Research
Differentiation and cancer
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1. Soares A, Rodrigues D, Cipriano E, Tavares A, Vilaca M, Silva D, Santos J, Mesquita A, Salgado M, Sottomayor C, Almeida R
Lack of expression of CDX2: Prognostic biomarker in stage IV colorectal cancer Annals of oncology : official journal of the European Society for Medical Oncology 31: S136-S136, 2020.  [Meeting Abstract] 
 
2. Raykova D, Kermpatsou D, Malmqvist T, Harrison PJ, Sander MR, Stiller C, Heldin J, Leino M, Ricardo S, Klemm A, David L, Spjuth O, Vemuri K, Dimberg A, Sundqvist A, Norlin M, Klaesson A, Kampf C, Söderberg O
A method for Boolean analysis of protein interactions at a molecular level. Nature communications 13: 4755, 2022.  [Article] 
 
3. Marcos NT, Magalhães A, Ferreira B, Oliveira MJ, Carvalho AS, Mendes N, Gilmartin T, Head SR, Figueiredo C, David L, Santos-Silva F, Reis CA
 doi: 10.1172/JCI34324 PMID: 18483624.
 
4. Nason R, Büll C, Konstantinidi A, Sun L, Ye Z, Halim A, Du W, Sørensen DM, Durbesson F, Furukawa S, Mandel U, Joshi HJ, Dworkin LA, Hansen L, David L, Iverson TM, Bensing BA, Sullam PM, Varki A, Vries E, de Haan CAM, Vincentelli R, Henrissat B, Vakhrushev SY, Clausen H, Narimatsu Y
Display of the human mucinome with defined O-glycans by gene engineered cells. Nature communications 12: 4070, 2021.  [Article] 
 
5. Pereira B, Le Borgne M, Chartier NT, Billaud M, Almeida R
MEX-3 proteins: recent insights on novel post-transcriptional regulators. Trends in biochemical sciences 38: 477-9, 2013.  [Editorial Material] 
 
6. Pinto R, Hansen L, Hintze J, Almeida R, Larsen S, Coskun M, Davidsen J, Mitchelmore C, David L, Troelsen JT, Bennett EP
 doi: 10.1093/nar/gkx371 PMID: 28472465.
 
7. Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H
 
8. Amaro HM, Barros R, Guedes AC, Sousa-Pinto I, Malcata FX
Microalgal compounds modulate carcinogenesis in the gastrointestinal tract. Trends in Biotechnology 31: 92-8, 2013.  [Review] 
 
9. Pereira B, Sousa S, Barros R, Carreto L, Oliveira P, Oliveira C, Chartier NT, Plateroti M, Rouault JP, Freund JN, Billaud M, Almeida R
 doi: 10.1093/nar/gkt087 PMID: 23408853.
 
10. Pereira B, Amaral AL, Dias A, Mendes N, Muncan V, Silva AR, Thibert C, Radu AG, David L, Máximo V, van den Brink GR, Billaud M, Almeida R
 
11. Ribeiro AS, Sousa B, Carreto L, Mendes N, Nobre AR, Ricardo S, Albergaria A, Cameselle-Teijeiro JF, Gerhard R, Söderberg O, Seruca R, Santos MA, Schmitt F, Paredes J
 doi: 10.1002/path.4143 PMID: 23180380.
 
12. Lopes N, Bergsland C, Bruun J, Bjørnslett M, Vieira AF, Mesquita P, Pinto R, Gomes R, Cavadas B, Bennett E, Pereira L, Lothe RA, Almeida R, David L
A panel of intestinal differentiation markers (CDX2, GPA33, and LI-cadherin) identifies gastric cancer patients with favourable prognosis. Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association 23: 811-823, 2020.  [Article] 
 
13. Huang YL, Liang CY, Ritz D, Coelho R, Septiadi D, Estermann M, Cumin C, Rimmer N, Schötzau A, Núñez López M, Fedier A, Konantz M, Vlajnic T, Calabrese D, Lengerke C, David L, Rothen-Rutishauser B, Jacob F, Heinzelmann-Schwarz V
 doi: 10.7554/eLife.59442 PMID: 33026975.
 
14. Ricardo S, Canão P, Martins D, Magalhães AC, Pereira M, Ribeiro-Junior U, de Mello ES, Alves VA, Pinto R, Leitão D, Alves G, Oliveira R, Wilton J, Costelha S, Meireles D, Cabanes D, David L, Schmitt F
 
15. Nunes M, Duarte D, Vale N, Ricardo S
 
16. Silva ML, Gutiérrez E, Rodríguez JA, Gomes C, David L
Construction and validation of a Sambucus nigra biosensor for cancer-associated STn antigen. Biosensors & bioelectronics 57: 254-61, 2014.  [Article] 
 
17. Nunes M, Silva PMA, Coelho R, Pinto C, Resende A, Bousbaa H, Almeida GM, Ricardo S
 
18. Almeida-Nunes DL, Mendes-Frias A, Silvestre R, Dinis-Oliveira RJ, Ricardo S
Immune Tumor Microenvironment in Ovarian Cancer Ascites. International journal of molecular sciences 23: ., 2022.  [Review] 
 
19. Nunes M, Pacheco F, Coelho R, Leitão D, Ricardo S, David L
 
20. Marques PI, Fonseca F, Sousa T, Santos P, Camilo V, Ferreira Z, Quesada V, Seixas S
Adaptive Evolution Favoring KLK4 Downregulation in East Asians. Molecular biology and evolution 33: 93-108, 2016.  [Article] 
 
21. Pádua D, Barros R, Amaral AL, Mesquita P, Freire AF, Sousa M, Maia AF, Caiado I, Fernandes H, Pombinho A, Pereira CF, Almeida R
 
22. Coelho R, Ricardo S, Amaral AL, Huang YL, Nunes M, Neves JP, Mendes N, López MN, Bartosch C, Ferreira V, Portugal R, Lopes JM, Almeida R, Heinzelmann-Schwarz V, Jacob F, David L
 
23. Almeida GM, Pereira C, Park JH, Lemos C, Campelos S, Gullo I, Martins D, Gonçalves G, Leitão D, Neto JL, André A, Borges C, Almeida D, Lee HJ, Kong SH, Kim WH, Carneiro F, Almeida R, Yang HK, Oliveira C
 
24. Duarte D, Nunes M, Ricardo S, Vale N
 
25. Ruvoën-Clouet N, Magalhaes A, Marcos-Silva L, Breiman A, Figueiredo C, David L, Le Pendu J
Increase in Genogroup II.4 Norovirus Host Spectrum by CagA-Positive Helicobacter pylori Infection. The Journal of infectious diseases 210: 183-91, 2014.  [Article] 
 
26. Solorzano L, Pereira C, Martins D, Almeida R, Carneiro F, Almeida GM, Oliveira C, Wahlby C
Towards Automatic Protein Co-Expression Quantification in Immunohistochemical TMA Slides. IEEE journal of biomedical and health informatics 25: 393-402, 2021.  [Article] 
 
27. Nunes M, Silva PMA, Coelho R, Pinto C, Resende A, Bousbaa H, Almeida GM, Ricardo S
 
28. Henriques TB, Dos Santos DZ, Dos Santos Guimarães I, Tessarollo NG, Lyra-Junior PCM, Mesquita P, Pádua D, Amaral AL, Cavadas B, Pereira L, Silva IV, Almeida RMDSG, Rangel LBA
 
29. Ricardo S, Marcos-Silva L, Pereira D, Pinto R, Almeida R, Söderberg O, Mandel U, Clausen H, Felix A, Lunet N, David L
 
30. Bruun J, Sveen A, Barros R, Eide PW, Eilertsen I, Kolberg M, Pellinen T, David L, Svindland A, Kallioniemi O, Guren MG, Nesbakken A, Almeida R, Lothe RA
 
31. Jantsch MF, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R
Positioning Europe for the EPITRANSCRIPTOMICS challenge. RNA biology 15: 829-831, 2018.  [Editorial Material] 
 
32. Pádua D, Figueira P, Ribeiro I, Almeida R, Mesquita P
The Relevance of Transcription Factors in Gastric and Colorectal Cancer Stem Cells Identification and Eradication. Frontiers in cell and developmental biology 8: 442, 2020.  [Review] 
 
33. Tsai MH, Lin X, Shumilov A, Bernhardt K, Feederle R, Poirey R, Kopp-Schneider A, Pereira B, Almeida R, Delecluse HJ
 
34. Magalhães A, Marcos-Pinto R, Nairn AV, Dela Rosa M, Ferreira RM, Junqueira-Neto S, Freitas D, Gomes J, Oliveira P, Santos MR, Marcos NT, Xiaogang W, Figueiredo C, Oliveira C, Dinis-Ribeiro M, Carneiro F, Moremen KW, David L, Reis CA
Helicobacter pylori chronic infection and mucosal inflammation switches the human gastric glycosylation pathways. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE 1852: 1928-39, 2015.  [Article] 
 
35. Amaro HM, Barros R, Tavares T, Almeida R, Pinto IS, Malcata FX, Guedes AC
 doi: 10.3390/md19110623 PMID: 34822494.
 
36. Gomes C, Almeida A, Ferreira JA, Silva L, Santos-Sousa H, Pinto-de-Sousa J, Santos LL, Amado F, Schwientek T, Levery SB, Mandel U, Clausen H, David L, Reis CA, Osório H
Glycoproteomic analysis of serum from patients with gastric precancerous lesions. Journal of proteome research 12: 1454-66, 2013.  [Article] 
 doi: 10.1021/pr301112x PMID: 23312025.
 
37. Burford B, Gentry-Maharaj A, Graham R, Allen D, Pedersen JW, Nudelman AS, Blixt O, Fourkala EO, Bueti D, Dawnay A, Ford J, Desai R, David L, Trinder P, Acres B, Schwientek T, Gammerman A, Reis CA, Silva L, Osório H, Hallett R, Wandall HH, Mandel U, Hollingsworth MA, Jacobs I, Fentiman I, Clausen H, Taylor-Papadimitriou J, Menon U, Burchell JM
 
38. Nunes M, Henriques Abreu M, Bartosch C, Ricardo S
Recycling the Purpose of Old Drugs to Treat Ovarian Cancer. International journal of molecular sciences 21: ., 2020.  [Review] 
 
39. Magalhães AC, Ricardo S, Moreira AC, Nunes M, Tavares M, Pinto RJ, Gomes MS, Pereira L
 
40. Koos B, Kamali-Moghaddam M, David L, Sobrinho-Simões M, Dimberg A, Nilsson M, Wählby C, Söderberg O
Next-generation pathology--surveillance of tumor microecology. Journal of molecular biology 427: 2013-22, 2015.  [Review] 
 
41. Ribeirinho-Soares S, Pádua D, Amaral AL, Valentini E, Azevedo D, Marques C, Barros R, Macedo F, Mesquita P, Almeida R
 
S100P is a molecular determinant of E-cadherin function in gastric cancer. Cell communication and signaling : CCS 17: 155, 2019.  [Article] 
 
43. Oliveira P, Carvalho J, Rocha S, Azevedo M, Reis I, Camilo V, Sousa B, Valente S, Paredes J, Almeida R, Huntsman D, Oliveira C
 doi: 10.1038/srep34860 PMID: 27721458.
 
44. Marcos-Silva L, Narimatsu Y, Halim A, Campos D, Yang Z, Tarp MA, Pereira PJ, Mandel U, Bennett EP, Vakhrushev SY, Levery SB, David L, Clausen H
Characterization of binding epitopes of CA125 monoclonal antibodies. Journal of proteome research 13: 3349-59, 2014.  [Article] 
 doi: 10.1021/pr500215g PMID: 24850311.
 
45. Pinto R, Barros R, Pereira-Castro I, Mesquita P, da Costa LT, Bennett EP, Almeida R, David L
CDX2 homeoprotein is involved in the regulation of ST6GalNAc-I gene in intestinal metaplasia. Laboratory investigation; a journal of technical methods and pathology 95: 718-27, 2015.  [Article] 
 
46. Lopes N, Bergsland CH, Bjørnslett M, Pellinen T, Svindland A, Nesbakken A, Almeida R, Lothe RA, David L, Bruun J
Digital image analysis of multiplex fluorescence IHC in colorectal cancer recognizes the prognostic value of CDX2 and its negative correlation with SOX2. Laboratory investigation; a journal of technical methods and pathology 100: 120-134, 2020.  [Article] 
 
47. Sadio A, Amaral AL, Nunes R, Ricardo S, Sarmento B, Almeida R, Tsukamoto H, das Neves J
 
48. Coelho R, Marcos-Silva L, Mendes N, Pereira D, Brito C, Jacob F, Steentoft C, Mandel U, Clausen H, David L, Ricardo S
 
49. Archampong TN, Asmah RH, Richards CJ, Martin VJ, Bayliss CD, Botão E, David L, Beleza S, Carrilho C
Gastro-duodenal disease in Africa: Literature review and clinical data from Accra, Ghana. World journal of gastroenterology 25: 3344-3358, 2019.  [Review] 
 
50. Ricardo S, Marcos-Silva L, David L
Mucin carriers of TF in ovarian cancer. Journal of cancer research and clinical oncology 142: 1867-8, 2016.  [Letter] 
 
51. Camilo V, Garrido M, Valente P, Ricardo S, Amaral AL, Barros R, Chaves P, Carneiro F, David L, Almeida R
 doi: 10.1111/his.12544 PMID: 25196071.
 
52. Camilo V, Barros R, Celestino R, Castro P, Vieira J, Teixeira MR, Carneiro F, Pinto-de-Sousa J, David L, Almeida R
 
53. Marcos-Silva L, Ricardo S, Chen K, Blixt O, Arigi E, Pereira D, Høgdall E, Mandel U, Bennett EP, Vakhrushev SY, David L, Clausen H
A novel monoclonal antibody to a defined peptide epitope in MUC16. Glycobiology 25: 1172-82, 2015.  [Article] 
 
54. Sadio A, Gustafsson JK, Pereira B, Gomes CP, Hansson GC, David L, Pêgo AP, Almeida R
 
55. de Oliveira JT, Ribeiro C, Barros R, Gomes C, de Matos AJ, Reis CA, Rutteman GR, Gärtner F
 
56. de Oliveira JT, Santos AL, Gomes C, Barros R, Ribeiro C, Mendes N, de Matos AJ, Vasconcelos MH, Oliveira MJ, Reis CA, Gärtner F
 
57. Bastos J, Peleteiro B, Barros R, Alves L, Severo M, de Fátima Pina M, Pinto H, Carvalho S, Marinho A, Guimarães JT, Azevedo A, La Vecchia C, Barros H, Lunet N
 doi: 10.1111/hel.12061 PMID: 23725608.
 
58. Ricardo S, Marcos-Silva L, Valente C, Coelho R, Gomes R, David L
Mucins MUC16 and MUC1 are major carriers of SLe(a) and SLe(x) in borderline and malignant serous ovarian tumors. Virchows Archiv : an international journal of pathology 468: 715-22, 2016.  [Article] 
 
59. Carrilho C, Gouveia P, Yokohama H, Lopes JM, Lunet N, Ferro J, Ismail M, Walboomers J, Sobrinho-Simões M, David L
Human papillomaviruses in intraepithelial neoplasia and squamous cell carcinoma of the conjunctiva: a study from Mozambique. European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP) 22: 566-8, 2013.  [Article] 
 
60. Mesquita P, Freire AF, Lopes N, Gomes R, Azevedo D, Barros R, Pereira B, Cavadas B, Pópulo H, Boaventura P, David L, Pereira L, Almeida R
Expression and Clinical Relevance of SOX9 in Gastric Cancer. Disease markers 2019: 8267021, 2019.  [Article] 
 
61. Huang YL, Liang CY, Ritz D, Coelho R, Septiadi D, Estermann M, Rimmer N, Vlajnic T, David L, Rothen-Rutishauser B, Jacob F, Heinzelmann-Schwarz V
Integrin alpha 2-collagen interaction promotes ovarian cancer metastasis GEBURTSHILFE UND FRAUENHEILKUNDE 80: E193-E193, 2020.  [Meeting Abstract] 
 
62. Barros R, Pereira D, Callé C, Camilo V, Cunha AI, David L, Almeida R, Dias-Pereira A, Chaves P
Dynamics of SOX2 and CDX2 Expression in Barrett's Mucosa. Disease markers 2016: 1532791, 2016.  [Article] 
 
63. Coelho R, Marcos-Silva L, Ricardo S, Ponte F, Costa A, Lopes JM, David L
 
64. Rodrigues JP, David L, Almeida R, Barros R, Freitas T, Silva J, Ponte A, Sousa M, Silva JC, Carvalho J
Mechanisms of regulation of normal and metaplastic intestinal differentiation. Histology and histopathology 33: 523-532, 2018.  [Review] 
 doi: 10.14670/HH-11-938 PMID: 29027178.
 
65. DE Oliveira JT, DE Matos AJ, Barros R, Ribeiro C, Chen A, Hespanhol V, Rutteman GR, Gärtner F
 PMID: 24778023.
 
66. Sousa AM, Grandgenett PM, David L, Almeida R, Hollingsworth MA, Santos-Silva F
Reflections on MUC1 glycoprotein: the hidden potential of isoforms in carcinogenesis. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 124: 913-924, 2016.  [Review] 
 doi: 10.1111/apm.12587 PMID: 27538373.
 
67. Monteiro LS, Delgado ML, Ricardo S, Garcez F, do Amaral B, Pacheco JJ, Lopes C, Bousbaa H
 doi: 10.1155/2014/905680 PMID: 24967412.
 
68. Sousa AM, Rei M, Freitas R, Ricardo S, Caffrey T, David L, Almeida R, Hollingsworth MA, Santos-Silva F
 
69. Rolim I, Rodrigues RV, Bettencourt A, Barros R, Camilo V, Dias Pereira A, Almeida R, Chaves P
Mid-Esophagus Columnar Metaplasia: What Is the Biopathogenic Pathway? International journal of surgical pathology 25: 262-265, 2017.  [Article] 
 
70. Pereira B, Billaud M, Almeida R
RNA-Binding Proteins in Cancer: Old Players and New Actors. Trends in cancer 3: 506-528, 2017.  [Review] 
 
71. Pimenta J, Ribeiro R, Almeida R, Costa PF, da Silva MA, Pereira B
Organ-on-Chip Approaches for Intestinal 3D In Vitro Modeling. Cellular and molecular gastroenterology and hepatology 13: 351-367, 2022.  [Review] 
 
72. Pádua D, Pinto DF, Figueira P, Pereira CF, Almeida R, Mesquita P
HMGA1 Has Predictive Value in Response to Chemotherapy in Gastric Cancer. Current oncology (Toronto, Ont.) 29: 56-67, 2021.  [Article] 
 
73. Pereira C, Park JH, Campelos S, Gullo I, Lemos C, Solorzano L, Martins D, Gonçalves G, Leitão D, Lee HJ, Kong SH, André A, Borges C, Almeida D, Wälbhy C, Almeida R, Kim WH, Carneiro F, Yang HK, Almeida GM, Oliveira C
 doi: 10.1002/ijc.33872 PMID: 34751446.
 
74. Amaral IF, Sousa SR, Neiva I, Marcos-Silva L, Kirkpatrick CJ, Barbosa MA, Pêgo AP
 doi: 10.4161/biom.24791 PMID: 23635535.