Publications

Find the most up to date publications on PubMed and Google Scholar.

(* Joint first author)

  • Sisu C*, Muir P*, Frankish A, Fiddes I, Diekhans M, Thybert D, Odom D, Flicek P, Keane T, Hubbard T, Harrow J, Gerstein M. 'Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history.' In Revision 2019 [BioRxiv]
  • Federico C, Owoka T, Ragusa D, Sturiale V, Caponnetto D, Leotta CG, Bruno F, Foster HA, Rigamonti S, Giudici G, Cazzaniga G, Bridger JM, Sisu C, Saccone S, Tosi S. 'Deletions of Chromosome 7q Affect Nuclear Organization and HLXB9Gene Expression in Hematological Disorders.' Cancers 2019,11 (4), 585 [Pubmed]
  • Chudasama D, Katopodis P, Stone N, Haskell J, Sheridan H, Gardner B, Urnovitz H, Schuetz E, Beck J, Hall M, Barr J, Sisu C, Rice A, Polychronis A, Anikin V, Karteris E. 'Liquid Biopsies in Lung Cancer: Four Emerging Technologies and Potential Clinical Applications.' Cancers 2019, 11 (3), 331 [Pubmed]
  • Rogers-Broadway KR, Kumar J, Sisu C, Wander G, Mazey E, Jeyaneethi J, Pados G, Tsolakidis D, Klonos E, Grunt T, Hall M, Chatterjee J, Karteris E 'Differential expression of mTOR components in endometriosis and ovarian cancer: Effects of rapalogues and dual kinase inhibitors on mTORC1 and mTORC2 stoichiometry.' International journal of molecular medicine 2019, 43 (1), 47-56. [Pubmed]
  • Jungreis I, Tress ML, Mudge J, Sisu C, Hunt T, Johnson R, Uszczynska-Ratajczak B, Lagarde J, Wright J, Muir P, Gerstein M, Guigo R, Kellis M, Frankish A, Flicek P, Gencode Consortium, 'Nearly all new protein-coding predictions in the CHESS database are not protein-coding', BioRxiv 2018 [BioRxiv]
  • Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P.'GENCODE reference annotation for the human and mouse genomes.' Nucleic Acids Res. 2019, 47 (D1), D766-D773. [Pubmed]
  • Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. 'Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.' Nat Genet. 2018, 50(11), 1574-1583. [Pubmed]
  • Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P. 'Repeat associated mechanisms of genome evolution and function revealed by the Mus caroliand Mus pahari genomes.' Genome Res. 2018, 28(4), 448-459. [Pubmed]
  • 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. 'A global reference for human genetic variation.' Nature. 2015, 526(7571), 68-74. [Pubmed]
  • Wang D, Yan KK, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein MB. Loregic: a method to characterize the cooperative logic of regulatory factors.' PLoS Comput Biol. 2015 11(4), e1004132. [Pubmed]
  • 1000 Genomes Project Consortium, Delaneau O, Marchini J. 'Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.' Nat Commun. 2014, 5, 3934 [Pubmed]
  • Gerstein MB*, Rozowsky J*, Yan KK*, Wang D*, Cheng C*, Brown JB*, Davis CA*, Hillier L*, Sisu C*, Li JJ*, Pei B*, Harmanci AO*, Duff MO*, Djebali S*, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. 'Comparative analysis of the transcriptome across distant species.' Nature 2014, 512(7515), 445-448. [Pubmed]
  • Sisu C*, Pei B*, Leng J*, Frankish A*, Zhang Y*, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J, Gerstein MB. 'Comparative analysis of pseudogenes across three phyla'. Proc Natl Acad Sci U S A 2014 111(37), 13361-13366. [Pubmed]
  • Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. 'Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.' Genome Biol. 2014, 15(6), R88. [Pubmed]
  • Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. 'Integrative annotation of variants from 1092 humans: application to cancer genomics.' Science. 2013, 342(6154), 1235587. [Pubmed]
  • 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. 'An integrated map of genetic variation from 1,092 human genomes.' Nature 2012 491(7422), 56-65. [Pubmed]
  • ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 489(7414), 57-74. [Pubmed]
  • Pei B*, Sisu C*, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. The GENCODE pseudogene resource. Genome Biol. 2012, 13(9), R51. [Pubmed]
  • Sisu C, Baron AJ, Branderhorst HM, Connell SD, Weijers CA, de Vries R, Hayes ED, Pukin AV, Gilbert M, Pieters RJ, Zuilhof H, Visser GM, Turnbull WB. The influence of ligand valency on aggregation mechanisms for inhibiting bacterial toxins. Chembiochem 2009, 10(2), 329-337. [Pubmed]
  • Albrecht B, Grant GH, Sisu C, Richards WG. Classification of proteins based on similarity of two-dimensional protein maps. Biophys Chem. 2008, 138(1-2), 11-22. [Pubmed]
  • Pukin AV, Branderhorst HM, Sisu C, Weijers CA, Gilbert M, Liskamp RM, Visser GM, Zuilhof H, Pieters RJ. Strong inhibition of cholera toxin by multivalent GM1 derivatives. Chembiochem 2007, 8(13), 1500-1503 [Pubmed]