Publications

 

A full list of publications with PDFs will be available soon.  Publications that aim to be transformative and/or created significant impact in citations are marked in bold.

 

PUBMED PUBLICATIONS

 

Google Scholar Publications

 

Recent publications –  from group members or graduate students working directly with collaborating researchers or co-advisors (it is common in mathematical or computational sciences to enable group members to conduct related but independent investigations with other colleagues).

Brian Haas

  • Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A.
    Genome Biol. 2019 Oct 21;20(1):213. doi: 10.1186/s13059-019-1842-9.
    PMID: 31639029 (thesis chapter I)

 

 

Jonathan Dreyfuss (BME Research Scientist, selected publications funded in part by the Diabetes Center, Regional Systems Biology Core Grant)

  • TGF-β2 is an exercise-induced adipokine that regulates glucose and fatty acid metabolism.Takahashi H, Alves CRR, Stanford KI, Middelbeek RJW, Pasquale Nigro, Ryan RE, Xue R, Sakaguchi M, Lynes MD, So K, Mul JD, Lee MY, Balan E, Pan H, Dreyfuss JM, Hirshman MF, Azhar M, Hannukainen JC, Nuutila P, Kalliokoski KK, Nielsen S, Pedersen BK, Kahn CR, Tseng YH, Goodyear LJ.Nature Metab. 2019 Feb;1(2):291-303. doi: 10.1038/s42255-018-0030-7. Epub 2019 Feb 11. PMID: 31032475
  • Characterization of Glycolytic Enzymes and Pyruvate Kinase M2 in Type 1 and 2 Diabetic Nephropathy. Gordin D, Shah H, Shinjo T, St-Louis R, Qi W, Park K, Paniagua SM, Pober DM, Wu IH, Bahnam V, Brissett MJ, Tinsley LJ, Dreyfuss JM, Pan H, Dong Y, Niewczas MA, Amenta P, Sadowski T, Kannt A, Keenan HA, King GL. Diabetes Care. 2019 Jul;42(7):1263-1273. doi: 10.2337/dc18-2585. Epub 2019 May 10.PMID: 3107641
  • Plasma FGF-19 Levels are Increased in Patients with Post-Bariatric Hypoglycemia. Mulla CM, Goldfine AB, Dreyfuss JM, Houten S, Pan H, Pober DM, Wewer Albrechtsen NJ, Svane MS, Schmidt JB, Holst JJ, Craig CM, McLaughlin TL, Patti ME. Obes Surg. 2019 Jul;29(7):2092-2099. doi: 10.1007/s11695-019-03845-0. PMID: 30976983
  • SGLT2 inhibition reprograms systemic metabolism via FGF21-dependent and -independent mechanisms. Osataphan S, Macchi C, Singhal G, Chimene-Weiss J, Sales V, Kozuka C, Dreyfuss JM, Pan H, Tangcharoenpaisan Y, Morningstar J, Gerszten R, Patti ME. JCI Insight. 2019 Mar 7;4(5). pii: 123130. doi: 10.1172/jci.insight.123130. eCollection 2019 Mar 7. PMID: 30843877
  • FoxO Transcription Factors Are Critical Regulators of Diabetes-Related Muscle Atrophy. O’Neill BT, Bhardwaj G, Penniman CM, Krumpoch MT, Suarez Beltran PA, Klaus K, Poro K, Li M, Pan H, Dreyfuss JM, Nair KS, Kahn CR. Diabetes. 2019 Mar;68(3):556-570. doi: 10.2337/db18-0416. Epub 2018 Dec 6. PMID: 30523026
  • Developmental and functional heterogeneity of white adipocytes within a single fat depot. Lee KY, Luong Q, Sharma R, Dreyfuss JM, Ussar S, Kahn CR. EMBO J. 2019 Feb 1;38(3). pii: e99291. doi: 10.15252/embj.201899291. Epub 2018 Dec 10. PMID: 30530479
  • The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response. Lavoie S, Conway KL, Lassen KG, Jijon HB, Pan H, Chun E, Michaud M, Lang JK, Gallini Comeau CA, Dreyfuss JM, Glickman JN, Vlamakis H, Ananthakrishnan A, Kostic A, Garrett WS, Xavier RJ. Elife. 2019 Jan 22;8. pii: e39982. doi: 10.7554/eLife.39982. PMID: 30666959
  • Metabolic Effects of Betaine: A Randomized Clinical Trial of Betaine Supplementation in Prediabetes. Grizales AM, Patti ME, Lin AP, Beckman JA, Sahni VA, Cloutier E, Fowler KM, Dreyfuss JM, Pan H, Kozuka C, Lee A, Basu R, Pober DM, Gerszten RE, Goldfine AB. J Clin Endocrinol Metab. 2018 Aug 1;103(8):3038-3049. doi: 10.1210/jc.2018-00507. PMID: 29860335
  • Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites. Fujisaka S, Avila-Pacheco J, Soto M, Kostic A, Dreyfuss JM, Pan H, Ussar S, Altindis E, Li N, Bry L, Clish CB, Kahn CR. Cell Rep. 2018 Mar 13;22(11):3072-3086. doi: 10.1016/j.celrep.2018.02.060.PMID: 29539432
  • Corrigendum: Adipose-derived circulating miRNAs regulate gene expression in other tissues. Thomou T, Mori MA, Dreyfuss JM, Konishi M, Sakaguchi M, Wolfrum C, Rao TN, Winnay JN, Garcia-Martin R, Grinspoon SK, Gorden P, Kahn CR. Nature. 2017 May 10;545(7653):252. doi: 10.1038/nature22319. No abstract available. PMID: 28492253
  • β Cell Aging Markers Have Heterogeneous Distribution and Are Induced by Insulin Resistance. Aguayo-Mazzucato C, van Haaren M, Mruk M, Lee TB Jr, Crawford C, Hollister-Lock J, Sullivan BA, Johnson JW, Ebrahimi A, Dreyfuss JM, Van Deursen J, Weir GC, Bonner-Weir S. Cell Metab. 2017 Apr 4;25(4):898-910.e5. doi: 10.1016/j.cmet.2017.03.015. PMID: 28380379
  • Domain-dependent effects of insulin and IGF-1 receptors on signalling and gene expression. Cai W, Sakaguchi M, Kleinridders A, Gonzalez-Del Pino G, Dreyfuss JM, O’Neill BT, Ramirez AK, Pan H, Winnay JN, Boucher J, Eck MJ, Kahn CR. Nature Commun. 2017 Mar 27;8:14892. doi: 10.1038/ncomms14892. PMID: 28345670
  • Evidence of stress in β cells obtained with laser capture microdissection from pancreases of brain dead donors. Ebrahimi A, Jung MH, Dreyfuss JM, Pan H, Sgroi D, Bonner-Weir S, Weir GC. Islets. 2017 Mar 4;9(2):19-29. doi: 10.1080/19382014.2017.1283083. PMID: 28252345
  • Adipose-derived circulating miRNAs regulate gene expression in other tissues.
    Thomou T, Mori MA, Dreyfuss JM, Konishi M, Sakaguchi M, Wolfrum C, Rao TN, Winnay JN, Garcia-Martin R, Grinspoon SK, Gorden P, Kahn CR. Nature. 2017 Feb 23;542(7642):450-455. doi: 10.1038/nature21365. Epub 2017 Feb 15. PMID: 28199304
  • Age-associated NF-κB signaling in myofibers alters the satellite cell niche and re-strains muscle stem cell function. Oh J, Sinha I, Tan KY, Rosner B, Dreyfuss JM, Gjata O, Tran P, Shoelson SE, Wagers AJ. Aging (Albany NY). 2016 Nov 14;8(11):2871-2896. doi: 10.18632/aging.101098. PMID: 27852976
  • Antibiotic effects on gut microbiota and metabolism are host dependent. Fujisaka S, Ussar S, Clish C, Devkota S, Dreyfuss JM, Sakaguchi M, Soto M, Konishi M, Softic S, Altindis E, Li N, Gerber G, Bry L, Kahn CR. J Clin Invest. 2016 Oct 24. pii: 86674. doi: 10.1172/JCI86674. PMID: 27775551
  • Defects in muscle branched-chain amino acid oxidation contribute to impaired lipid metabolism. Lerin C, Goldfine AB, Boes T, Liu M, Kasif S, Dreyfuss JM, De Sousa-Coelho AL, Daher G, Manoli I, Sysol JR, Isganaitis E, Jessen N, Goodyear LJ, Beebe K, Gall W, Venditti CP, Patti ME. Mol Metab. 2016 Aug 6;5(10):926-36. doi: 10.1016/j.molmet.2016.08.001. PMID: 27689005
  • Dietary Betaine Supplementation Increases Fgf21 Levels to Improve Glucose Homeostasis and Reduce Hepatic Lipid Accumulation in Mice. Ejaz A, Martinez-Guino L, Goldfine AB, Ribas-Aulinas F, De Nigris V, Ribó S, Gonzalez-Franquesa A, Garcia-Roves PM, Li E, Dreyfuss JM, Gall W, Kim JK, Bottiglieri T, Villarroya F, Gerszten RE, Patti ME, Lerin C. Diabetes. 2016 Apr;65(4):902-12. doi: 10.2337/db15-1094.
  • Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence. Steinbaugh MJ, Narasimhan SD, Robida-Stubbs S, Moronetti Mazzeo LE, Dreyfuss JM, Hourihan JM, Raghavan P, Operaña TN, Esmaillie R, Blackwell TK. Elife. 2015 Aug 24;4. doi: 10.7554/eLife.07836. PMID: 26196144
  • Clonal analyses and gene profiling identify genetic biomarkers of the thermogenic potential of human brown and white preadipocytes. Xue R, Lynes MD, Dreyfuss JM, Shamsi F, Schulz TJ, Zhang H, Huang TL, Townsend KL, Li Y, Takahashi H, Weiner LS, White AP, Lynes MS, Rubin LL, Goodyear LJ, Cypess AM, Tseng YH. Nature Med. 2015 Jul;21(7):760-8. doi: 10.1038/nm.3881. Epub 2015 Jun 15. PMID:26076036
  • Associations of cord blood metabolites with early childhood obesity risk.Isganaitis E, Rifas-Shiman SL, Oken E, Dreyfuss JM, Gall W, Gillman MW, Patti ME. Int J Obes (Lond). 2015 Mar 25. doi: 10.1038/ijo.2015.39. PMID: 25804930

Michael Molla (BME Research Scientist, selected publications)

  • Genetic insulin resistance is a potent regulator of gene expression and proliferation in human iPS cells. Iovino S, Burkart AM, Kriauciunas K, Warren L, Hughes KJ, Molla M, Lee YK, Patti ME, Kahn CR. Diabetes. 2014 Dec;63(12):4130-42. doi: 10.2337/db14-0109. Epub 2014 Jul 24. PMID: 25059784
  • Anatomical localization, gene expression profiling and functional characterization of adult human neck brown fat. Cypess AM, White AP, Vernochet C, Schulz TJ, Xue R, Sass CA, Huang TL, Roberts-Toler C, Weiner LS, Sze C, Chacko AT, Deschamps LN, Herder LM, Truchan N, Glasgow AL, Holman AR, Gavrila A, Hasselgren PO, Mori MA, Molla M, Tseng YH. Nat Med. 2013 May;19(5):635-9. doi: 10.1038/nm.3112. Epub 2013 Apr 21. PMID: 23603815
  • An unbiased assessment of the role of imprinted genes in an intergenerational model of developmental programming. Radford EJ, Isganaitis E, Jimenez-Chillaron J, Schroeder J, Molla M, Andrews S, Didier N, Charalambous M, McEwen K, Marazzi G, Sassoon D, Patti ME, Ferguson-Smith AC. PLoS Genet. 2012;8(4):e1002605. doi: 10.1371/journal.pgen.1002605. Epub 2012 Apr 12. PMID: 22511876

Clark Freifeld  (joint PhD student with John Brownstein, selected publications during PhD)

 

Esther Rheinbay,  (jointly co-mentored PhD student with  Brad Bernstein, selected publications)

  • H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Ku M, Jaffe JD, Koche RP, Rheinbay E, Endoh M, Koseki H, Carr SA, Bernstein BE. Genome Biol. 2012 Oct 3;13(10):R85. doi: 10.1186/gb-2012-13-10-r85. PMID: 23034477
  • Imp2 controls oxidative phosphorylation and is crucial for preserving glioblastoma cancer stem cells. Janiszewska M, Suvà ML, Riggi N, Houtkooper RH, Auwerx J, Clément-Schatlo V, Radovanovic I, Rheinbay E, Provero P, Stamenkovic I. Genes Dev. 2012 Sep 1;26(17):1926-44. doi: 10.1101/gad.188292.112. Epub 2012 Aug 16. PMID: 22899010
  • A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma.
  • Rheinbay E, Louis DN, Bernstein BE, Suvà ML. Cancer Cell. 2012 Mar 20;21(3):329-31. doi: 10.1016/j.ccr.2012.03.001. PMID: 22439930
  • Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Aiden AP, Rivera MN, Rheinbay E, Ku M, Coffman EJ, Truong TT, Vargas SO, Lander ES, Haber DA, Bernstein BE. Cell Stem Cell. 2010 Jun 4;6(6):591-602. doi: 10.1016/j.stem.2010.03.016. PMID: 20569696

Richard Park (joint PhD Student with Peter Park)

  • Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ. Genome Res. 2013 Feb;23(2):217-27. doi: 10.1101/gr.140301.112. Epub 2012 Nov 6. PMID: 23132910
  • Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Nature. 2011 Mar 24;471(7339):480-5. doi: 10.1038/nature09725. Epub 2010 Dec 22. PMID: 21179089

Publications

 

  1. High-throughput mediation analysis (Hitman) of human proteome and metabolome identifies mediators of post-surgical diabetes controlJonathan M Dreyfuss1,2,3*, Yixing Yuchi3,4,5*, Xuehong Dong3,4, 6, Vissarion Efthymiou3,4, Hui Pan1,2, Donald C. Simonson3,7, AshleyVernon3,8, Florencia Halperin3,7, Pratik Aryal3, 9, Anish Konkar10, 11, Yinong Sebastian10, Brandon W Higgs10, 12, Joseph Grimsby10, 13, Cristina M. Rondinone10, 14, Simon Kasif2, Barbara B. Kahn3,9, Kathleen Foster4, Randy Seeley15, Allison Goldfine3,4,7,16, Vera Djordjilović17, Mary-Elizabeth Patti3,4**mediators of improved glycemia after gastric bypass surgery Jonathan M Dreyfuss, Yixing Yuchi, Hui Pan, Xuehong Dong, Donald C. Simonson, Ashley Vernon, Pratik Aryal, Anish Konkar, Yinong Sebastian, Brandon W Higgs, Joseph Grimsby, Cristina M. Rondinone, Simon Kasif , Barbara B. Kahn, Kathleen Foster, Allison Goldfine, Mary-Elizabeth Patti (to appear).
  2. Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector
    View ORCID ProfileBrian J. Haas, Alexander Dobin, Mahmoud Ghandi, Anne Van Arsdale, Timothy Tickle, James T. Robinson, Riaz Gillani, Simon Kasif, Aviv Regev (submitted)
  3. We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data, Simon Kasif ,Richard J. Roberts, PLoS Biology, 2020.
  4. Artificial Tikkun Olam: AI Can Be Our Best Friend in Building an Open Human-Computer Society, Kasif, S.arXiv:2010.12015, 2020
  5. Analysis of brain region-specific co-expression networks reveals clustering of established and novel genes associated with Alzheimer disease. Lancour D, Dupuis J, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GC, Crovella M, Farrer LA, Kasif S. Alzheimers Res Ther. 2020 Sep 2;12(1):103. doi: 10.1186/s13195-020-00674-7.
  6. Identifying Human Interactors of SARS-CoV-2 Proteins and Drug Targets for COVID-19 using Network-Based Label Propagation, Jeffrey Law et al, aRxiv, 2020
  7. Rate Estimation and Identification of COVID-19 Infections: Towards Rational Policy Making During Early and Late Stages of Epidemics, Richard Beigel, Simon Kasif, medRxiv 2020
  8. Single-cell transcriptional networks in differentiating preadipocytes suggest drivers associated with tissue heterogeneity.Ramirez AK, Dankel SN, Rastegarpanah B, Cai W, Xue R, Crovella M, Tseng YH, Kahn CR, Kasif S.Nature Commun. 2020 Apr 30;11(1):2117. doi: 10.1038/s41467-020-16019-9.PMID: 32355218
  9. In the Land of Risks: Nature vs Man Made Threats, S. Kasif, in review.
  10. Evolution of Knowledge Networks: Towards Reproducibility, Provenance and Causal Paths in Biology and Medicine, Kasif S. Roberts, RJ., to appear.
  11. Novel mediation analysis of human plasma proteome and metabolome reveals mediators of improved glycemia after gastric bypass surgery Jonathan Dreyfuss, Yixing Yang, Hui Pan, Xuehong Dong, Donald C Simonson, Ashley Vernon, Pratik Aryal, Anish Konkar, Yinong Sebastian, Brandon W Higgs, Joseph Grimsby, Christina M Rondinone, Simon Kasif, Barbara B Kahn, Kathleen Foster, Allison Goldfine, Mary Elizabeth Patti,BioRxiv, 817494, 2019
  12. Membrane Metallo-Endopeptidase (Neprilysin) Regulates Inflammatory Response and Insulin Signaling in White Preadipocytes Ramirez AK, Dankel S, Cai W, Sakaguchi M, Kasif S, Kahn CR. Mol Metab. 2019 Apr;22:21-36. doi: 10.1016/j.molmet.2019.01.006. Epub 2019 Jan 25. PMID: 30795914
  13. One for all and all for One: Improving replication of genetic studies through network diffusion. Lancour D, Naj A, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GD, Crovella M, Farrer LA, Kasif S. PLoS Genet. 2018 Apr 23;14(4):e1007306. doi: 10.1371/journal.pgen.1007306. eCollection 2018 Apr. PMID: 29684019
  14. Integrative Analysis of Human Plasma Proteome/Metabolome Reveals Central Role for Phospholipid, Retinol, and Histidine Metabolism after Gastric Bypass, Jonathan Dreyfuss, Yixing Yuchi, Hui Pan, Donald C Simonson, Ashley H Vernon, Pratik Aryal, Barbara Kahn, Kathleen Foster, Simon Kasif, Allison Goldfine, Mary E Patti,  Diabetes, Volume 67, Supplement 1,2018/7/1
  15. Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes. Ramirez AK, Lynes MD, Shamsi F, Xue R, Tseng YH, Kahn CR, Kasif S, Dreyfuss JM. Cell Rep. 2017 Dec 12;21(11):3040-3048. doi: 10.1016/j.celrep.2017.11.065. PMID: 29241534 (Best Graduate Student Paper award to Alfred Ramirez). One of the very few papers providing experimental validation of flux modeling in human cells. 
  16. Unexpected Properties of Short Genomic Tandem Repeats I Glotova, M Molla, AL Delcher, S Kasif bioRxiv, 165308
  17. Not All Experimental Questions Are Created Equal: Accelerating Biological Data to Knowledge Transformation (BD2K) via Science Informatics, Active Learning and Artificial Intelligence, Kasif,S, Letovsky S, Roberts, RJ,  Steffen,M,  bioRxiv, 2017 (**Can computers help biologists come up with high impact biology questions**)
  18. Unexpected Properties of Short Genomic Tandem Repeats. ,Glotova, I, Molla, M, Delcher, AL, Kasif, S,  bioRxiv, 165308, (2017)
  19. Defects in muscle branched-chain amino acid oxidation contribute to impaired lipid metabolism. Lerin C, Goldfine AB, Boes T, Liu M, Kasif S, Dreyfuss JM, De Sousa-Coelho AL, Daher G, Manoli I, Sysol JR, Isganaitis E, Jessen N, Goodyear LJ, Beebe K, Gall W, Venditti CP, Patti ME. Mol Metab. 2016 Aug 6;5(10):926-36. doi: 10.1016/j.molmet.2016.08.001. eCollection 2016 Oct. PMID: 27689005
  20. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. Chang YC, Hu Z, Rachlin J, Anton BP, Kasif S, Roberts RJ, Steffen M.Nucleic Acids Res. 2015 Dec 3. pii: gkv1324. [Epub ahead of print] PMID: 26635392. (**first database that allows searching of knowledge gaps – SEARCHING THE SPACE THAT WE DON’T KNOW **)
  21. Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes. Nogiec C, Burkart A, Dreyfuss JM, Lerin C, Kasif S, Patti ME. Mol Metab. 2015 Jan 2;4(3):151-63. doi: 10.1016/j.molmet.2014.12.012. eCollection 2015 Mar. PMID: 25737951 (COVER). (** first FBA modeling modeling of insulin resistance with experimental validations **) 
  22. Identification of rare germline copy number variations over-represented in five human cancer types. Park RW, Kim TM, Kasif S, Park PJ. Mol Cancer. 2015 Feb 3;14(1):25. [Epub ahead of print] PMID: 25644941
  23. Objective: Biochemical Function. Anton BP, Kasif S, Roberts RJ, Steffen M. Nature Frontiers in Genetics, 2014
  24. Hypermutable DNA chronicles the evolution of human colon cancer. Naxerova K, Brachtel E, Salk JJ, Seese AM, Power K, Abbasi B, Snuderl M, Chiang, S, Kasif S, Jain RK. Proc Natl Acad Sci U S A. 2014 PMID: 24753616
  25. Reconstructing and reprogramming the developmental hierarchy of glioblastoma, Mario L. Suvà*, Esther Rheinbay* et al, Cell, 2014. (** reprogramming cancer stem cells along the malignancy axis based on clues provided by epigenomic signatures and analysis **)
  26. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE. Cell Reports. 2013 May 30;3(5):1567-79.  2013.04.021. Epub 2013 May 23. PMID: 23707066
  27. The COMBREX project: design, methodology, and initial results. Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova  IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O’Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg, SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S. PLoS Biology. 2013 Aug;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. PMID: 24013487 (** the first COMBREX CONSORTIUM paper catalyzing experimental gene function prediction **)

  28. Systems biology characterization of engineered tissues. Rajagopalan P, Kasif S, Murali TM. Annu Rev Biomed Eng. 2013;15:55-70. doi: 10.1146/annurev-bioeng-071811-150120. PMID: 23862675
  29. To supplement or not to supplement: a metabolic network framework for human nutritional supplements. Nogiec CD, Kasif S. PLoS One. 2013;8(8):e68751. doi: 10.1371/journal.pone.0068751. PMID: 23967053 (**a first of a kind attempt to study nutritional supplements using in-silico modeling **)

  30. Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. Choi HP, Juarez S, Ciordia S, Fernandez M, Bargiela R, Albar JP, Mazumdar V, Anton BP, Kasif S, Ferrer M, Steffen M. PLoS One. 2013 Jun 18;8(6):e66605. Print 2013. PMID: 23825549
  31. Deep sequencing of the oral microbiome reveals s signatures of periodontal disease, Bo Liu1,2*, Lina Faller3*, Niels Klitgord3*, Varun Mazumdar3*, Mohammad Ghodsi1,2,Daniel D. Sommer1, Theodore R. Gibbons1,4, Todd J. Treangen1,10, Yi-Chien Chang3,Shan Li5, O. Colin Stine5, Hatice Hasturk8, Simon Kasif3,7,9, Daniel Segrè3,6,7#,  Mihai Pop1,2,4#, Salomon Amar3,8#,, PLOS One, 2012
  32. Network Signatures of Insulin Resistance and Life Span, M. Liu, M. Mori, IS. Kohane, ME Patti, A. Goldfine, CR Kahn, S. Kasif, in preparation.
  33.  Thousands of new genes with strong computational support found in bacterial genomes, Derrick E. Wood, Henry Lin, Ami Levy-Moonshine, Rajiswari Swaminathan, Yi-Chien Chang, Brian P. Anton, Lais Osmani4, Martin Steffen, Simon Kasif, and Steven L. Salzberg, Biology Direct, 2012.
  34. Bridging Computation and Experiments: Using Computers to Drive Biology, (in revision), Science.
  35. Towards a Personal Repeatome: A Genome-Wide Survey of Length Variation in Short Tandem Repeats in Human Gene Transcripts, in preparation.
  36. A Critical Assessment of Genomic and Clinical Breast Cancer Biomarkers. Chang-Jiun Wu, Tianxi Cai, Zoltan Szallasi, Kamila Naxerova, Martin Steffen, L.J. Wei, Isaac S. Kohane*, Simon Kasif*, co-corresponding authors, in revision.
  37. Integrative Pheno-genomic module discovery with application to breast cancer, Chang-Jiun Wu, Tianxi Cai, Isaac S. Kohane*, Simon Kasif*, in revision.
  38. A Systems Biology Approach Links Inflammation to the Predisposition to Metabolic Diseases in Mouse Strains, Marcelo Mori*, Manway Liu*, Simon Kasif, Ron Kahn, Diabetes 2010.

  39. Transcriptome Analysis Reveals Parallel Dysregulation of Oxidative Metabolism and Inflammation in Muscle and Adipose Tissue With Progression of Insulin Resistance in Humans, Mary-Elizabeth Patti, Manway Liu, Wanzhu Jin, Carles Lerin, Jonathan Dreyfuss, Martha Vokes, Joshua Schroeder, Elizabeth Tatro, Peter Park, Isaac Kohane, Igor Leykin, Simon Kasif, and Allison Goldfine, in preparation.

  40. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG,   Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segr D, Salzberg , SL, Delisi C, Steffen M, Kasif S. Nucleic Acids Res. 2010 Nov 21. PMID: 21097892
  41. Functional Characterization of the YmcB and YqeV tRNA Methylthiotransferases of\ Bacillus subtilis Brian P. Anton, Susan Russell, Patrick A. Limbach, Simon Kasif,  Elisabeth A. Raleigh, and Richard J. Roberts, Nucleic Acid Research 2010.
  42. Drug Response Phosphorylation Signatures of Lung Cancer, Chang-Jiun Wu, Martin Steffen, Simon Kasif in preparation.
  43. The Evolution of Gene Annotation, Simon Kasif and Martin Steffen, Nature Chemical Biology, Jan 2010.
  44. A Predictive phosphorylation signature of lung cancer. Chang-Jiun Wu, Tianxi Cai, Klarisa Rikova, David Merberg, Simon Kasif,* Martin Steffen*, co-corresponding authors,  PLoS ONE, Nov 2009. (** phosphorylation signatures are as predictive as gene expression signatures for cancer classification – not surprising but overlooked **)

  45. Triplet repeat length bias and variation in the human transcriptome,  Molla M*, Delcher A*, Cantor CR, Kasif S, Proc. of National Academy of Sciences, Oct. 2009, PMID: 19805156 (** a surprising pattern is detected in long studied triplet repeats that contribute to multiple human diseases **)

  46. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS. Bioinformatics. 2009 Dec 1;25(23):3121-7. Epub 2009 Sep 28.PMID: 19786482
  47. Seeing the Forest for the Trees: Using the Gene Ontology to Restructure Hierarchical clustering.  Dotan-Cohen D, Kasif S, Melkman AA, Kasif S, Bioinformatics, 2009
  48. Biological process linkage networks. Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S. PLoS ONE. 2009;4(4):e5313. Epub 2009 Apr 23. PMID 19390589 (** the paper suggests complex patterns of interconnection in biological systems and points to  new directions in biological research focusing on cross-pathway network interactions **)

  49. Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice. Isganaitis E, Jimenez-Chillaron J, Woo M, Chow A, DeCoste J, Vokes M, Liu M, Kasif S, Zavacki AM, Leshan RL, Myers MG, Patti ME. Diabetes. 2009 May;58(5):1192-200. Epub 2009 Feb 10. PMID: 19208909
  50. Quantitative analysis of single nucleotide polymorphisms within copy number variation. Lee S, Kasif S, Weng Z, Cantor CR. PLoS ONE. 2008;3(12):e3906. Epub 2008 Dec 18. PMID: 19093001
  51. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE. PLoS Genet. 2008 Oct;4(10):e1000242. Epub 2008 Oct 31. PMID: 18974828
  52. Formula dissection: A parallel algorithm for constraint satisfaction. Reif, J. H., Kasif, S., and Sherlekar, D.  Comput. Math. Appl. 55, 6 (Mar. 2008), 1170- 1177 (republished from a 1987 conference version). (** a very early 1985 paper on recursive decomposition for model checking of logical formulae and constraint systems**)

  53. Integration of relational and hierarchical network information for protein function prediction. Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED. BMC Bioinformatics. 2008 Aug 22; 9:350. PMID: 18721473 (** Does the GO hierarchy help prediction protein function **)

  54. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS. Genome Biol. 2008;9(7):R108. Epub 2008 Jul 8. PMID: 18611264 (** the relationship of developmental and oncogenic processes is studied across cancers **)

  55. Anton BP, Saleh L, Benner JS, Raleigh EA, Kasif S, Roberts RJ.RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1826-31. Epub 2008 Feb 5. PMID: 18252828
  56. Context specific protein function prediction. Nariai N, Kasif S. Genome Inform. 2007; 18:173-82. PMID: 18546485

  57. Tullai JW, Schaffer ME, Mullenbrock S, Sholder G, Kasif S, Cooper GM. Immediate-early and delayed primary response genes are distinct in function and genomic architecture, J Biol Chem. 2007 Jun 15;
  58. Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet. 2007 Jun 15;3(6):e96. PMID: 17571924 (** one of the earliest papers on modeling disease as network anomaly specifically focusing on Diabetes **)

  59. Nariai N, Kolaczyk ED, Kasif S. Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS ONE. 2007 Mar 28;2:e337. PMID: 17396164
  60. Zhang L, Kasif S, Cantor AC. Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3061-6. Epub 2007 Feb 20. PMID: 17360609
  61. Tullai JW, Chen J, Schaffer ME, Kamenetsky E, Kasif S, Cooper GM. Glycogen synthase kinase-3 represses cyclic AMP response element-binding protein (CREB)-targeted immediate early genes in quiescent cells. J Biol Chem. 2007 Mar 30;282(13):9482-91. Epub 2007 Feb 3. PMID: 17277356
  62. Alon N, Asodi V, Cantor C, Kasif S, Rachlin J. Multi-node graphs: a framework for multiplexed biological assays. J Comput Biol. 2006 Dec;13(10):1659-72. PMID: 17238837 (** multi-node graphs are a new computer science data structure **)

  63. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles., PLoS Biol. 2007 Jan 9;5(1):e8 PMID: 17214507 (** first of a kind large scale experimental validation of computational regulatory network predictions **)

  64. Murali TM, Wu CJ, Kasif S. The art of gene function prediction. Nature Biotechnology. 2006 Dec;24(12):1474-5. PMID: 17160037
  65. Gustafson AM, Snitkin ES, Parker SC, DeLisi C, Kasif S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics. 2006 Oct 19;7:265. PMID: 17052348 (** a critique of the network degree method for predicting essentiality and multiple new better proposals **)

  66. Lee S, Kasif S. The complete genome sequence of a dog: a perspective. Bioessays. 2006 Jun;28(6):569-73. PMID: 16700068
  67. Rachlin J, Cohen DD, Cantor C, Kasif S. Biological context networks: a mosaic view of the interactome. Nature/Embo. Mol Syst Biol. 2006;2:66. Epub 2006 Nov 28. PMID: 17130868 (** first of a kind biological context networks are proposed **)

  68. Lee S, Kohane I, Kasif S. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. BMC Genomics. 2005 Nov 27;6:168. PMID: 16309559
  69. Zheng Y, Anton BP, Roberts RJ, Kasif S. Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics. 2005 Oct 3;6:243. PMID: 16202130
  70. Szustakowski JD, Kasif S, Weng Z. Less is more: towards an optimal universal description of protein folds. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii66-ii71. PMID: 16204127 (** a proposal to use minimum description language (MDL) and methods to describe the protein universe **)

  71. Rachlin J, Ding C, Cantor C, Kasif S. Computational tradeoffs in multiplex PCR assay design for SNP genotyping. BMC Genomics. 2005 Jul 25;6:102.PMID: 16042802 (** a rigorous study of multiplex PCR design pointing to theoretical phase transitions  **)

  72. Wu CJ, Kasif S.  GEMS: a web server for biclustering analysis of expression data. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W596-9. PMID: 15980544
  73. Rachlin J, Ding C, Cantor C, Kasif S.  MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W544-7. PMID: 15980531
  74. Zheng Y, Roberts RJ, Kasif S, Guan C.  Characterization of two new aminopeptidases in Escherichia coli. J Bacteriol. 2005 Jun;187(11):3671-7. PMID: 15901689
  75. Noga Alon, Richard Beigel and Simon Kasif and Steven Rudich and Benny Sudakov, “Learning a Hidden Matching“, SIAM Journal of Computing, 2004.
  76. Zheng Y, Roberts RJ, Kasif S.  Identification of genes with fast-evolving regions in microbial genomes. Nucleic Acids Res. 2004 Dec 2;32(21):6347-57. Print 2004. PMID: 15576679
  77. Zhang L, Kasif S, Cantor CR, Broude NE. GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16855-60. Epub 2004 Nov 17. PMID: 15548610
  78. Tullai JW, Schaffer ME, Mullenbrock S, Kasif S, Cooper GM. Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem. 2004 May 7;279(19):20167-77. Epub 2004 Feb 9. PMID: 14769801 (** a very early attempt to integrate multiple computational analysis for predicting regulatory networks and  first of a kind experimental validation of regulatory network predictions **)

  79. Zheng Y, Roberts RJ, Kasif S.  Segmentally variable genes: a new perspective on adaptation. PLoS Biol. 2004 Apr;2(4):E81. Epub 2004 Apr 13. PMID: 15094797

  80. Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2888-93. Epub 2004 Feb 23. PMID: 4981259

  81. Wu CJ, Fu Y, Murali TM, Kasif S.  Gene expression module discovery using Gibbs sampling. Genome Inform. 2004;15(1):239-48. PMID: 15712126
  82. Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J.  topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D520-2. PMID: 14681472
  83. Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S. RankGene: identification of diagnostic genes based on expression data. Bioinformatics. 2003 Aug 12;19(12):1578-9. PMID: 12912841 (** many methods to rank diagnostic genes **)

  84. Wu J, Kasif S, DeLisi C.  Identification of functional links between genes using phylogenetic profiles. Bioinformatics. 2003 Aug 12;19(12):1524-30. PMID: 12912833
  85. Zhang L, Pavlovic V, Cantor CR, Kasif S. Human-mouse gene identification by comparative evidence integration and evolutionary analysis. Genome Res. 2003 Jun;13(6A):1190-202. Epub 2003 May 12. PMID: 12743024
  86. Pervouchine DD, Graber JH, Kasif S. On the normalization of RNA equilibrium free energy to the length of the sequence.  Nucleic Acids Res. 2003 May 1;31(9):e49. PMID: 12711694
  87. Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J.  Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol. 2003 Apr 11;327(5):1021-30. PMID: 12662927
  88. Letovsky S, Kasif S.  Predicting protein function from protein/protein interaction data: a probabilistic approach.  Bioinformatics. 2003;19 Suppl 1:i197-204. PMID: 12855458 (** a formalization of network based protein function prediction using Markov Random Fields **)

  89. Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res. 2002 Oct 15;30(20):e106. PMID: 12384608
  90. Zheng Y, Roberts RJ, Kasif S. Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol. 2002 Oct 10;3(11):RESEARCH0060. Epub 2002 Oct 10. PMID: 12429059
  91. Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S.  Computational identification of operons in microbial genomes. Genome Res. 2002 Aug;12(8):1221-30. PMID: 12176930

  92. Walker M, Pavlovic V, Kasif S A comparative genomic method for computational identification of prokaryotic translation initiation sites. Nucleic Acids Res. 2002 Jul 15;30(14):3181-91. PMID: 12136100
  93. Pavlovic V, Garg A, Kasif S. A Bayesian framework for combining gene predictions. Bioinformatics. 2002 Jan;18(1):19-27. PMID: 11836207
  94. Lander ES et al,  Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921. (** the public human genome project ** )

  95. Cai D, Delcher A, Kao B, Kasif S. Modeling splice sites with Bayes networks. Bioinformatics. 2000 Feb;16(2):152-8. PMID: 10842737 (** Using Bayes nets to track cross sequence dependencies **)

  96. Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL.  Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics. 1999 Dec 15;62(3):500-7. PMID: 10644449
  97. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999 Dec 1;27(23):4636-41. PMID: 10556321

  98. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes. Nucleic Acids Res. 1999 Jun 1;27(11):2369-76. PMID: 10325427 (** the first open access bacterial whole genome alignment – analysis system **)

  99. Salzberg SL, Delcher AL, Kasif S, White O.  Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 1998 Jan 15;26(2):544-8. PMID: 9421513 (** a widely used bacterial gene finding system, helped popularize variable length models in sequence analysis **

  100. Bright, J., Kasif, L. Stiller, “Data Intensive Algorithms for Search Problems”, accepted for publication in IEEE Transactions on Computers.
  101. Kasif, S.,  “Datascope: Mining Biological Sequences”, special issue on Data Mining, IEEE Intelligent Systems,  pp. 38–45, 1999.
  102. Kasif, S., Salzberg, S., Waltz, D., J. Rachlin, and Aha, D., “Towards of a Framework for Memory-Based Reasoning”, Artificial Intelligence, pp. 287–311, 1998. (** a very early proposal for probabilistic kernels based on Bayes Nets **)

  103. Kasif, S., “Towards a Constraint-Based Engineering Framework for Algorithm Design and Application”, Journal of Constraints, 1997.
  104. Delcher, A, A. Grove, S. Kasif and J. Pearl, “Logarithmic Time Queries and Updates in Probabilistic Networks”, Journal of Artificial Intelligence Research, Vol. 4., pp. 37–59, 1996. (** a novel factorization of Bayes nets that supports parallel, incremental and limited memory implementations **)

  105. Waltz, D. and S. Kasif, “On Reasoning from Data”, Computing Surveys, 1996.
  106. Salzberg, S., D. Heath, A. Delcher and S. Kasif, “Best Case Analysis of Nearest Neighbours Algorithms”, IEEE Transaction on Pattern Analysis and Machine Intelligence, 17:6, pp.599–608, June 1995.
  107. Delcher, A. and S. Kasif, “Term Matching on a Mesh-Connected Array of Processors”, Annals of Mathematics and Artificial Intelligence, Volume 14, pp.177–186, 1995.
  108. Murthy, S., S. Kasif and S. Salzberg, “ System for Induction of Oblique Decision Trees”, Journal of Artificial Intelligence Research, 2:1, pp.1–33, 1994. (** a very popular decision tree system **)

  109. Heath, D., S. Kasif, S. R. Kosaraju, S. Salzberg and G. Sullivan, “Learning Nested Concept Classes with Limited Memory”, Journal of Experimental and Theoretical AI, 1996 (accepted 1992, early version AAAI 1991). (** one of the earliest data mining papers in the data streaming model **)

  110. Kasif, S., “Optimal Parallel Algorithms for Quad-Tree Problems”, Journal of Computer Vision and Image Processing, pp.281–285, May 1994.
  111. Kasif, S. and A. Delcher, “Analysis of Local Consistency in Parallel Constraint Networks”, Artificial Intelligence, 69, pp.307–327, 1994.
  112. Heath, D. and S. Kasif, “On Voronoi Covers with Applications to Machine Learning”, Computational Geometry: Theory and Applications, pp. 289-305, Nov. 1993.
  113. Kasif, S., S. Banerjee, A. Delcher and G. Sullivan, “Some Results on the Complexity of Symmetric Connectionist Networks”, Annals of Mathematics and Artificial Intelligence, pp.327-344, Nov. 1993.
  114. Delcher, A. and S. Kasif,  “Efficient Parallel Term Matching and Anti-Unification”, Journal of Automated Reasoning, pp.  391–406, 1992.
  115. Kasif, S., “On the Parallel Complexity of Discrete Relaxation in Constraint Networks”, Artificial Intelligence, pp. 275-286, October 1990. (** Waltz filtering, discrete relaxation are inherently sequential **)

  116. Delcher, A. and S. Kasif, “Some Results On the Complexity of Maintaining Data Flow Dependencies in Parallel Logic Programs”, Journal of Logic Programming, pp.229–241, April 1989.
  117. Kasif, S., “Control and Data Driven Execution of Logic Programs: A Comparison”, Journal of Parallel Programming.Vol.15, No.1, pp.73–100, February 1987.
  118. Kasif, S., L. Kitchen and A. Rosenfeld, “A Hough Transform Technique for Subgraph Isomorphism”, Pattern Recognition Letters. Vol.2, pp.83–88, December 1983. (** an early proposal for using graph walks for matching graphs – naive in retrospect given the work on graph diffusions and graph Laplacians  but follows the same intuition **)

  119. Kasif, S. and A. Rosenfeld, “Pyramid Linking as a Special Case of Isodata”, IEEE Transactions on Systems, Man and Cybernetics, Vol.SMC-13, No.1, January 1983. (** analysis of convergence  in very early unsupervised DEEP LEARNING architectures **)

 

Books, Books Chapters and Special Reports

 

  1.  S. Kasif and A. Delcher, “Analysis of Local Consistency in Parallel Constraint Networks”, Principle and Practice of Constraint Programming, published by MIT press, editors Pascal van Henteryck and V.J. Saraswat, 1994.
  2. Heath, D., S. Kasif and S. Salzberg, “Committees of Decision Trees”, Cognitive Technology, North Holland Publishers, 1995
  3. Simon Kasif and Stuart Russell (Eds.), Proceedings of the AAAI Fall Symposium on Learning Complex Behaviors, AAAI Press, 1996.

  4. J. Flannagan, T. Huang, P. Jones, and S. Kasif, “Human Centered Systems: Information, Interactivity and Intelligence”, Executive NSF Steering Committee Report, July, 1997.
  5. R. Grossman, S. Kasif, J. Ullman, et al,  “Data Mining”, Executive Committee NSF Report, 1998.
  6. Kasif, S. and A. Delcher, “Biological Data Modeling using Probabilistic Networks”, in Salzberg, S., D. Searls, and S. Kasif, “Computational Methods in Molecular Biology”, Elsevier, Publ. 1998.
  7. S. Salzberg, D. Searls and S. Kasif, eds, “Computational Methods in Molecular Biology”, Elsevier Publ. 1998. (2nd Printing, February 1999).
  8. Beth Logan, Pedro Moreno, Baris Suzek, Zhiping Weng and Simon Kasif, “A Study of Remote Homology Detection“, Cambridge Research Laboratory, Technical Report, CRL 2001/05, June 2001 (first version summer 2000). (** a very early proposal for using simple sequence kernels for protein similarity, remote homology and function prediction .. very simple but shown to beat BLAST and other more sophisticated approaches … **)

  9. Rich Roberts, Peter Karp, Simon Kasif and Stuart Linn, “An Experimental Approach to Gene Function”, Executive Report, American Academy for Microbiology.

  10. Satoru Miyano Jill Mesirov, Simon Kasif, Sorin Istrail Pavel Pevzner, Michael Waterman, Research in Computational Molecular Biology: 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings Lecture Notes in Bioinformatics.

 

 

Papers in Peer-Reviewed Conferences

Publications in very selective conferences with acceptance rates of 25% or less are marked with asterisks *. These papers are typically considered equal to a journal publication in Computer Science.

 

  1. *Eisinger, N., S. Kasif and J. Minker, “Logic Programming: A Parallel Approach”, First International Logic Programming Conf., Faculte des Sciences de Luminy Marseille, France, pp.71–77, September 1982.
  2. Kasif, S., M. Kohli and J. Minker, “PRISM—A Parallel Inference System Based on Logic”, Logic Programming Workshop, pp.123–152, Portugal, June 1983.
  3. *Kasif, S., M. Kohli and J. Minker, “Control Facilities of PRISM—A Parallel Inference System Based on Logic”, International Joint Conf. on Artificial Intelligence, August 1983.

  4.  Chakravarthy, U. S., S. Kasif, M. Kohli, J. Minker and D. Cao, “Logic Programming on ZMOB: A Highly Parallel Machine”, Proc. 1982 International Conf. on Parallel Processing, IEEE Press, pp.347—349 New York, 1982.
  5. *Kasif, S. and A. Rosenfeld, “The Fixpoints of Images and Scenes”, Conf. on Computer Vision and Pattern Recognition, pp.454-456, June 1983.
  6. *Kasif, S. and J. Minker, “The Intelligent Channel:  A Scheme for Result Sharing in Parallel Logic Programs”, International Joint Conf. on Artificial Intelligence, pp.29-31, August 1985.
  7. *Kasif, S., “On the Parallel Complexity of Some Constraint Satisfaction Problems”, National Conf. on Artificial Intelligence (AAAI-86), pp.349-353, August 1986.

  8. Kasif, S., J. Reif and D. Sherlekar, “Formula Dissection: A Parallel Algorithm for Constraint Satisfaction”, IEEE Workshop on Computer Architecture for Pattern Analysis and Machine Intelligence, pp.51-57, October 1987.

  9. Delcher, A. and S. Kasif, “On the Complexity of Incremental Parallel Computations in Artificial Intelligence”, IEEE Workshop on Computer Architecture for Pattern Analysis and Machine Intelligence, pp.59-64, October 1987.

  10. Kasif, S., “Efficient Parallel Quad-Tree Algorithms”, Proc. of 1988 ICAI, Tel Aviv, Israel, pp.353-363, December 1988.
  11. Delcher, A. and S. Kasif, “Parallel Term Matching on Mesh Connected Computers”, Proc. of 1988 ICAI, Tel Aviv, Israel, pp.~441-452, December 1988.
  12. *Kasif, S., “Parallel Solutions to Constraint Satisfaction Problems”, IEEE Conf. on Principles of Knowledge Representation and Reasoning, pp. 180-187, May 1989.
  13. *Delcher, A. and S. Kasif, “Parallel Term Matching and Anti-Unification”, International Conf. on Logic Programming, pp.355–369, June 1990.
  14. *Heath, D., S. Kasif, S. R. Kosaraju, S. Salzberg and G. Sullivan, “Learning Nested Concept Classes with Limited Storage”, Proceedings of the International Joint Conference on Artificial Intelligence(IJCAI-91), pp. 777-782, 1991.

  15. *Salzberg, S., D. Heath, A. Delcher and S. Kasif, “Learning with a Helpful Teacher”, Proceedings of the International Joint Conference on Artificial Intelligence, (IJCAI-91), pp. 705-711, 1991. (** an early proposal for optimizing the number of examples needed to TEACH a concept **)

  16. *S. Kasif and A. Delcher, “Improved Decision Making in Game Trees: Recovering from Pathology”, Proceedings of the National Conference on Artificial Intelligence (AAAI-92), pp. 513-518, July 1992. (** an early proposal for a simple kind of Deep Learning in Game Playing in AI **)

  17. D. Heath, S. Kasif and S. Salzberg, “Learning Oblique Decision Trees”, Computational Learning Theory and Natural Learning Systems, 1992.
  18. Kasif, S. and A. Delcher, “Analysis of Local Consistency in Parallel Constraint Networks”, International Conference on Artificial Intelligence and Vision, pp. 217-231, 1992.
  19. S. Kasif, “Iterative Focusing and Hashing: An Alternative to Alpha-Beta”, International Conference on Artificial Intelligence and Vision, pp. 59-72, 1992.
  20. *D. Heath, S. Kasif and S. Salzberg, “Learning Oblique Decision Trees”, Proceedings of the International Joint Conference on Artificial Intelligence, (IJCAI 93), pp. 1002–1007, August 1993.
  21. *Murthy, S., S. Kasif, S. Salzberg and R. Beigel, “OC1: A Randomized Algorithm for Building Oblique Decision Trees”, Proceedings of the National Conference on Artificial Intelligence, (AAAI-93), pp. 322–327, July 93.

  22. Heath, D., S. Kasif and S. Salzberg, “k-DT: A Multi-Tree Learning Method”, Proceedings of the Second International Workshop on Multi-strategy Learning (pp. 138–149), Harpers Ferry, West Virginia, 1993.
  23. *Delcher, A., S. Kasif, H. Goldberg and W. Xsu, “Protein Secondary-Structure Modeling with Probabilistic Networks”, International Conference on Intelligent Systems and Molecular Biology, pp. 109–117, 1993.

  24. *Delcher, A., S. Kasif, H. Goldberg and W. Xsu, “Application of Probabilistic Causal Trees to Analysis of Protein Secondary Structure”, Proceedings of the National Conference on Artificial Intelligence, pp. 316–321, July 1993.

  25. *Bright, J., Kasif, L. Stiller, “Exploiting Algebraic Structure in Parallel State-Space Search”, Proc. of the 11-th National Conf. on Artificial Intelligence, July 1994, (AAAI-94), pp. 1341-1346, preliminary version presented in the AAAI Symposium on Massively Parallel AI”, March 1993.
  26. *Rachlin, J., S. Kasif, S. Salzberg and D. Aha, “Toward of a better understanding of Memory-Based Classifiers”,  (plenary talk), Proceeding of the 11-th Intern. Conf. on Machine Learning, pp. 242–250, July 1994.
  27. *Fulton, T., S. Kasif and S. Salzberg, “Efficient Algorithms for Finding Multi-Way Splits for Decision Trees”, JHU TR, December 1993, Proceeding of the 12-th Intern. Conf. on Machine Learning, July 1995.
  28. *Delcher, A, A. Grove, S. Kasif and J. Pearl, “Logarithmic Time Queries and Updates in Probabilistic Networks”, Proceedings of the 1995 Conference on Uncertainty in AI, August 1995.

  29. D. Dobkin, D. Gunopoulous,  S. Kasif, “Induction of Low-Depth Decision Trees”, International Conference on Mathematics and Artificial Intelligence, 1996,
  30. S. Weiss, S. Kasif, and E. Brill, “Towards a Framework for Adaptive Information Retrieval”, AAAI Spring Symposium on Information Retrieval (1996).
  31. *T. Fulton, S., Kasif, S. Salzberg, and D. Waltz, “Local Induction of Decision Trees”, Proceedings of the 1996 Conference of Knowledge Discovery in Databases”, August 1996.
  32. R. Grossman, S. Bailey, S. Kasif, “Papyrous: A System for Distributed Data Mining”, Workshop on Distributed Data Mining, NYC, 1998.
  33. *Beigel, R., N. Alon, S. Apaydin, L. Fortnow, and S. Kasif, “An Optimal Multiplex PCR Protocol for Closing Gaps in Whole Genomes”, RECOMB, April 2001.
  34. * Noga Alon, Richard Beigel and Simon Kasif and Steven Rudich and Benny Sudakov, “Learning a Hidden Matching”, Foundations of Computer Science, FOCS 2002.
  35. T.M. Murali and S. Kasif, “Extracting Conserved Gene Expression Motifs from from Microarray Data”, Pacific Symposium on Biocomputing, January 2003.
  36. B. Logan, P. Moreno, B. Suzek, Z. Weng, and S. Kasif, “Remote Homology Detection Using Feature Vectors Formed Using Alignments of Small Motifs”, RECOMB 2002 (poster and patent 2000).
  37. D. Pervouchine, J. Graber, and S. Kasif, “Stable RNA Secondary Structure of Human Donor Splice Sites”, RECOMB 2002 (poster)
  38. M. Walker, V. Pavlovic, and S. Kasif, “A Comparative Genomic Method for Computational Identification of Prokaryotic Translation Initiation Sites”, RECOMB 2002 (poster)
  39. Y. Zheng, R. J. Roberts, and S. Kasif, “Computational Identification of Operons in Microbial Genomes”, RECOMB 2002 (poster).
  40. M. Walker and S. Kasif, Active Learning Strategies for Compound Screening, Presented Talk, ACS National Meeting, March 2005.
  41. Murali TM, Kasif S.  Extracting conserved gene expression motifs from gene expression data. Pac Symp Biocomput. 2003;:77-88. PMID: 12603019

  42. *S. Letovsky and S. Kasif, “A Probabilistic Approach to Gene Function Assignment and Propagation in Protein Interaction Networks”, June 2003, ISMB 2003.

  43. Nariai N, Kasif S. “Context Specific Protein Function Prediction“, Genome Informatics, pp 173–182, 2007.

 

Selected Unpublished Technical Reports and Conference Presentations

  1. SIMON KASIF, PARALLEL SEARCHING AND MERGING ON ZMOB(U) MARYLAND UNIV COLLEGE PARK CENTER FOR AUTOMATION RESEARCH SIMON KASIF JUN 1984 CAR-TR-64. 
  2. Zhang, L., Pavlovic, E. Green, G. Cantor, C.R. and S. Kasif, “Novel Human Gene Discovery using Cross-Species Analysis: Is the Mouse the Right Reference Point?”.
  3. B. Logan, P. Moreno, B, Suzek , Z. Weng and S. Kasif, “Learning Remote-Homology Using Probabilistic Feature Vectors“, Cambridge Research Lab TR 2000.

  4. Walker, M. and Kasif. S., “Comparative Analysis of lipid biosynthesis and metabolism component of the DnaA regulon”.
  5. Joseph D. Szustakowski, Ulas Karaoz, Serafim Batzouglou, James Galagan, Tarjei Mikkelsen, Zhiping Weng, Joel H. Graber, S. Kasif, On the Organization of Ancient and Modern Genes in the Human Genome.
  6. Megon Walker, Terrence Wu, Andreas Bender, Simon Kasif. Descriptor Biclustering Improves Compound Classification with Partial Least Squares, Unpublished Manuscript, April 2007.