear coefficient Ieee Photonics Technology Letters. 26: 1557-1560. DOI: 10.1109/LPT.2014.2329134  1
2014 Baldi P, Castaldi P, Mimmo N, Simani S. Generic wind estimation and compensation based on NLGA and RBF-NN 2014 European Control Conference, Ecc 2014. 1729-1734. DOI: 10.1109/ECC.2014.6862272  1
2014 Baldi P, Rossi M. Representation of Gaussian isotropic spin random fields Stochastic Processes and Their Applications. 124: 1910-1941. DOI: 10.1016/j.spa.2014.01.007  1
2014 Mastrolembo Ventura B, Serpelloni E, Argnani A, Bonforte A, Bürgmann R, Anzidei M, Baldi P, Puglisi G. Fast geodetic strain-rates in eastern Sicily (southern Italy): New insights into block tectonics and seismic potential in the area of the great 1693 earthquake Earth and Planetary Science Letters. 404: 77-88. DOI: 10.1016/J.Epsl.2014.07.025  1
2014 Baldi P, Berti M, Montalto R. KAM for quasi-linear KdV Comptes Rendus Mathematique. 352: 603-607. DOI: 10.1016/j.crma.2014.04.012  1
2014 Baldi P, Berti M, Montalto R. KAM for autonomous quasi-linear perturbations of KdV Annales De L'Institut Henri Poincare. Annales: Analyse Non Lineaire/Nonlinear Analysis. DOI: 10.1016/j.anihpc.2015.07.003  1
2014 Baldi P. A note on standard completeness for some extensions of uninorm logic Soft Computing. 18: 1463-1470. DOI: 10.1007/s00500-014-1265-1  1
2014 Baldi P, Berti M, Montalto R. KAM for quasi-linear and fully nonlinear forced perturbations of Airy equation Mathematische Annalen. 359: 471-536. DOI: 10.1007/s00208-013-1001-7  1
2014 Napolitano F, Tagliaferri R, Baldi P. An adaptive reference point approach to efficiently search large chemical databases Smart Innovation, Systems and Technologies. 26: 63-74. DOI: 10.1007/978-3-319-04129-2_7  1
2014 Baldi P, Castaldi P, Mimmo N, Simani S. A new aerodynamic decoupled frequential FDIR methodology for satellite actuator faults International Journal of Adaptive Control and Signal Processing. 28: 812-832. DOI: 10.1002/acs.2379  1
2014 Sadowski P, Baldi P, Whiteson D. Searching for higgs boson decay modes with deep learning Advances in Neural Information Processing Systems. 3: 2393-2401.  1
2014 Baldi P, Wang W. Message from the general chairs Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. iii-iv.  1
2013 Wolters PJ, Schouten HJ, Velasco R, Si-Ammour A, Baldi P. Evidence for regulation of columnar habit in apple by a putative 2OG-Fe(II) oxygenase. The New Phytologist. 200: 993-9. PMID 24571666 DOI: 10.1111/nph.12580  1
2013 Eckel-Mahan KL, Patel VR, de Mateo S, Orozco-Solis R, Ceglia NJ, Sahar S, Dilag-Penilla SA, Dyar KA, Baldi P, Sassone-Corsi P. Reprogramming of the circadian clock by nutritional challenge. Cell. 155: 1464-78. PMID 24360271 DOI: 10.1016/J.Cell.2013.11.034  1
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  1
2013 Fooshee D, Andronico A, Baldi P. ReactionMap: an efficient atom-mapping algorithm for chemical reactions. Journal of Chemical Information and Modeling. 53: 2812-9. PMID 24160861 DOI: 10.1021/Ci400326P  1
2013 Aguilar-Arnal L, Hakim O, Patel VR, Baldi P, Hager GL, Sassone-Corsi P. Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nature Structural & Molecular Biology. 20: 1206-13. PMID 24056944 DOI: 10.1038/Nsmb.2667  1
2013 Fujikawa T, Berglund ED, Patel VR, Ramadori G, Vianna CR, Vong L, Thorel F, Chera S, Herrera PL, Lowell BB, Elmquist JK, Baldi P, Coppari R. Leptin engages a hypothalamic neurocircuitry to permit survival in the absence of insulin. Cell Metabolism. 18: 431-44. PMID 24011077 DOI: 10.1016/J.Cmet.2013.08.004  1
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  1
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  1
2013 Baldi PC, Giambartolomei GH. Pathogenesis and pathobiology of zoonotic brucellosis in humans. Revue Scientifique Et Technique (International Office of Epizootics). 32: 117-25. PMID 23837370  1
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  1
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  1
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  1
2013 Miraglia MC, Scian R, Samartino CG, Barrionuevo P, Rodriguez AM, Ibañez AE, Coria LM, Velásquez LN, Baldi PC, Cassataro J, Delpino MV, Giambartolomei GH. Brucella abortus induces TNF-α-dependent astroglial MMP-9 secretion through mitogen-activated protein kinases. Journal of Neuroinflammation. 10: 47. PMID 23587438 DOI: 10.1186/1742-2094-10-47  1
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  1
2013 Masri S, Patel VR, Eckel-Mahan KL, Peleg S, Forne I, Ladurner AG, Baldi P, Imhof A, Sassone-Corsi P. Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proceedings of the National Academy of Sciences of the United States of America. 110: 3339-44. PMID 23341599 DOI: 10.1073/Pnas.1217632110  1
2013 Baldi PC, Giambartolomei GH. Immunopathology of Brucella infection. Recent Patents On Anti-Infective Drug Discovery. 8: 18-26. PMID 22812614 DOI: 10.2174/157489113805290737  1
2013 Baldi P, Berti M, Montalto R. A note on KAM theory for quasi-linear and fully nonlinear forced KdV Atti Della Accademia Nazionale Dei Lincei, Classe Di Scienze Fisiche, Matematiche E Naturali, Rendiconti Lincei Matematica E Applicazioni. 24: 437-450. DOI: 10.4171/RLM/660  1
2013 Baldi P, Rossi M. On Lévy's Brownian motion indexed by elements of compact groups Colloquium Mathematicum. 133: 227-236. DOI: 10.4064/cm133-2-9  1
2013 Baldi P, Pisani C. Simple simulation schemes for cir and Wishart processes International Journal of Theoretical and Applied Finance. 16. DOI: 10.1142/S0219024913500453  1
2013 Baldi P, Castaldi P, Mimmo N, Simani S. Satellite attitude active FTC based on Geometric Approach and RBF Neural Network Conference On Control and Fault-Tolerant Systems, Systol. 667-673. DOI: 10.1109/SysTol.2013.6693907  1
2013 Dolbilov MA, Shur VY, Shishkina EV, Angudovich ES, Ushakov AD, Baldi P, De Micheli MP. Formation of nanodomain structure in front of the moving domain wall in lithium niobate single crystal modified by proton exchange Ferroelectrics. 442: 82-91. DOI: 10.1080/10584587.2013.776408  1
2013 Cenni N, Viti M, Baldi P, Mantovani E, Bacchetti M, Vannucchi A. Present vertical movements in Central and Northern Italy from GPS data: Possible role of natural and anthropogenic causes Journal of Geodynamics. 71: 74-85. DOI: 10.1016/j.jog.2013.07.004  1
2013 Baldi P. Periodic solutions of fully nonlinear autonomous equations of Benjamin-Ono type Annales De L'Institut Henri Poincare. Annales: Analyse Non Lineaire/Nonlinear Analysis. 30: 33-77. DOI: 10.1016/j.anihpc.2012.06.001  1
2013 Baldi P, Wolters PJ, Komjanc M, Viola R, Velasco R, Salvi S. Genetic and physical characterisation of the locus controlling columnar habit in apple (Malus × domestica Borkh.) Molecular Breeding. 31: 429-440. DOI: 10.1007/s11032-012-9800-1  1
2013 Stepanenko O, Quillier E, Krasnokutska I, Baldi P, De Micheli MP. Nonlinear effects in lithium niobate proton exchanged embedded waveguides Optics Infobase Conference Papers 1
2013 Baldi PL, Iannello P, Riva S, Antonietti A. Cognitive reflection and socially biased decisions Studia Psychologica. 55: 265-271.  1
2013 Baldi P, Sadowski P. Understanding dropout Advances in Neural Information Processing Systems 1
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  1
2012 Wanke MM, Cairó F, Rossano M, Laiño M, Baldi PC, Monachesi NE, Comercio EA, Vivot MM. Preliminary study of an immunochromatography test for serological diagnosis of canine brucellosis. Reproduction in Domestic Animals = Zuchthygiene. 47: 370-2. PMID 23279541 DOI: 10.1111/rda.12108  1
2012 Pollak CN, Delpino MV, Fossati CA, Baldi PC. Outer membrane vesicles from Brucella abortus promote bacterial internalization by human monocytes and modulate their innate immune response. Plos One. 7: e50214. PMID 23189190 DOI: 10.1371/journal.pone.0050214  1
2012 Baldi P, Muthuchelian K, La Porta N. Leaf plasticity to light intensity in Italian cypress (Cupressus sempervirens L.): adaptability of a Mediterranean conifer cultivated in the Alps. Journal of Photochemistry and Photobiology. B, Biology. 117: 61-9. PMID 23079539 DOI: 10.1016/j.jphotobiol.2012.09.006  1
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  1
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  1
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  1
2012 Patel VR, Eckel-Mahan K, Sassone-Corsi P, Baldi P. CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics. Nature Methods. 9: 772-3. PMID 22847108 DOI: 10.1038/Nmeth.2111  1
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  1
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  1
2012 Sequeira A, Martin MV, Rollins B, Moon EA, Bunney WE, Macciardi F, Lupoli S, Smith EN, Kelsoe J, Magnan CN, van Oven M, Baldi P, Wallace DC, Vawter MP. Mitochondrial mutations and polymorphisms in psychiatric disorders. Frontiers in Genetics. 3: 103. PMID 22723804 DOI: 10.3389/Fgene.2012.00103  1
2012 Ficorella C, Bruera G, Cannita K, Porzio G, Baldi PL, Tinari N, Natoli C, Ricevuto E. Triplet chemotherapy in patients with metastatic colorectal cancer: toward the best way to safely administer a highly active regimen in clinical practice. Clinical Colorectal Cancer. 11: 229-37. PMID 22694897 DOI: 10.1016/j.clcc.2012.05.001  1
2012 Baldi P, Lu Z. Complex-valued autoencoders. Neural Networks : the Official Journal of the International Neural Network Society. 33: 136-47. PMID 22622264 DOI: 10.1016/J.Neunet.2012.04.011  1
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  1
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  1
2012 Ferrero MC, Fossati CA, Rumbo M, Baldi PC. Brucella invasion of human intestinal epithelial cells elicits a weak proinflammatory response but a significant CCL20 secretion. Fems Immunology and Medical Microbiology. 66: 45-57. PMID 22553918 DOI: 10.1111/j.1574-695X.2012.00985.x  1
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  1
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  1
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  1
2012 Eckel-Mahan KL, Patel VR, Mohney RP, Vignola KS, Baldi P, Sassone-Corsi P. Coordination of the transcriptome and metabolome by the circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 109: 5541-6. PMID 22431615 DOI: 10.1073/Pnas.1118726109  1
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  1
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  1
2012 Delpino MV, Barrionuevo P, Macedo GC, Oliveira SC, Genaro SD, Scian R, Miraglia MC, Fossati CA, Baldi PC, Giambartolomei GH. Macrophage-elicited osteoclastogenesis in response to Brucella abortus infection requires TLR2/MyD88-dependent TNF-α production. Journal of Leukocyte Biology. 91: 285-98. PMID 22075930 DOI: 10.1189/jlb.04111185  1
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  1
2012 Tudini M, Palluzzi E, Cannita K, Mancini M, Santomaggio A, Bruera G, Baldi PL, Pelliccione M, Ricevuto E, Ficorella C. Modulation of GemOx chemotherapy according to CIRS in elderly patients with advanced pancreatic cancer. Oncology Reports. 27: 423-32. PMID 22020810 DOI: 10.3892/or.2011.1517  1
2012 Baldi P, Castaldi P, Mimmo N, Simani S. Aerodynamic decoupled FDI for frequency faults in earth satellite engines Ifac Proceedings Volumes (Ifac-Papersonline). 8: 1095-1100. DOI: 10.3182/20120829-3-MX-2028.00178  1
2012 Alibart O, De Micheli M, Baldi P. Single WDM channel efficient wavelength shifting and/or amplification using counterpropagating optical parametric amplifiers Optics Communications. 285: 3886-3889. DOI: 10.1016/j.optcom.2012.05.042  1
2012 Cenni N, Mantovani E, Baldi P, Viti M. Present kinematics of Central and Northern Italy from continuous GPS measurements Journal of Geodynamics. 58: 62-72. DOI: 10.1016/j.jog.2012.02.004  1
2012 Bruera G, Cannita K, Giuliante F, Baldi PL, Vicentini R, Marchetti P, Nuzzo G, Antonucci A, Ficorella C, Ricevuto E. Effectiveness of liver metastasectomies in patients with metastatic colorectal cancer treated with FIr-B/FOx triplet chemotherapy plus bevacizumab Clinical Colorectal Cancer. 11: 119-126. DOI: 10.1016/j.clcc.2011.11.002  1
2012 Baldi P. Boolean autoencoders and hypercube clustering complexity Designs, Codes, and Cryptography. 65: 383-403. DOI: 10.1007/S10623-012-9719-X  1
2012 Marsella M, Baldi P, Coltelli M, Fabris M. The morphological evolution of the Sciara del Fuoco since 1868: Reconstructing the effusive activity at Stromboli volcano Bulletin of Volcanology. 74: 231-248. DOI: 10.1007/s00445-011-0516-6  1
2012 Baldi P, Ciabattoni A, Spendier L. Standard completeness for extensions of MTL: An automated approach Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7456: 154-167. DOI: 10.1007/978-3-642-32621-9_12  1
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.  1
2012 Stepanenko O, Quillier E, Tronche H, Baldi P, Aschiéri P, Benchabane S, Micheli MD. Towards proton exchanged photonic wires in LiNbO3 Advances in Optical Materials, Aiom 2012. IF1A.6.  1
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  1
2011 Baldi P, Müller KR, Schneider G. Editorial: Charting Chemical Space: Challenges and Opportunities for Artificial Intelligence and Machine Learning. Molecular Informatics. 30: 751. PMID 27467407 DOI: 10.1002/Minf.201180003  1
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  1
2011 Marchesini MI, Connolly J, Delpino MV, Baldi PC, Mujer CV, DelVecchio VG, Comerci DJ. Brucella abortus choloylglycine hydrolase affects cell envelope composition and host cell internalization. Plos One. 6: e28480. PMID 22174816 DOI: 10.1371/journal.pone.0028480  1
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  1
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  1
2011 Tang B, Di Lena P, Schaffer L, Head SR, Baldi P, Thomas EA. Genome-wide identification of Bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling. Plos One. 6: e23691. PMID 21912641 DOI: 10.1371/Journal.Pone.0023691  1
2011 Boehnke SE, Berg DJ, Marino RA, Baldi PF, Itti L, Munoz DP. Visual adaptation and novelty responses in the superior colliculus. The European Journal of Neuroscience. 34: 766-79. PMID 21864319 DOI: 10.1111/j.1460-9568.2011.07805.x  1
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  1
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  1
2011 Scian R, Barrionuevo P, Giambartolomei GH, De Simone EA, Vanzulli SI, Fossati CA, Baldi PC, Delpino MV. Potential role of fibroblast-like synoviocytes in joint damage induced by Brucella abortus infection through production and induction of matrix metalloproteinases. Infection and Immunity. 79: 3619-32. PMID 21730088 DOI: 10.1128/IAI.05408-11  1
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  1
2011 Ferrero MC, Bregante J, Delpino MV, Barrionuevo P, Fossati CA, Giambartolomei GH, Baldi PC. Proinflammatory response of human endothelial cells to Brucella infection. Microbes and Infection / Institut Pasteur. 13: 852-61. PMID 21621633 DOI: 10.1016/j.micinf.2011.04.010  1
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  1
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  1
2011 Scian R, Barrionuevo P, Giambartolomei GH, Fossati CA, Baldi PC, Delpino MV. Granulocyte-macrophage colony-stimulating factor- and tumor necrosis factor alpha-mediated matrix metalloproteinase production by human osteoblasts and monocytes after infection with Brucella abortus. Infection and Immunity. 79: 192-202. PMID 20956574 DOI: 10.1128/IAI.00934-10  1
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  1
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  1
2011 Baldi P, Casula G, Cenni N, Loddo F, Pesci A, Bacchetti M. Vertical and horizontal crustal movements in Central and Northern Italy Bollettino Di Geofisica Teorica Ed Applicata. 52: 667-685. DOI: 10.4430/bgta0021  1
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  1
2011 Baldi P, Toland JF. Steady periodic water waves under nonlinear elastic membranes Journal Fur Die Reine Und Angewandte Mathematik. 67-112. DOI: 10.1515/CRELLE.2011.015  1
2011 Baldi P, Baronio R, De Cristofaro E, Gasti P, Tsudik G. Countering GATTACA: Efficient and secure testing of fully-sequenced human genomes Proceedings of the Acm Conference On Computer and Communications Security. 691-702. DOI: 10.1145/2046707.2046785  1
2011 Baldi P, Castaldi P, Mimmo N, Torre A, Simani S. A new longitudinal flight path control with adaptive wind shear estimation and compensation Proceedings of the Ieee Conference On Decision and Control. 6852-6857. DOI: 10.1109/CDC.2011.6160900  1
2011 Baldi P, Caramellino L. General Freidlin-Wentzell Large Deviations and positive diffusions Statistics and Probability Letters. 81: 1218-1229. DOI: 10.1016/j.spl.2011.03.020  1
2011 Baldi P, Pedron L, Hietala AM, La Porta N. Cold tolerance in cypress (Cupressus sempervirens L.): A physiological and molecular study Tree Genetics and Genomes. 7: 79-90. DOI: 10.1007/s11295-010-0316-8  1
2011 Baldi P, Müller KR, Schneider G. Charting chemical space: Challenges and opportunities for artificial intelligence and machine learning Molecular Informatics. 30: 751-752. DOI: 10.1002/minf.201180003  1
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  1
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 1
2011 Baldi P. Possessive expressions in Oscan and Umbrian Stuf - Sprachtypologie Und Universalienforschung. 64: 103-113.  1
2010 Bruera G, Santomaggio A, Cannita K, Baldi PL, Tudini M, De Galitiis F, Mancini M, Marchetti P, Antonucci A, Ficorella C, Ricevuto E. "Poker" association of weekly alternating 5-fluorouracil, irinotecan, bevacizumab and oxaliplatin (FIr-B/FOx) in first line treatment of metastatic colorectal cancer: a phase II study. Bmc Cancer. 10: 567. PMID 20958992 DOI: 10.1186/1471-2407-10-567  1
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  1
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  1
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  1
2010 Whisenant TC, Ho DT, Benz RW, Rogers JS, Kaake RM, Gordon EA, Huang L, Baldi P, Bardwell L. Computational prediction and experimental verification of new MAP kinase docking sites and substrates including Gli transcription factors. Plos Computational Biology. 6. PMID 20865152 DOI: 10.1371/Journal.Pcbi.1000908  1
2010 Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics. 42: 833-9. PMID 20802477 DOI: 10.1038/Ng.654  1
2010 Wallach JC, Delpino MV, Scian R, Deodato B, Fossati CA, Baldi PC. Prepatellar bursitis due to Brucella abortus: case report and analysis of the local immune response. Journal of Medical Microbiology. 59: 1514-8. PMID 20724508 DOI: 10.1099/jmm.0.016360-0  1
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  1
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  1
2010 Ferrero MC, Fossati CA, Baldi PC. Direct and monocyte-induced innate immune response of human lung epithelial cells to Brucella abortus infection. Microbes and Infection / Institut Pasteur. 12: 736-47. PMID 20478392 DOI: 10.1016/j.micinf.2010.05.002  1
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  1
2010 Delpino MV, Barrionuevo P, Scian R, Fossati CA, Baldi PC. Brucella-infected hepatocytes mediate potentially tissue-damaging immune responses. Journal of Hepatology. 53: 145-54. PMID 20452697 DOI: 10.1016/j.jhep.2010.02.028  1
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  1
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  1
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  1
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  1
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  1
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  1
2010 Baldi P, Toland JF. Bifurcation and secondary bifurcation of heavy periodic hydroelastic travelling waves Interfaces and Free Boundaries. 12: 1-22. DOI: 10.4171/IFB/224  1
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  1
2010 Berg D, Boehnke S, Marino R, Baldi P, Munoz D, Itti L. The role of bottom-up and top-down influences in directing primate gaze shifts Journal of Vision. 7: 632-632. DOI: 10.1167/7.9.632  1
2010 Boehnke S, Berg D, Baldi P, Itti L, Munoz D. Adaptation and habituation of visual responses in the superficial and intermediate layers of the superior colliculus (SC) Journal of Vision. 7: 188-188. DOI: 10.1167/7.9.188  1
2010 Berg DJ, Boehnke S, Marino R, Baldi P, Munoz D, Itti L. Characterizing surprise in humans and monkeys Journal of Vision. 6: 211-211. DOI: 10.1167/6.6.211  1
2010 Fabris M, Baldi P, Anzidei M, Pesci A, Bortoluzzi G, Aliani S. High resolution topographic model of Panarea Island by fusion of photogrammetric, lidar and bathymetric digital terrain models Photogrammetric Record. 25: 382-401. DOI: 10.1111/j.1477-9730.2010.00600.x  1
2010 Baldi P, Castaldi P, Simani S, Bertoni G. Fault diagnosis and control reconfiguration for satellite reaction wheels Conference On Control and Fault-Tolerant Systems, Systol'10 - Final Program and Book of Abstracts. 143-148. DOI: 10.1109/SYSTOL.2010.5676066  1
2010 Napolitano F, Tagliaferri R, Baldi P. A scalable reference-point based algorithm to efficiently search large chemical databases Proceedings of the International Joint Conference On Neural Networks. DOI: 10.1109/IJCNN.2010.5596608  1
2010 Aboussouan P, Alibart O, Ostrowsky DB, Baldi P, Tanzilli S. High-visibility two-photon interference at a telecom wavelength using picosecond-regime separated sources Physical Review a - Atomic, Molecular, and Optical Physics. 81. DOI: 10.1103/PhysRevA.81.021801  1
2010 Dolbilov MA, Shishkin EI, Shur VY, Tascu S, Baldi P, De Micheli MP. Abnormal domain growth in lithium niobate with surface layer modified by proton exchange Ferroelectrics. 398: 108-114. DOI: 10.1080/00150193.2010.489840  1
2010 Baldi P, Castaldi P, Mimmo N, Simani S. Fault diagnosis and control reconfiguration in earth satellite model engines Iet Seminar Digest. 2010: 114-119. DOI: 10.1049/ic.2010.0266  1
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  1
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  1
2010 Serpelloni E, Bürgmann R, Anzidei M, Baldi P, Mastrolembo Ventura B, Boschi E. Strain accumulation across the Messina Straits and kinematics of Sicily and Calabria from GPS data and dislocation modeling Earth and Planetary Science Letters. 298: 347-360. DOI: 10.1016/J.Epsl.2010.08.005  1
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  1
2010 Javanmardi S, Lopes C, Baldi P. Modeling user reputation in wikis Statistical Analysis and Data Mining. 3: 126-139. DOI: 10.1002/Sam.V3:2  1
2010 Javanmardi S, Lopes C, Baldi P. Modeling user reputation in wikis: Modeling User Reputation in Wikis Statistical Analysis and Data Mining. 3: 126-139. DOI: 10.1002/Sam.10070  1
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.  1
2010 Mantovani E, Cenni N, Baldi P, Viti M. GPS measurements in central-northern Italy for deterministic estimate of seismic hazard | Misure GPS nell'Italia centro-settentrionale per la stima deterministica della pericolosità sismica Ingegneria Sismica. 27: 69-76.  1
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  1
2009 Castaldini D, Bassi P, Aschieri P, Tascu S, De Micheli M, Baldi PA. High performance mode adapters based on segmented SPE:LiNbO3 waveguides. Optics Express. 17: 17868-73. PMID 19907575 DOI: 10.1364/OE.17.017868  1
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  1
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  1
2009 Baldi P, Hirschberg DS. An intersection inequality sharper than the tanimoto triangle inequality for efficiently searching large databases. Journal of Chemical Information and Modeling. 49: 1866-70. PMID 19601605 DOI: 10.1021/Ci900133J  1
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  1
2009 Russo T, Baldi P, Parisi A, Magnifico G, Mariani S, Cataudella S. Lévy processes and stochastic von Bertalanffy models of growth, with application to fish population analysis. Journal of Theoretical Biology. 258: 521-9. PMID 19459236 DOI: 10.1016/J.Jtbi.2009.01.033  1
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  1
2009 Delpino MV, Comerci DJ, Wagner MA, Eschenbrenner M, Mujer CV, Ugalde RA, Fossati CA, Baldi PC, Delvecchio VG. Differential composition of culture supernatants from wild-type Brucella abortus and its isogenic virB mutants. Archives of Microbiology. 191: 571-81. PMID 19436993 DOI: 10.1007/s00203-009-0484-9  1
2009 Ferrero MC, Fossati CA, Baldi PC. Smooth Brucella strains invade and replicate in human lung epithelial cells without inducing cell death. Microbes and Infection / Institut Pasteur. 11: 476-83. PMID 19397873 DOI: 10.1016/j.micinf.2009.01.010  1
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  1
2009 Pedron L, Baldi P, Hietala AM, La Porta N. Genotype-specific regulation of cold-responsive genes in cypress (Cupressus sempervirens L.). Gene. 437: 45-53. PMID 19374025 DOI: 10.1016/j.gene.2008.12.012  1
2009 Delpino MV, Fossati CA, Baldi PC. Proinflammatory response of human osteoblastic cell lines and osteoblast-monocyte interaction upon infection with Brucella spp. Infection and Immunity. 77: 984-95. PMID 19103778 DOI: 10.1128/IAI.01259-08  1
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  1
2009 Xie X, Rigor P, Baldi P. MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics (Oxford, England). 25: 167-74. PMID 19017655 DOI: 10.1093/Bioinformatics/Btn605  1
2009 Itti L, Baldi P. Bayesian surprise attracts human attention. Vision Research. 49: 1295-306. PMID 18834898 DOI: 10.1016/J.Visres.2008.09.007  1
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  1
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  1
2009 Javanmardi S, Ganjisaffar Y, Lopes C, Baldi P. User contribution and trust in Wikipedia 2009 5th International Conference On Collaborative Computing: Networking, Applications and Worksharing, Collaboratecom 2009. DOI: 10.4108/ICST.COLLABORATECOM2009.8376  1
2009 Baldi P, Kerkyacharian G, Marinucci D, Picard D. Subsampling needlet coefficients on the sphere Bernoulli. 15: 438-463. DOI: 10.3150/08-BEJ164  1
2009 Baldi P, Kerkyacharian G, Marinucci D, Picard D. Adaptive density estimation for directional data using needlets Annals of Statistics. 37: 3362-3395. DOI: 10.1214/09-AOS682  1
2009 Baldi P, Kerkyacharian G, Marinucci D, Picard D. Asymptotics for spherical needlets Annals of Statistics. 37: 1150-1171. DOI: 10.1214/08-AOS601  1
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  1
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  1
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  1
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  1
2009 Russo T, Mariani S, Baldi P, Parisi A, Magnifico G, Clausen LW, Cataudella S. Progress in modelling herring populations: An individual-based model of growth Ices Journal of Marine Science. 66: 1718-1725. DOI: 10.1093/Icesjms/Fsp204  1
2009 Baldi P, Casula G, Cenni N, Loddo F, Pesci A. GPS-based monitoring of land subsidence in the Po Plain (Northern Italy) Earth and Planetary Science Letters. 288: 204-212. DOI: 10.1016/j.epsl.2009.09.023  1
2009 Jurdak R, Baldi P, Lopes CV. Software-driven sensor networks for short-range shallow water applications Ad Hoc Networks. 7: 837-848. DOI: 10.1016/j.adhoc.2008.07.012  1
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  1
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 1
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  1
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  1
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  1
2008 Wallach JC, Ferrero MC, Victoria Delpino M, Fossati CA, Baldi PC. Occupational infection due to Brucella abortus S19 among workers involved in vaccine production in Argentina. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. 14: 805-7. PMID 18727806 DOI: 10.1111/j.1469-0691.2008.02029.x  0.01
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  1
2008 Baldi P, Benz RW. BLASTing small molecules--statistics and extreme statistics of chemical similarity scores. Bioinformatics (Oxford, England). 24: i357-65. PMID 18586735 DOI: 10.1093/bioinformatics/btn187  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2007 Einhäuser W, Mundhenk TN, Baldi P, Koch C, Itti L. A bottom-up model of spatial attention predicts human error patterns in rapid scene recognition. Journal of Vision. 7: 6.1-13. PMID 17997675 DOI: 10.1167/7.10.6  1
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  1
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  1
2007 Delpino MV, Estein SM, Fossati CA, Baldi PC. Partial protection against Brucella infection in mice by immunization with nonpathogenic alphaproteobacteria. Clinical and Vaccine Immunology : Cvi. 14: 1296-301. PMID 17715332 DOI: 10.1128/CVI.00459-06  0.01
2007 Delpino MV, Estein SM, Fossati CA, Baldi PC, Cassataro J. Vaccination with Brucella recombinant DnaK and SurA proteins induces protection against Brucella abortus infection in BALB/c mice. Vaccine. 25: 6721-9. PMID 17686554 DOI: 10.1016/j.vaccine.2007.07.002  0.01
2007 Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins. 69: 137-51. PMID 17680686 DOI: 10.1002/Prot.21675  1
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  1
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  1
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  1
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  1
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  1
2007 Larsen LS, Zhang M, Beliakova-Bethell N, Bilanchone V, Lamsa A, Nagashima K, Najdi R, Kosaka K, Kovacevic V, Cheng J, Baldi P, Hatfield GW, Sandmeyer S. Ty3 capsid mutations reveal early and late functions of the amino-terminal domain. Journal of Virology. 81: 6957-72. PMID 17442718 DOI: 10.1128/Jvi.02207-06  1
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  1
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  1
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  1
2007 Wang N, Baldi PF, Gaut BS. Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae. Molecular Phylogenetics and Evolution. 43: 1066-75. PMID 17196839 DOI: 10.1016/J.Ympev.2006.11.019  1
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  1
2007 Posadas DM, Martín FA, Sabio y García JV, Spera JM, Delpino MV, Baldi P, Campos E, Cravero SL, Zorreguieta A. The TolC homologue of Brucella suis is involved in resistance to antimicrobial compounds and virulence. Infection and Immunity. 75: 379-89. PMID 17088356 DOI: 10.1128/IAI.01349-06  0.01
2007 Delpino MV, Marchesini MI, Estein SM, Comerci DJ, Cassataro J, Fossati CA, Baldi PC. A bile salt hydrolase of Brucella abortus contributes to the establishment of a successful infection through the oral route in mice. Infection and Immunity. 75: 299-305. PMID 17088355 DOI: 10.1128/IAI.00952-06  0.01
2007 Lemos OAL, Bajracharya SK, Ossher J, Morla RS, Masiero PC, Baldi P, Lopes CV. CodeGenie: Using test-cases to search and reuse source code Ase'07 - 2007 Acm/Ieee International Conference On Automated Software Engineering. 525-526. DOI: 10.1145/1321631.1321726  1
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  1
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  1
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  1
2007 Brandon M, Procaccio V, Ruiz-Pesini E, Mishmar D, Lott M, Baldi P, Wallace DC. 74 Mitomaster – Analytical tool for clinical mitochondrial sequence data Mitochondrion. 7: 425. DOI: 10.1016/J.Mito.2007.08.078  1
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  1
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  1
2006 Castro HA, González SR, Prat MI, Baldi PC. [Detection of anti-Brucella spp. antibodies in swine by agglutination techniques and indirect ELISA in the Buenos Aires and La Pampa provinces, Argentina]. Revista Argentina De MicrobiologíA. 38: 75-8. PMID 17037254  0.01
2006 Brandon M, Baldi P, Wallace DC. Mitochondrial mutations in cancer. Oncogene. 25: 4647-62. PMID 16892079 DOI: 10.1038/Sj.Onc.1209607  1
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  1
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  1
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  1
2006 Delpino MV, Cassataro J, Fossati CA, Goldbaum FA, Baldi PC. Brucella outer membrane protein Omp31 is a haemin-binding protein. Microbes and Infection / Institut Pasteur. 8: 1203-8. PMID 16517201 DOI: 10.1016/j.micinf.2005.11.008  0.01
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  1
2006 Wanke MM, Delpino MV, Baldi PC. Use of enrofloxacin in the treatment of canine brucellosis in a dog kennel (clinical trial). Theriogenology. 66: 1573-8. PMID 16476476 DOI: 10.1016/j.theriogenology.2006.01.034  0.01
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  1
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  1
2006 Wang ET, Kodama G, Baldi P, Moyzis RK. Global landscape of recent inferred Darwinian selection for Homo sapiens. Proceedings of the National Academy of Sciences of the United States of America. 103: 135-40. PMID 16371466 DOI: 10.1073/Pnas.0509691102  1
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  1
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  1
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  1
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  1
2005 Baldi P. Chemoinformatics, drug design, and systems biology. Genome Informatics. International Conference On Genome Informatics. 16: 281-5. PMID 16913067 DOI: 10.11234/Gi1990.16.2_281  0.01
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  1
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  1
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  1
2005 Baldi P, Rosen-Zvi M. On the relationship between deterministic and probabilistic directed Graphical models: from Bayesian networks to recursive neural networks. Neural Networks : the Official Journal of the International Neural Network Society. 18: 1080-6. PMID 16157470 DOI: 10.1016/J.Neunet.2005.07.007  0.01
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  1
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  1
2005 Cheng J, Baldi P. Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics (Oxford, England). 21: i75-84. PMID 15961501 DOI: 10.1093/Bioinformatics/Bti1004  1
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  1
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  1
2005 Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP. Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. The Journal of Biological Chemistry. 280: 15084-96. PMID 15699038 DOI: 10.1074/jbc.M414030200  1
2005 Sokolchik I, Tanabe T, Baldi PF, Sze JY. Polymodal sensory function of the Caenorhabditis elegans OCR-2 channel arises from distinct intrinsic determinants within the protein and is selectively conserved in mammalian TRPV proteins. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 25: 1015-23. PMID 15673683 DOI: 10.1523/JNEUROSCI.3107-04.2005  0.12
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  1
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  1
2005 Hampson SE, Gaut BS, Baldi P. Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics (Oxford, England). 21: 1339-48. PMID 15585535 DOI: 10.1093/Bioinformatics/Bti168  1
2005 Cheng J, Scharenbroich L, Baldi P, Mjolsness E. Sigmoid: A software infrastructure for pathway bioinformatics and systems biology Ieee Intelligent Systems. 20: 68-75. DOI: 10.1109/Mis.2005.51  1
2005 Jurdak R, Baldi P, Lopes CV. State-driven energy optimization in wireless sensor networks Proceedings - 2005 Systems Communications: Icw 2005, Wireless - Ichsn 2005, High Speed Networks - Icmcs 2005, Multimedia Communications Systems - Senet 2005, Sensor Networks. 2005: 356-363. DOI: 10.1109/ICW.2005.76  1
2005 Itti L, Baldi P. A principled approach to detecting surprising events in video Proceedings - 2005 Ieee Computer Society Conference On Computer Vision and Pattern Recognition, Cvpr 2005. 631-637. DOI: 10.1109/CVPR.2005.40  1
2005 Baldi P. Surprise: A Shortcut for Attention? Neurobiology of Attention. 24-28. DOI: 10.1016/B978-012375731-9/50009-4  0.01
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  1
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  1
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  1
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  1
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  1
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  1
2004 Jurdak R, Lopes CV, Baldi P. An acoustic identification scheme for location systems Proceedings - the Ieee/Acs International Conference On Pervasive Services, Icps2004. 61-70.  1
2003 McLysaght A, Baldi PF, Gaut BS. Extensive gene gain associated with adaptive evolution of poxviruses. Proceedings of the National Academy of Sciences of the United States of America. 100: 15655-60. PMID 14660798 DOI: 10.1073/Pnas.2136653100  1
2003 Weiss GA, Roth TA, Baldi PF, Sidhu SS. Comprehensive mutagenesis of the C-terminal domain of the M13 gene-3 minor coat protein: the requirements for assembly into the bacteriophage particle. Journal of Molecular Biology. 332: 777-82. PMID 12972250 DOI: 10.1016/S0022-2836(03)00950-1  1
2003 Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP. Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. The Journal of Biological Chemistry. 278: 29837-55. PMID 12754220 DOI: 10.1074/Jbc.M213060200  1
2003 Hampson S, McLysaght A, Gaut B, Baldi P. LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Research. 13: 999-1010. PMID 12695327 DOI: 10.1101/Gr.814403  1
2003 Hatfield GW, Hung SP, Baldi P. Differential analysis of DNA microarray gene expression data. Molecular Microbiology. 47: 871-7. PMID 12581345 DOI: 10.1046/J.1365-2958.2003.03298.X  1
2003 Baldi P, Batchelder WH. Bounds on variances of estimators for multinomial processing tree models Journal of Mathematical Psychology. 47: 467-470. DOI: 10.1016/S0022-2496(03)00036-1  1
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  1
2002 Pollastri G, Baldi P. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics (Oxford, England). 18: S62-70. PMID 12169532 DOI: 10.1093/BIOINFORMATICS/18.SUPPL_1.S62  1
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  1
2002 Hampson S, Kibler D, Baldi P. Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinformatics (Oxford, England). 18: 513-28. PMID 12016049 DOI: 10.1093/Bioinformatics/18.4.513  1
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  1
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  1
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  1
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  1
2001 Baldi P, Long AD. A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics (Oxford, England). 17: 509-19. PMID 11395427 DOI: 10.1093/Bioinformatics/17.6.509  1
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  1
2001 Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, Baldi P. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. The Journal of Biological Chemistry. 276: 19937-44. PMID 11259426 DOI: 10.1074/Jbc.M010192200  1
2000 Gallo K, Baldi P, De Micheli M, Ostrowsky DB, Assanto G. Cascading phase shift and multivalued response in counterpropagating frequency-nondegenerate parametric amplifiers. Optics Letters. 25: 966-8. PMID 18064242  0.01
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  1
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  1
1999 Aschiéri P, Rastogi V, Chanvillard L, Baldi P, De Micheli MP, Ostrowsky DB, Bellanca G, Bassi P, Thyagarajan K, Shenoy MR. Experimental observation of longitudinal modulation of mode fields in periodically segmented waveguides. Applied Optics. 38: 5734-7. PMID 18324084  0.01
1999 Baldi P, Brunak S, Frasconi P, Soda G, Pollastri G. Exploiting the past and the future in protein secondary structure prediction. Bioinformatics (Oxford, England). 15: 937-46. PMID 10743560  1
1999 Baldi P, Brunak S, Chauvin Y, Pedersen AG. Structural basis for triplet repeat disorders: A computational analysis Bioinformatics. 15: 918-929. PMID 10743558  1
1999 Pedersen AG, Baldi P, Chauvin Y, Brunak S. The biology of eukaryotic promoter prediction - A review Computers and Chemistry. 23: 191-207. PMID 10404615 DOI: 10.1016/S0097-8485(99)00015-7  1
1998 Pedersen AG, Baldi P, Chauvin Y, Brunak S. DNA structure in human RNA polymerase II promoters Journal of Molecular Biology. 281: 663-673. PMID 9710538 DOI: 10.1006/Jmbi.1998.1972  1
1998 Baldi P, Vanier MC, Bower JM. On the use of Bayesian methods for evaluating compartmental neural models. Journal of Computational Neuroscience. 5: 285-314. PMID 9663553 DOI: 10.1023/A:1008887028637  1
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  1
1996 Baldi P, Chauvin Y. Hybrid Modeling, HMM/NN Architectures, and Protein Applications Neural Computation. 8: 1541-1565. PMID 8823946 DOI: 10.1162/Neco.1996.8.7.1541  1
1994 Baldi P, Atiya AF. How delays affect neural dynamics and learning Ieee Transactions On Neural Networks. 5: 612-621. PMID 18267834 DOI: 10.1109/72.298231  0.01
1994 Baldi P, Chauvin Y. Hidden Markov Models of the G-protein-coupled receptor family. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 1: 311-336. PMID 8790474 DOI: 10.1089/Cmb.1994.1.311  1
1994 Baldi P, Chauvin Y, Hunkapiller T, Mcclure MA. Hidden Markov models of biological primary sequence information Proceedings of the National Academy of Sciences of the United States of America. 91: 1059-1063. PMID 8302831 DOI: 10.1073/Pnas.91.3.1059  1
1991 Baldi P, Chauvin Y. Temporal Evolution of Generalization during Learning in Linear Networks. Neural Computation. 3: 589-603. PMID 31167336 DOI: 10.1162/Neco.1991.3.4.589  1
1991 Venkatesht SS, Baldi P. Programmed interactions in higher-order neural networks: The outer-product algorithm☆ Journal of Complexity. 7: 443-479. DOI: 10.1016/0885-064X(91)90030-2  0.01
1990 Baldi P, Posner EC. Graph coloring bounds for cellular radio Computers & Mathematics With Applications. 19: 91-97. DOI: 10.1016/0898-1221(90)90361-M  0.01
1988 Baldi P, Heiligenberg W. How sensory maps could enhance resolution through ordered arrangements of broadly tuned receivers. Biological Cybernetics. 59: 313-8. PMID 3196776 DOI: 10.1007/Bf00332921  1
1987 Baldi P. Symmetries and learning in neural network models. Physical Review Letters. 59: 1976-1978. PMID 10035383 DOI: 10.1103/Physrevlett.59.1976  0.01
1987 Baldi P, Venkatesh SS. Number of stable points for spin-glasses and neural networks of higher orders. Physical Review Letters. 58: 913-916. PMID 10035071 DOI: 10.1103/Physrevlett.58.913  0.04
1986 Baldi P, Baum EB. Bounds on the size of ultrametric structures. Physical Review Letters. 56: 1598-1600. PMID 10032718 DOI: 10.1103/Physrevlett.56.1598  0.01
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