Names highlighted in bold indicate current or past Bakel Lab members. * indicates equally contributing authors. † indicates corresponding authors.

For the latest publication information please see here.

2022

• Ramírez JD, Castañeda S, Ballesteros N, Muñoz M, Hernández M, Banu R, Shrestha P, Chen F, Shi H, van Bakel H, Simon V, Cordon-Cardo C, Sordillo EM, Paniz-Mondolfi AE.
  Hotspots for SARS-CoV-2 Omicron variant spread: Lessons from New York City.
  J Med Virol. 2022 Jul;94(7):2911-2914.
• Kirkpatrick Roubidoux E, Sano K, McMahon M, Carreño JM, Capuano C, Jiang K, Simon V, van Bakel H, Wilson P, Krammer F.
  Novel Epitopes of the Influenza Virus N1 Neuraminidase Targeted by Human Monoclonal Antibodies.
  J Virol. 2022 May 11;96(9):e0033222.
• DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Fischer WM, Florence WC, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli S, Turner SA, Vakaki MA, van Bakel H, VanBlargan LA, Vincent LR, Wallace ZS, Wang L, Wang M, Wang P, Wang W, Weaver SC, Webby RJ, Weiss CD, Wentworth DE, Weston SM, Whelan SPJ, Whitener BM, Wilks SH, Xie X, Ying B, Yoon H, Zhou B, Hertz T, Smith DJ, Diamond MS, Post DJ, Suthar MS.
  Defining the risk of SARS-CoV-2 variants on immune protection.
  Nature. 2022 May;605(7911):640-652.
• Reategui Schwarz E, van de Guchte A, Dupper AC, Caban AB, Nadkarni D, Fox L, Mills A, Obla A, Chacko KI, Oussenko I, Samaroo F, Polanco Jb>, Silvera R, Smith ML, Patel G, Gitman M, Alburquerque B, Chung M, Sullivan MJ, van Bakel H, Altman DR.
  Everybody nose: molecular and clinical characteristics of nasal colonization during active methicillin-resistant Staphylococcus aureus bloodstream infection.
  BMC Infect Dis. 2022 Apr 24;22(1):400.
• Hernandez MM, Banu R, Gonzalez-Reiche AS, van de Guchte A, Khan Z, Shrestha P, Cao L, Chen F, Shi H, Hanna A, Alshammary H, Fabre S, Amoako A, Obla A, Alburquerque B, Patiño LH, Ramírez JD, Sebra R, Gitman MR, Nowak MD, Cordon-Cardo C, Schutzbank TE, Simon V, van Bakel H, Sordillo EM, Paniz-Mondolfi AE.
  Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach.
  J Med Virol. 2022 Apr;94(4):1606-1616.
• Escalera A, Gonzalez-Reiche AS, Aslam S, Mena I, Laporte M, Pearl RL, Fossati A, Rathnasinghe R, Alshammary H, van de Guchte A, Farrugia K, Qin Y, Bouhaddou M, Kehrer T, Zuliani-Alvarez L, Meekins DA, Balaraman V, McDowell C, Richt JA, Bajic G, Sordillo EM, Dejosez M, Zwaka TP, Krogan NJ, Simon V, Albrecht RA, van Bakel H, García-Sastre A, Aydillo T.
  Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission.
  Cell Host Microbe. 2022 Mar 9;30(3):373-387.e7.
• Tan J, O'Dell G, Hernandez MM, Sordillo EM, Kahn Z, Kriti D, van Bakel H, Ellebedy AH, Wilson PC, Simon V, Krammer F, McMahon M.
  Human Anti-neuraminidase Antibodies Reduce Airborne Transmission of Clinical Influenza Virus Isolates in the Guinea Pig Model.
  J Virol. 2022 Jan 26;96(2):e0142121.
• Halfmann PJ, Iida S, Iwatsuki-Horimoto K, Maemura T, Kiso M, Scheaffer SM, Darling TL, Joshi A, Loeber S, Singh G, Foster SL, Ying B, Case JB, Chong Z, Whitener B, Moliva J, Floyd K, Ujie M, Nakajima N, Ito M, Wright R, Uraki R, Warang P, Gagne M, Li R, Sakai-Tagawa Y, Liu Y, Larson D, Osorio JE, Hernandez-Ortiz JP, Henry AR, Ciouderis K, Florek KR, Patel M, Odle A, Wong LR, Bateman AC, Wang Z, Edara VV, Chong Z, Franks J, Jeevan T, Fabrizio T, DeBeauchamp J, Kercher L, Seiler P, Gonzalez-Reiche AS, Sordillo EM, Chang LA, van Bakel H, Simon V, Douek DC, Sullivan NJ, Thackray LB, Ueki H, Yamayoshi S, Imai M, Perlman S, Webby RJ, Seder RA, Suthar MS, García-Sastre A, Schotsaert M, Suzuki T, Boon ACM, Diamond MS, Kawaoka Y.
  SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters.
  Nature. 2022 Jan 21;.
• Encinas P, Del Real G, Dutta J, Khan Z, van Bakel H, Del Burgo MÁM, García-Sastre A, Nelson MI.
  Evolution of influenza A virus in intensive and free-range swine farms in Spain.
  Virus Evol. 2022 Jan;7(2):veab099.

2021

• Carreño JM, Alshammary H, Tcheou J, Singh G, Raskin A, Kawabata H, Sominsky L, Clark J, Adelsberg DC, Bielak D, Gonzalez-Reiche AS, Dambrauskas N, Vigdorovich V, Srivastava K, Sather DN, Sordillo EM†, Bajic G†, van Bakel H†, Simon V†, Krammer F†.
  Activity of convalescent and vaccine serum against SARS-CoV-2 Omicron.
  Nature. 2021 Dec 31;.
• Diamond M, Halfmann P, Maemura T, Iwatsuki-Horimoto K, Iida S, Kiso M, Scheaffer S, Darling T, Joshi A, Loeber S, Foster S, Ying B, Whitener B, Floyd K, Ujie M, Nakajima N, Ito M, Wright R, Uraki R, Li R, Sakai Y, Liu Y, Larson D, Osorio J, Hernandez-Ortiz J, ÄŒiuoderis K, Florek K, Patel M, Bateman A, Odle A, Wong LY, Wang Z, Edara VV, Chong Z, Thackray L, Ueki H, Yamayoshi S, Imai M, Perlman S, Webby R, Seder R, Suthar M, Garcia-Sastre A, Schotsaert M, Suzuki T, Boon A, Kawaoka Y, Douek D, Moliva J, Sullivan N, Gagne M, Ransier A, Case J, Jeevan T, Franks J, Fabrizio T, DeBeauchamp J, Kercher L, Seiler P, Singh G, Warang P, Gonzalez-Reiche AS, Sordillo E, van Bakel H, Simon V.
  The SARS-CoV-2 B.1.1.529 Omicron virus causes attenuated infection and disease in mice and hamsters.
  Res Sq. 2021 Dec 29;.
• Holmes G, Gonzalez-Reiche AS, Saturne M, Motch Perrine SM, Zhou X, Borges AC, Shewale B, Richtsmeier JT, Zhang B, van Bakel H, Jabs EW.
  Single-cell analysis identifies a key role for Hhip in murine coronal suture development.
  Nat Commun. 2021 Dec 8;12(1):7132.
• Letizia AG, Arnold CE, Adhikari BN, Voegtly LJ, Glang L, Rice GK, Goforth CW, Schilling MA, Weir DL, Malagon F, Ramos I, Vangeti S, Gonzalez-Reiche AS, Cer RZ, Sealfon SC, van Bakel H, Bishop-Lilly KA.
  Immunological and Genetic Investigation of SARS-CoV-2 Reinfection in an Otherwise Healthy, Young Marine Recruit.
  Pathogens. 2021 Dec 8;10(12).
• Hernandez MM, Banu R, Gonzalez-Reiche AS, van de Guchte A, Khan Z, Shrestha P, Cao L, Chen F, Shi H, Hanna A, Alshammary H, Fabre S, Amoako A, Obla A, Alburquerque B, Patiño LH, Ramírez JD, Sebra R, Gitman MR, Nowak MD, Cordon-Cardo C, Schutzbank TE, Simon V, van Bakel H, Sordillo EM, Paniz-Mondolfi AE.
  Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach.
  J Med Virol. 2021 Dec 7;.
• Neira V, Brito B, Agüero B, Berrios F, Valdés V, Gutierrez A, Ariyama N, Espinoza P, Retamal P, Holmes EC, Gonzalez-Reiche AS, Khan Z, van de Guchte A, Dutta J, Miorin L, Kehrer T, Galarce N, Almonacid LI, Levican J, van Bakel H, García-Sastre A, Medina RA.
  A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners.
  Emerg Microbes Infect. 2021 Dec;10(1):376-383.
• Carreño JM, Alshammary H, Singh G, Raskin A, Amanat F, Amoako A, Gonzalez-Reiche AS, van de Guchte A, Study Group P, Srivastava K, Sordillo EM, Sather DN, van Bakel H†, Krammer F†, Simon V†.
  Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients.
  EBioMedicine. 2021 Nov;73:103626.
• Gitman MR, Alburquerque B, Chung M, van de Guchte A, Sullivan MJ, Obla A, Polanco J, Oussenko I, Smith ML, Samaroo F, Barackman D, Altman DR, Sordillo EM, van Bakel H.
  Modified methicillin-resistant Staphylococcus aureus detected in neonatal intensive care patients.
  J Antimicrob Chemother. 2021 Oct 11;76(11):2774-2777.
• Patiño LH, Ballesteros N, Muñoz M, Castañeda S, Hernández C, Gomez S, Florez C, Rico A, Pardo L, Hernandez-Pereira CE, Delgado-Noguera L, Grillet ME, Hernandez MM, Khan Z, van de Guchte A, Dutta J, Gonzalez-Reiche AS, Simon V, van Bakel H, Sordillo EM, Ramírez JD, Paniz-Mondolfi AE.
  SARS-CoV-2 in Transit: Characterization of SARS-CoV-2 Genomes From Venezuelan Migrants in Colombia.
  Int J Infect Dis. 2021 Sep;110:410-416.
• Silvas JA, Vasquez DM, Park JG, Chiem K, Allué-Guardia A, Garcia-Vilanova A, Platt RN, Miorin L, Kehrer T, Cupic A, Gonzalez-Reiche AS, Bakel HV, García-Sastre A, Anderson T, Torrelles JB, Ye C, Martinez-Sobrido L.
  Contribution of SARS-CoV-2 Accessory Proteins to Viral Pathogenicity in K18 Human ACE2 Transgenic Mice.
  J Virol. 2021 Aug 10;95(17):e0040221.
• IMPACC Manuscript Writing Team; IMPACC Network Steering Committee.
  Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study.
  Sci Immunol. 2021 Aug 10;6(62).
• Liu H, Plancarte M, Ball EE, Weiss CM, Gonzales-Viera O, Holcomb K, Ma ZM, Allen AM, Reader JR, Duignan PJ, Halaska B, Khan Z, Kriti D, Dutta J, van Bakel H, Jackson K, Pesavento PA, Boyce WM, Coffey LL.
  Respiratory Tract Explant Infection Dynamics of Influenza A Virus in California Sea Lions, Northern Elephant Seals, and Rhesus Macaques.
  J Virol. 2021 Jul 26;95(16):e0040321.
• Amanat F, Thapa M, Lei T, Ahmed SMS, Adelsberg DC, Carreño JM, Strohmeier S, Schmitz AJ, Zafar S, Zhou JQ, Rijnink W, Alshammary H, Borcherding N, Reiche AG, Srivastava K, Sordillo EM, van Bakel H, Turner JS, Bajic G, Simon V, Ellebedy AH, Krammer F.
  SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2.
  Cell. 2021 Jul 22;184(15):3936-3948.e10.
• Letizia AG, Smith DR, Ge Y, Ramos I, Sealfon RSG, Goforth C, Gonzalez-Reiche AS, Vangeti S, Weir DL, Alshammary H, Chen HW, George MC, Soares-Schanoski A, Lizewski RA, Lizewski SE, Marayag J, Miller CM, Nunez E, Porter CK, Ana ES, Schilling M, Sugiharto VA, Sun P, Termini M, van de Guchte A, Troyanskaya OG, van Bakel H, Sealfon SC.
  Viable virus shedding during SARS-CoV-2 reinfection.
  Lancet Respir Med. 2021 May 5:S2213-2600(21)00219-8.
• Ballesteros N, Muñoz M, Patiño LH, Hernández C, González-Casabianca F, Carroll I, Santos-Vega M, Cascante J, Angel A, Feged-Rivadeneira A, Palma-Cuero M, Flórez C, Gomez S, van de Guchte A, Khan Z, Dutta J, Obla A, Alshammary HA, Gonzalez-Reiche AS, Hernandez MM, Sordillo EM, Simon V, van Bakel H, Paniz-Mondolfi AE, Ramírez JD.
  Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin.
  PLoS Negl Trop Dis. 2021 Apr;15(4):e0009327.
• Livanos AE*, Jha D*, Cossarini F*, Gonzalez-Reiche AS*, Tokuyama M*, Aydillo T*, Parigi TL*, Ladinsky MS, Ramos I, Dunleavy K, Lee B, Dixon R, Chen ST, Martinez-Delgado G, Nagula S, Bruce EA, Ko HM, Glicksberg BS, Nadkarni G, Pujadas E, Reidy J, Naymagon S, Grinspan A, Ahmad J, Tankelevich M, Bram Y, Gordon R, Sharma K, Houldsworth J, Britton GJ, Chen-Liaw A, Spindler MP, Plitt T, Wang P, Cerutti A, Faith JJ, Colombel JF, Kenigsberg E, Argmann C, Merad M, Gnjatic S, Harpaz N, Danese S, Cordon-Cardo C, Rahman A, Schwartz RE, Kumta NA, Aghemo A, Bjorkman PJ, Petralia F†, van Bakel H†, Garcia-Sastre A†, Mehandru S†.
  Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms.
  Gastroenterology. 2021 Mar 4
• Roubidoux EK, Carreño JM, McMahon M, Jiang K, van Bakel H, Wilson P, Krammer F.
  Mutations in the Hemagglutinin Stalk Domain Do Not Permit Escape from a Protective, Stalk-Based Vaccine-Induced Immune Response in the Mouse Model.
  mBio. 2021 Feb 16;12(1).
• Kirkpatrick Roubidoux E, McMahon M, Carreño JM, Capuano C, Jiang K, Simon V, van Bakel H, Wilson P, Krammer F.
  Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase.
  mSphere. 2021 Feb 10;6(1).
• Stadlbauer D*, Tan J*, Jiang K*, Hernandez MM, Fabre S, Amanat F, Teo C, Arunkumar GA, McMahon M, Capuano C, Twyman K, Jhang J, Nowak MD, Simon V†, Sordillo EM†, van Bakel H†, Krammer F.†
  Repeated cross-sectional sero-monitoring of SARS-CoV-2 in New York City.
  Nature. 2021 Feb;590(7844):146-150.
• Ramírez JD, Florez C, Muñoz M, Hernández C, Castillo A, Gomez S, Rico A, Pardo L, Barros EC, Castañeda S, Ballesteros N, Martínez D, Vega L, Jaimes JE, Cruz-Saavedra L, Herrera G, Patiño LH, Teherán AA, Gonzalez-Reiche AS, Hernandez MM, Sordillo EM, Simon V, van Bakel H, Paniz-Mondolfi A.
  The arrival and spread of SARS-CoV-2 in Colombia.
  J Med Virol. 2021 Feb;93(2):1158-1163.

2020

• Aydillo T, Gonzalez-Reiche AS, Aslam S, van de Guchte A, Khan Z, Obla A, Dutta J, van Bakel H, Aberg J, García-Sastre A, Shah G, Hohl T, Papanicolaou G, Perales MA, Sepkowitz K, Babady NE, Kamboj M.
  Shedding of Viable SARS-CoV-2 after Immunosuppressive Therapy for Cancer.
  N Engl J Med. 2020 Dec 24;383(26):2586-2588.
• Letizia AG*, Ramos I*, Obla A*, Goforth C, Weir DL, Ge Y, Bamman MM, Dutta J, Ellis E, Estrella L, George MC, Gonzalez-Reiche AS, Graham WD, van de Guchte A, Gutierrez R, Jones F, Kalomoiri A, Lizewski R, Lizewski S, Marayag J, Marjanovic N, Millar EV, Nair VD, Nudelman G, Nunez E, Pike BL, Porter C, Regeimbal J, Rirak S, Santa Ana E, Sealfon RSG, Sebra R, Simons MP, Soares-Schanoski A, Sugiharto V, Termini M, Vangeti S, Williams C, Troyanskaya OG*†, van Bakel H*†, Sealfon SC*†.
  SARS-CoV-2 Transmission among Marine Recruits during Quarantine.
  N Engl J Med. 2020 Dec 17;383(25):2407-2416.
• Paniz-Mondolfi A, Muñoz M, Florez C, Gomez S, Rico A, Pardo L, Barros EC, Hernández C, Delgado L, Jaimes JE, Pérez L, Teherán AA, Alshammary HA, Obla A, Khan Z, Dutta J, van de Guchte A, Gonzalez-Reiche AS, Hernandez MM, Sordillo EM, Simon V, van Bakel H, Llewellyn MS, Ramírez JD.
  SARS-CoV-2 spread across the Colombian-Venezuelan border.
  Infect Genet Evol. 2020 Dec;86:104616.
• Javaid W*, Ehni J*, Gonzalez-Reiche AS*, Carreño JM, Hirsch E, Tan J, Khan Z, Kriti D, Ly T, Kranitzky B, Barnett B, Cera F, Prespa L, Moss M, Albrecht RA, Mustafa A, Herbison I, Hernandez MM, Pak TR, Alshammary H, Sebra R, Smith M, Krammer F, Gitman MR, Sordillo EM*†, Simon V*†, van Bakel H*†.
  Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology.
  Clin Infect Dis. 2020 Nov 30
• Nelson MI, Perofsky A, McBride DS, Rambo-Martin BL, Wilson MM, Barnes JR, van Bakel H, Khan Z, Dutta J, Nolting JM, Bowman AS.
  A Heterogeneous Swine Show Circuit Drives Zoonotic Transmission of Influenza A Viruses in the United States.
  J Virol. 2020 Nov 23;94(24).
• Berbel Caban A, Pak TR, Obla A, Dupper AC, Chacko KI, Fox L, Mills A, Ciferri B, Oussenko I, Beckford C, Chung M, Sebra R, Smith M, Conolly S, Patel G, Kasarskis A, Sullivan MJ, Altman DR, van Bakel H.
  PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks.
  Genome Med. 2020 Nov 16;12(1):96.
• Kirkpatrick E, Henry C, McMahon M, Jiang K, Strohmeier S, van Bakel H, Wilson PC, Krammer F.
  Characterization of Novel Cross-Reactive Influenza B Virus Hemagglutinin Head Specific Antibodies That Lack Hemagglutination Inhibition Activity.
  J Virol. 2020 Nov 9;94(23).
• Simon V, van Bakel H, Sordillo EM.
  Positive, again! What to make of "re-positive" SARS-CoV-2 molecular test results.
  EBioMedicine. 2020 Oct;60:103011.
• Samuels BD, Aho R, Brinkley JF, Bugacov A, Feingold E, Fisher S, Gonzalez-Reiche AS, Hacia JG, Hallgrimsson B, Hansen K, Harris MP, Ho TV, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Leslie EJ, Li H, Liao EC, Long H, Lu N, Maas RL, Marazita ML, Mohammed J, Prescott S, Schuler R, Selleri L, Spritz RA, Swigut T, van Bakel H, Visel A, Welsh I, Williams C, Williams TJ, Wysocka J, Yuan Y, Chai Y.
  FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research.
  Development. 2020 Sep 21;147(18).
• Gonzalez-Reiche AS, Hernandez MM, Sullivan MJ, Ciferri B, Alshammary H, Obla A, Fabre S, Kleiner G, Polanco J, Khan Z, Alburquerque B, van de Guchte A, Dutta J, Francoeur N, Melo BS, Oussenko I, Deikus G, Soto J, Sridhar SH, Wang YC, Twyman K, Kasarskis A, Altman DR, Smith M, Sebra R, Aberg J, Krammer F, García-Sastre A, Luksza M, Patel G, Paniz-Mondolfi A, Gitman M, Sordillo EM*†, Simon V*†, van Bakel H*†.
  Introductions and early spread of SARS-CoV-2 in the New York City area.
  Science. 2020 Jul 17;369(6501):297-301.
• Holmes G*, Gonzalez-Reiche AS*, Lu N*, Zhou X*, Rivera J, Kriti D, Sebra R, Williams AA, Donovan MJ, Potter SS, Pinto D, Zhang B*, van Bakel H*†, Jabs EW*.
  Integrated Transcriptome and Network Analysis Reveals Spatiotemporal Dynamics of Calvarial Suturogenesis.
  Cell Rep. 2020 Jul 7;32(1):107871.
• Agüero B, Mena J, Berrios F, Tapia R, Salinas C, Dutta J, van Bakel H, Mor SK, Brito B, Medina RA, Neira V.
  First report of porcine respirovirus 1 in South America.
  Vet Microbiol. 2020 Jul;246:108726.
• Ho JSY, Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung L, Zheng S, Chang M, Fstkchyan Y, Clohisey S, Dinan AM, Gibbs J, Gifford R, Shen R, Gu Q, Irigoyen N, Campisi L, Huang C, Zhao N, Jones JD, van Knippenberg I, Zhu Z, Moshkina N, Meyer L, Noel J, Peralta Z, Rezelj V, Kaake R, Rosenberg B, Wang B, Wei J, Paessler S, Wise HM, Johnson J, Vannini A, Amorim MJ, Baillie JK, Miraldi ER, Benner C, Brierley I, Digard P, Łuksza M, Firth AE, Krogan N, Greenbaum BD, MacLeod MK, van Bakel H, Garcìa-Sastre A, Yewdell JW, Hutchinson E, Marazzi I.
  Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection.
  Cell. 2020 Jun 25;181(7):1502-1517.e23.
• Mitchell J. Sullivan, Harm van Bakel
  Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes
  https://joss.theoj.org/papers/10.21105/joss.02451

2019

• Wu M, Kriti D, van Bakel H, Jabs EW, Holmes G.
  Laser Capture Microdissection of Mouse Embryonic Cartilage and Bone for Gene Expression Analysis.
  J Vis Exp. 2019 Dec 18;(154). doi: 10.3791/60503.
• Oliveira PH, Ribis JW, Garrett EM, Trzilova D, Kim A, Sekulovic O, Mead EA, Pak T, Zhu S, Deikus G, Touchon M, Lewis-Sandari M, Beckford C, Zeitouni NE, Altman DR, Webster E, Oussenko I, Bunyavanich S, Aggarwal AK, Bashir A, Patel G, Wallach F, Hamula C, Huprikar S, Schadt EE, Sebra R, van Bakel H, Kasarskis A, Tamayo R, Shen A, Fang G.
  Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis.
  Nat Microbiol. 2019 Nov 25. doi: 10.1038/s41564-019-0613-4
• Imai M, Yamashita M, Sakai-Tagawa Y, Iwatsuki-Horimoto K, Kiso M, Murakami J, Yasuhara A, Takada K, Ito M, Nakajima N, Takahashi K, Lopes TJS, Dutta J, Khan Z, Kriti D, van Bakel H, Tokita A, Hagiwara H, Izumida N, Kuroki H, Nishino T, Wada N, Koga M, Adachi E, Jubishi D, Hasegawa H, Kawaoka Y.
  Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets.
  Nat Microbiol. 2019 Nov 25. doi: 10.1038/s41564-019-0609-0.
• Dupper AC, Sullivan MJ, Chacko KI, Mishkin A, Ciferri B, Kumaresh A, Berbel Caban A, Oussenko I, Beckford C, Zeitouni NE, Sebra R, Hamula C, Smith M, Kasarskis A, Patel G, McBride RB, van Bakel H, Altman DR.
  Blurred Molecular Epidemiological Lines Between the Two Dominant Methicillin-Resistant Staphylococcus aureus Clones.
  Open Forum Infect Dis. 2019 Jun 27;6(9):ofz302. doi: 10.1093/ofid/ofz302.
• Sullivan MJ, Altman DR, Chacko KI, Ciferri B, Webster E, Pak TR, Deikus G, Lewis-Sandari M, Khan Z, Beckford C, Rendo A, Samaroo F, Sebra R, Karam-Howlin R, Dingle T, Hamula C, Bashir A, Schadt E, Patel G, Wallach F, Kasarskis A, Gibbs K*, van Bakel H*†.
  A complete genome screening program of clinical methicillin-resistant Staphylococcus aureus isolates identifies the origin and progression of a neonatal intensive care unit outbreak.
  J Clin Microbiol. 2019 Oct 2. pii: JCM.01261-19.
  • Press coverage includes: PacBio Blog
• Furusawa Y, Yamada S, da Silva Lopes TJ, Dutta J, Khan Z, Kriti D, van Bakel H, Kawaoka Y.
  Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment.
  MBio. 2019 Oct 1;10(5). pii: e01794-19.
• Bergervoet SA, Pritz-Verschuren SBE, Gonzales JL, Bossers A, Poen MJ, Dutta J, Khan Z, Kriti D, van Bakel H, Bouwstra R, Fouchier RAM, Beerens N.
  Circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands, 2006-2016.
  Sci Rep. 2019 Sep 23;9(1):13681.
• Zhong G, Fan S, Lopes TJS, Le MQ, van Bakel H, Dutta J, Smith GJD, Jayakumar J, Nguyen HLK, Hoang PVM, Halfmann P, Hatta M, Su YCF, Neumann G, Kawaoka Y.
  Isolation of Highly Pathogenic H5N1 Influenza Viruses in 2009-2013 in Vietnam.
  Front Microbiol. 2019 Jun 25;10:1411.
• Sause WE, Balasubramanian D, Irnov I, Copin R, Sullivan MJ, Sommerfield A, Chan R, Dhabaria A, Askenazi M, Ueberheide B, Shopsin B, van Bakel H, Torres VJ.
  The purine biosynthesis regulator PurR moonlights as a virulence regulator in Staphylococcus aureus.
  Proc Natl Acad Sci U S A. 2019 Jun 19.
• Motch Perrine SM, Wu M, Stephens NB, Kriti D, van Bakel H, Jabs EW, Richtsmeier JT.
  Mandibular dysmorphology due to abnormal embryonic osteogenesis in FGFR2-related craniosynostosis mice.
  Dis Model Mech. 2019 May 30;12(5).
• Takada K, Kawakami C, Fan S, Chiba S, Zhong G, Gu C, Shimizu K, Takasaki S, Sakai-Tagawa Y, Lopes TJS, Dutta J, Khan Z, Kriti D, van Bakel H, Yamada S, Watanabe T, Imai M, Kawaoka Y.
  A humanized MDCK cell line for the efficient isolation and propagation of human influenza viruses.
  Nat Microbiol. 2019 Apr 29.
• Yang X, Yuan T, Ma R, Chacko KI, Smith M, Deikus G, Sebra R, Kasarskis A, van Bakel H, Franzblau SG, Sampson NS.
  Mce3R Stress-Resistance Pathway Is Vulnerable to Small-Molecule Targeting That Improves Tuberculosis Drug Activities.
  ACS Infect Dis. 2019 May 3.
• Copin R, Sause WE, Fulmer Y, Balasubramanian D, Dyzenhaus S, Ahmed JM, Kumar K, Lees J, Stachel A, Fisher JC, Drlica K, Phillips M, Weiser JN, Planet PJ, Uhlemann AC, Altman DR, Sebra R, van Bakel H, Lighter J, Torres VJ, Shopsin B.
  Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus.
  Proc Natl Acad Sci U S A. 2019 Jan 11. pii: 201814265. doi: 10.1073/pnas.

2018

• Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Moran Losada P, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE; PsychENCODE Consortium, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH.
  Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.
  Science 2018 Dec 14;362(6420). pii: eaat8127.
• Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR†, Page JE† and van Bakel H†.
  A physical and genetic map of Cannabis sativa identifies extensive rearrangement at the THC/CBD acid synthase locus.
  Genome Res. 2018 Nov, doi:10.1101/gr.242594.118
  • Press coverage includes: The Star, Live Science, Inverse, Daily Mail
• Rimondi A, Gonzalez-Reiche AS, Olivera VS, Decarre J, Castresana GJ, Romano M, Nelson MI, van Bakel H, Pereda AJ, Ferreri L, Geiger G, Perez DR.
  Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina (2006-2016).
  Emerg Microbes Infect. 2018 Nov 28;7(1):194.
• Holmes G, O'Rourke C, Motch Perrine SM, Lu N, van Bakel H, Richtsmeier JT, Jabs EW.
  Midface and upper airway dysgenesis in FGFR2-related craniosynostosis involves multiple tissue-specific and cell cycle effects.
  Development. 2018 Oct 5;145(19)
• Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, Ma Y, Rialdi A, Albrecht R, Fenouil R, Sánchez-Aparicio MT, Ayllon J, Ravisankar S, Haddad B, Ho JSY, Low D, Jin J, Yurchenko V, Prinjha RK, Tarakhovsky A, Squatrito M, Pinto D, Allette K, Byun M, Smith ML, Sebra R, Guccione E, Tumpey T, Krogan N, Greenbaum B, van Bakel H, García-Sastre A, Marazzi I.
  Influenza virus infection causes global RNAPII termination defects.
  Nat Struct Mol Biol. 2018 Sep;25(9):885-893.
• Altman DR*, Sullivan MJ*, Chacko KI, Balasubramanian D, Pak TR, Sause WE, Kumar K, Sebra R, Deikus G, Attie O, Rose H, Lewis M, Fulmer Y, Bashir A, Kasarskis A, Schadt EE, Richardson AR, Torres VJ, Shopsin B†, van Bakel H†.
  Genome plasticity of agr-defective Staphylococcus aureus during clinical infection.
  Infect Immun.2018 Jul 30. pii: IAI.00331-18. doi: 10.1128/IAI.00331-18.
• Mena J, Brito B, Moreira R, Tadich T, González I, Cruces J, Ortega R, van Bakel H, Rathnasinghe R, Pizarro-Lucero J, Medina R, Neira V.
  Re-emergence of H3N8 Equine Influenza A virus in Chile
  Transbound Emerg Dis.2018 Jul 28. doi: 10.1111/tbed.12984.
• Voorhees IEH, Dalziel BD, Glaser A, Dubovi EJ, Murcia PR, Newbury S, Toohey-Kurth K, Su S, Kriti D, Van Bakel H, Goodman LB, Leutenegger C, Holmes EC, Parrish CR.
  Multiple incursions and recurrent epidemic fade-out of H3N2 canine influenza A virus in the United States.
  J Virol. 2018 Jun 6. pii: JVI.00323-18. doi: 10.1128/JVI.00323-18.
• Venkatesh D, Poen MJ, Bestebroer TM, Scheuer RD, Vuong O, Chkhaidze M, Machablishvili A, Mamuchadze J, Ninua L, Fedorova NB, Halpin RA, Lin X, Ransier A, Stockwell TB, Wentworth DE, Kriti D, Dutta J, van Bakel H, Puranik A, Slomka MJ, Essen S, Brown IH, Fouchier RAM, Lewis NS.
  Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem.
  J Virol. 2018 May 16. pii: JVI.00433-18. doi: 10.1128/JVI.00433-18.
• Gandal MJ, Haney JR, Parikshak NN, Leppa V, Ramaswami G, Hartl C, Schork AJ, Appadurai V, Buil A, Werge TM, Liu C, White KP; CommonMind Consortium; PsychENCODE Consortium; iPSYCH-BROAD Working Group, Horvath S, Geschwind DH.
  Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap.
  Science. 2018 Feb 9;359(6376):693-697.
• Chacko KI, Sullivan MJ, Beckford C, Altman DR, Ciferri B, Pak TR, Sebra R, Kasarskis A, Hamula CL, van Bakel H.
  The genetic basis of emerging vancomycin, linezolid, and daptomycin heteroresistance in a case of persistent Enterococcus faecium bacteremia.
  Antimicrob Agents Chemother. 2018 Jan 16. pii: AAC.02007-17.

2017

• Woods E, Cohen G, Bressman E, Lin D, Zeitouni NE, Beckford C, Hamula C, van Bakel H, Sullivan M, Altman DR, and Caplivski D.
  Community-Acquired Cavitary Pseudomonas Pneumonia Linked to Use of a Home Humidifier.
  Case Rep Infect Dis. 2017 Dec 28. Volume 2017, Article ID 5474916.
• Eisfeld AJ*, Halfmann PJ*, Wendler JP*, Kyle JE*, Burnum-Johnson KE*, Peralta Z*, Maemura T, Walters KB, Watanabe T, Fukuyama S, Yamashita M, Jacobs JM, Kim YM, Casey CP, Stratton KG, Webb-Robertson BM, Gritsenko MA, Monroe ME, Weitz KK, Shukla AK, Tian M, Neumann G, Reed JL, van Bakel H†, Metz TO†, Smith RD†, Waters KM†, N'jai A, Sahr F†, Kawaoka Y†.
  Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis.
  Cell Host Microbe. 2017 Nov 15. pii: S1931-3128(17)30446-8.
• Pak TR, Chacko KI, O'Donnell T, Huprikar SS, van Bakel H, Kasarskis A, Scott ER.
  Estimating Local Costs Associated With Clostridium difficile Infection Using Machine Learning and Electronic Medical Records.
  Infect Control Hosp Epidemiol. 2017 Nov 6:1-9.
• Navarro JAR, Phillips-Mora W, Arciniegas-Leal A, Mata-QuirósA, Haiminen N, Mustiga G, Livingstone-III D, van Bakel H, Kuhn DN, Parida L, Kasarskis A and Motamayor JC.
  Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases.
  Front Plant Sci. 14 Nov 2017
• Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang ZZ, Laffleur B, Kaake RM, McGregor MJ, Haas K, Pefanis E, Albrecht RA, Pache L, Chanda S, Jen J, Ochando J, Byun M, Basu U, García-Sastre A, Krogan N, van Bakel H, Marazzi I.
  The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity.
  Cell. 2017 May 4;169(4):679-692.e14.
• Gonzalez-Reiche AS, Nelson MI, Angel M, Müller ML, Ortiz L, Dutta J, van Bakel H, Cordon-Rosales C, Perez DR.
  Evidence of Intercontinental Spread and Uncommon Variants of Low-Pathogenicity Avian Influenza Viruses in Ducks Overwintering in Guatemala.
  mSphere. 2017 Apr 5;2(2).

2016

• Barriga GP, Boric-Bargetto D, Cortez-San Martin M, Neira V, van Bakel H, Thompsom M, Tapia R, Toro-Ascuy D, Moreno L, Vasquez Y, Sallaberry M, Torres-Pérez F, González-Acuña D, and Medina RA.
  Avian influenza virus H5 strain with North American and Eurasian lineage genes in an Antarctic penguin.
  Emerg Infect Dis. 2016 Dec.
• Mena I, Nelson MI, Quezada-Monroy F, Dutta J, Cortes-Fernández R, Lara-Puente JH, Castro-Peralta F, Cunha LF, Trovão NS, Lozano-Dubernard B, Rambaut A, van Bakel H, García-Sastre A.
  Origins of the 2009 H1N1 influenza pandemic in swine in Mexico.
  eLife, 2016; 5 DOI: 10.7554/eLife.16777
• Brinkley JF, Fisher S, Harris MP, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Maas RL, Marazita ML, Selleri L, Spritz RA, van Bakel H, Visel A, Williams TJ, Wysocka J; FaceBase Consortium, Chai Y.
  The FaceBase Consortium: A comprehensive resource for craniofacial researchers.
  Development. 2016 Jun 10. pii: dev.135434.
• Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JS, Martinez-Gil L, Fenouil R, Chen X, Edwards M, Metreveli G, Jordan S, Peralta Z, Munoz-Fontela C, Bouvier N, Merad M, Jin J, Weirauch M, Heinz S, Benner C, van Bakel H, Basler C, García-Sastre A, Bukreyev A, Marazzi I.
  Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation.
  Science. 2016 Apr 28. pii: aad7993.
• Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist JF, Noel J, Sachs DH, Hamilton J, Leon PE, Chawdury A, Tripathi S, Melegari C, Campisi L, Hai R, Metreveli G, Gamarnik AV, García-Sastre A, Greenbaum B, Simon V, Fernandez-Sesma A, Krogan NJ, Mulder LC, van Bakel H, Tortorella D, Taunton J, Palese P, Marazzi I.
  Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection.
  Immunity 2016 Jan 19;44(1):46-58. doi: 10.1016/j.immuni.2015.12.017

2015

• The PsychENCODE project consortium
  The PsychENCODE project.
  Nat Neurosci. 2015 Nov 25;18(12):1707-12. doi: 10.1038/nn.4156.
• Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G, Hand J, Patel G, Wallach F, Schadt EE, Huprikar S, van Bakel H, Kasarskis A, Bashir A.
  Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia.
  Antimicrob Agents Chemother. 2015 Aug 31. pii: AAC.01723-15.
• Miller MS, Rialdi A, Ho JSY, Tilove M, Martinez-Gil L, Moshkina NP, Peralta Z, Noel J, Melegari C, Maestre AM, Mitsopoulos P, Madrenas J, Heinz S, Benner C, Young JAT, Feagins AR, Basler C, Fernandez-Sesma A, Becherel OJ, Lavin MF, Harm van Bakel*†, Ivan Marazzi*†.
  Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis.
  Nat Immunol. 2015 Mar 30;doi:10.1038/ni.3132
  • Press coverage includes: Fox News, Alzforum, ALS News Today, Neuroscience News
• Devos M, Mommaerts E, Migeot V, van Bakel H, Hermand D
  Fission yeast Cdk7 controls gene expression through both its CAK and CTD kinase activities.
  Mol Cell Biol. 2015 Feb 17; doi:10.1128/MCB.00024-15
• Nonnenmacher M, van Bakel H, Hajjar RJ, Weber T.
  High Capsid-Genome Correlation Facilitates Creation of AAV Libraries for Directed Evolution.
  Mol Ther. 2015 Jan 13; doi:10.1038/mt.2015.3

2014

• Holmes G, van Bakel H, Zhou X, Losic B, Jabs EW.
  BCL11B expression in intramembranous osteogenesis during murine craniofacial suture development.
  Gene Expr Patterns. 2014 Dec 12;17(1):16-25.
• Teixeira A, Yen B, Gusella GL, Thomas AG, Mullen MP, Aberg J, Chen X, Hoshida Y, van Bakel H, Schadt E, Basler CF, García-Sastre A, Mosoian A
  Prothymosin alpha variants isolated from CD8+ T cells and cervicovaginal fluids suppress HIV replication through type I IFN induction.
  J Infect Dis. 2014 Nov 17. doi:10.1093/infdis/jiu643
• Altman DR*, Sebra R*, Hand J, Attie O, Deikus G, Carpini KWD, Patel G, Rana M, Arvelakis A, Grewal P, Dutta J, Rose H, Shopsin B, Daefler S, Schadt E, Kasarskis A, van Bakel H*, Bashir A*, Huprikar S*.
  Transmission of Methicillin-Resistant Staphylococcus aureus via Deceased Donor Liver Transplantation Confirmed by Whole Genome Sequencing
  Am J Transplant. 2014 Sep 22. doi: 10.1111/ajt.12897
• Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR.
  Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity.
  Cell. 2014 Sep 11;158(6):1431-1443.
• Kemmeren P, Sameith K, van de Pasch LA, Benschop JJ, Lenstra TL, Margaritis T, O'Duibhir E, Apweiler E, van Wageningen S, Ko CW, van Heesch S, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ, Bouwmeester D, van Hooff SR, van Bakel H, Sluiters E, Bakker LV, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Holstege FC
  Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.
  Cell. 2014 Apr 24;157(3):740-52.
• Bongers G, Pacer ME, Geraldino TH, Chen L, He Z, Hashimoto D, Furtado GC, Ochando J, Kelley KA, Clemente JC, Merad M, van Bakel H, Lira SA.
  Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice.
  J Exp Med. 2014 March 3
  • Insight by Christian Jobin: Do bugs define cancer geography?
  • Press coverage includes: The Scientist

2013

• Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, van Bakel H, Schadt EE, Reijo-Pera RA, Underwood JG, Wong WH.
  Characterization of the human ESC transcriptome by hybrid sequencing.
  Proc Natl Acad Sci U S A. 2013 Nov 26.
• de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR.
  A unified model for yeast transcript definition.
  Genome Res. 2013 Oct 29.
• van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, Nislow C.
  A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription.
  PLoS Genet. 2013 May;9(5):e1003479.
• Srikumar T, Lewicki MC, Costanzo M, Tkach JM, van Bakel H, Tsui K, Johnson ES, Brown GW, Andrews BJ, Boone C, Giaever G, Nislow C and Raught B.
  Global analysis of SUMO chain function reveals multiple roles in chromatin regulation.
  J Cell Biol. 2013 Apr 1;201(1):145-63.

2012

• Xu M, Soloveychik M, Ranger M, Schertzberg M, Shah Z, Raisner R, Venkatasubrahmanyan S, Tsui K, Gebbia M, Hughes T, van Bakel H, Nislow C, Madhani HD, Meneghini MD.
  Timing of Transcriptional Quiescence during Gametogenesis Is Controlled by Global Histone H3K4 Demethylation.
  Dev Cell. 2012 Nov 13;23(5):1059-71.
• Drogat J, Migeot V, Mommaerts E, Mullier C, Dieu M, van Bakel H, Hermand D.
  Cdk11-CyclinL Controls the Assembly of the RNA Polymerase II Mediator Complex.
  Cell Rep. 2012 Nov 29;2(5):1068-76.

 

2011

• Kurat CF, Lambert JP, van Dyk D, Tsui K, van Bakel H, Kaluarachchi S, Friesen H, Kainth P, Nislow C, Figeys D, Fillingham J, Andrews BJ.
  Restriction of histone gene transcription to S‐phase by phosphorylation of a chromatin boundary protein.
  Genes Dev. 2011 Dec 1;25(23):2489-501.
• van Bakel H, Stout JM, Cote A, Tallon CM, Sharpe AG, Hughes TR, Page JE.
  The draft genome and transcriptome of Cannabis sativa.
  Genome Biol. 2011 Oct 20;12(10):R102.
  • With editorial by Naomi Attar: How hemp got high.
  • Press coverage includes: Nature News, ScienceShot, Science Daily, NBC News, Huffington Post, CBC News, The Globe and Mail, OpenHelix Blog, GenomeWeb, Volkskrant
• van Bakel H, Nislow C, Blencowe BJ, Hughes TR.
  Response to "The Reality of Pervasive Transcription".
  PLoS Biol. 2011 Jul 12;9(7): e1001102.
• Lam KN, van Bakel H, Cote A, van der Ven A, Hughes TR.
  Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays.
  Nucl Acids Res. 2011 Jun;39(11):4680-90.
• Stead MB, Marshburn S, Mitra J, Pena-Castillo L, Ray D, van Bakel H, Hughes TR, Kushner SR.
  Analysis of E. coli RNase E and RNase III activity in vivo using tiling microarrays.
  Nucleic Acids Res. 2011 Apr;39(8):3188-203.
• van Bakel H.
  Interactions of transcription factors with chromatin.
  Subcell Biochem. 2011 52:223-59.

2010

• van Bakel H, Nislow C, Blencowe B, Hughes TR.
  Most "Dark Matter" transcripts are associated with known genes.
  PLoS Biol. 2010 May 18;8(5):e1000371.
  • With editorial by Richard Robinson: Dark Matter Transcripts: Sound and Fury, Signifying Nothing?
  • With comments in: Nature Reviews Genetics, Nature Methods
  • Press coverage includes: Nature News
• van Bakel H*, Coudreuse D*, Dewez M, Soutourina J, Parnell T, Vandenhaute J, Cairns B, Werner M and Hermand D.
  A gene-specific requirement of RNA polymerase II CTD phosphorylation on serine 2 for sexual differentiation in fission yeast.
  Current Biol. 2010 Jun 22;20(12):1053-64.
• Gordon BRG, Li Y, Wanga L, Sintsovaa A, van Bakel H, Tian S, Navarre WW, Xia B, and Liu J.
  Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis.
  Proc Natl Acad Sci USA. 2010 Mar 16;107(11):5154-9.

2009

• van Bakel H*, Khanna M*, Calarco JA, Babak T, Guo G, Emili A, Greenblatt J, Hughes TR, Krogan N and Blencowe B.
  A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.
  RNA. 2009 Dec;15(12):2174-85.
• van Bakel H, Hughes TR.
  Establishing legitimacy and function in the new transcriptome.
  Brief Funct Genomic Proteomic. 2009 Nov;8(6):424-36.
• Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J, Andrews BJ.
  A two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression.
  Mol Cell. 2009 Aug 14;35(3):340-51.

2008

• Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Yeo AL, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, and Hughes TR.
  A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.
  Mol Cell. 2008 Dec 26;32(6):878-87.
• van Werven FJ, van Bakel H, van Teeffelen HAAM, Altelaar AF, Groot Koerkamp M, Heck AJR, Holstege FCP and Timmers M.
  Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome.
  Genes Dev. 2008 Sep 1;22(17):2359-69.
• van Bakel H*, van Werven F*, Radonjic M, Brok M, van Leenen D, Holstege FCP, Timmers M.
  Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification.
  Nucl Acids Res. 2008 Mar;36(4):e21.

2007

• van Bakel H*†, Rustici G*, Holstege FCP, Wijmenga C, Bahler J.
  Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
  Genome Biol. 2007;8(5):R73.
• Diosdado B, van Bakel H, Strengman E, Franke L, van Oort E, Mulder CJ, Wijmenga C, Wapenaar MC.
  Neutrophil recruitment and barrier impairment in celiac disease: a genomic study.
  Clin Gastroenterol Hepatol. 2007 May;5(5):574-81.
• Muller P, van Bakel H, van de Sluis B, Holstege F, Wijmenga C, Klomp LW.
  Gene expression profiling of liver cells after copper overload in vivo and in vitro reveals new copper-regulated genes.
  J Biol Inorg Chem. 2007 May;12(4):495-507.

2006

• van Bakel H, Wijmenga C.
  Family matters: gene regulation by metal-dependent transcription factors.
  Top Curr Genet. 2006;14:341-94.
• Franke L, van Bakel H, Fokkens L, de Jong E, Peterson M, Wijmenga C.
  Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes.
  Am J Hum Genet. 2006 Jun;78(6):1011-25.

2005

• van Bakel H, Strengman E, Wijmenga C, Holstege FCP.
  Gene expression profiling and phenotype analyses of S. cerevisiae in response to changing copper reveals six genes with new roles in copper and iron metabolism.
  Physiol Genomics. 2005 Aug 11;22(3):356-67.
• van de Peppel J, Kettelarij N, van Bakel H, Kockelkorn TTJP, van Leenen D, Holstege FCP.
  Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets.
  Mol Cell. 2005 Aug 19;19(4):511-22.

2004

• van Bakel H, Holstege FCP.
  In control: systematic assessment of microarray performance.
  EMBO Rep. 2004 Oct;5(10):964-9.
• Franke L, van Bakel H, Diosdado B, van Belzen M, Wapenaar M, Wijmenga C.
  Team: a tool for the integration of expression, and linkage and association maps.
  Eur J Hum Genet. 2004 Aug;12(8):633-8.

2003

• van Bakel H, Huynen M, Wijmenga C.
  Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway.
  Bioinformatics. 2004 Nov 1;20(16):2644-55.
• van Tilburg JH, Wijmenga C, van Bakel H, Rozeman L, Pearson PL, van Haeften TW.
  Relationship of beta2-adrenergic receptor polymorphism with obesity in type 2 diabetes.
  Diabetes Care. 2003 Jan;26(1):251-2.
• van de Peppel J, Kemmeren P, van Bakel H, Radonjic M, van Leenen D, Holstege FCP.
  Monitoring global messenger RNA changes in externally controlled microarray experiments.
  EMBO Rep. 2003 Apr;4(4):387-93.

2002

• Staal FJ, van der Luijt RB, Baert MR, van Drunen J, van Bakel H, Peters E, de Valk I, van Amstel HK, Taphoorn MJ, Jansen GH, van Veelen CW, Burgering B, Staal GE.
  A novel germline mutation of PTEN associated with brain tumours of multiple lineages.
  Br J Cancer. 2002 May 20;86(10):1586-91.