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John J. Cotter

Fax +1.617.261.3175
John Cotter concentrates his practice in patent and complex intellectual property trials and appeals. He has tried patent, trademark, and other IP cases and argued Markman and summary judgment hearings; argued appeals at the Federal, First, and Eleventh Circuits; handled inter partes disputes at the U.S. Patent and Trademark Office; and has taken U.S. and overseas arbitrations to judgment.

Mr. Cotter’s patent cases have involved technologies including HIV antiviral drugs; electronic and optical switching technology; wireless and mobile communications; medical ventilators and blood analyzers; diagnostic medical tests; software and computer systems for FDA clinical trials, medical records, and security; and surgical devices. He advises clients on IP strategy, rights ownership, indemnification, and licensing; internal investigations involving technology and trade secrets; Hatch-Waxman/ANDA patent litigation; exemptions from infringement for FDA-related activities; and global litigation strategies.

Mr. Cotter’s trademark litigation experience spans from internationally famous to regional and niche brands, for consumer and industrial products, pharmaceuticals, and medical instruments. In the copyright, licensing, trade secrets, and internet areas, John has litigated the leading case on internet trespass; a pro bono artists’ and musicians’ rights lawsuit resulting in the City of Boston rescinding unconstitutional regulations; entertainment and patent royalty disputes, and software copyright cases including under the Digital Millennium Copyright Act.

His pro bono work also includes trying cases for political asylum seekers in immigration court, and assisting victims of cyber harassment.

Professional Background

Mr. Cotter was K&L Gates’ first firm-wide practice group coordinator for intellectual property litigation from 2006-2011. Prior to joining K&L Gates, he was the co-chair of and partner in the patent and intellectual property practice group of Testa, Hurwitz & Thibeault, LLP. Prior to practicing law, Mr. Cotter was an engineer with General Electric’s Aircraft Engine Group.


  • Best Lawyers in America, Litigation - Intellectual Property, 2013 - 2020; Litigation - Patent, 2014 - 2018

Professional/Civic Activities

  • American Bar Association (Intellectual Property Law and Litigation Sections)
  • American Intellectual Property Law Association
  • Boston Bar Association
  • Federal Circuit Bar Association
  • Intellectual Property Owners Association
  • International Trademark Association
  • New York Intellectual Property Law Association

Speaking Engagements

Mr. Cotter has spoken before client, legal, and industry groups including the International Trademark Association (INTA), the Biotechnology Industry Organization (BIO), the Boston Patent Law Association, the Practicing Law Institute, the Licensing Executives Society (LES), and law schools and universities. Examples include:
  • “What to Look for in Contingency Fee Arrangements When Deciding to Enforce University Patent Rights,” Association of University Technology Managers (AUTM) Eastern Region Meeting, Raleigh, NC October 4, 2019.
  • “Today’s Legal Challenges in R&D – Review of Recent Litigation and IP Protection in Field Research,” Client Seminar, Irvine, CA, April 17, 2019.
  • "Primer on Intellectual Property Law for Advertising and Marketing," Client Seminar, Boston, MA, March 2014.
  • Leahy-Smith America Invents Act: One Year Later”, Client CLE Presentation at annual meeting of in-house IP lawyers, Franklinton NC, October 2013.
  • "Securing and Defending IP Rights," European Private Equity and Venture Capital Association (EVCA), Course for Investment Professionals, Paris, France, April 23, 2009.
  • "Hot Topics in Patent Litigation," Client CLE Presentation, Reston, VA, November 12, 2007.
  • "The Changing World of Intellectual Property Law," Financial Technology Forum (a division of Institutional Investor, Inc.), Boston, MA, November 16, 2005.
  • "Intellectual Property Insurance and Risk Management Strategies," Licensing Executives Society, Boston, October 20, 2004.
  • "Hatch Waxman Patent Litigation Update," S.G. Cowen & Co. 7th Annual Pharmaceutical and Biotechnology Therapeutic Categories Review Conference and 4th Patent Forum, New York, October 12-13, 2004.
  • Host for International Trademark Association Roundtables, Boston, various dates, 2000-2003.
  • "Clickwrap and Click-Through; Licensing and Contract Issues," Harvard University Extension School, Cambridge, MA, April 14, 2003.
  • "Avoiding Evidence Pitfalls: Demonstrative Evidence," Macaronis Institute for Trial and Appellate Advocacy, Suffolk University Law School, Boston, April 17, 2003.
  • "Unwanted Access: Online Trespass and Other Contact," ABA’s National Cybercrime Conference at John Marshall Law School, Chicago, May 10, 2002.
  • "I.P. for I.T.," Northeastern University's High Tech MBA Program, Dedham, MA, June 1, 2002.
  • "Pharmaceutical and Health Care Breakout Session," International Trademark Association Annual Meeting, San Francisco, May 7, 2001.
  • "Fair Use, Public Domain or Privacy? Should the Digital Exchange of Copyrighted Works be Permitted or Prevented?," Fordham University Law School's Symposium on Digital Exchange of Copyrighted Works, New York, October 6, 2000, transcript published at Vol. IX, No. 2, Fordham Intellectual Property, Media, and Entertainment Law Journal, Winter 2001.
  • "Using and Misusing Third Party Resources," Practising Law Institute's 5th Annual Internet Law Institute, New York, July 9, 2001.
  • "The Infringement Continuum: The Expanding Definitional View," American Conference Institute's Intellectual Property on the Internet Seminar, Washington, D.C., November 14, 2000.
  • "Property Rights in Cyberspace," Yale Law School's Law and Technology Society Roundtable, New Haven, November 13, 2000.
  • "Trademark Law," Suffolk University Law School, Boston, Fall 1999.
  • "Patent Infringement Risks:  Financial Consequences and Funding Remedies," Biotechnology Industry Organization BIO ’98 Conference, New York, June 18, 1998.
  • "Selected Permanent Injunction Issues in Patent Litigation," Boston Patent Law Association Litigation Committee Seminar, Boston, April 8, 1998.
  • "Development, Enforcement and Defensive Strategies for Intellectual Property," Conference on Latest Developments in Intellectual Property, Burlington, MA, March 19, 1998.

Additional Information

  • Quoted in "Technology Cases to Watch in 2008," Technology Law 360, Portfolio Media, January 1, 2008.
  • Quoted in "Let the Music Play," Boston Globe Magazine, May 15, 2005.
  • Quoted in "Sidewalk shows must go on: Hub give street performers a pass – for now," by J. M. Lawrence, Boston Herald, December 23, 2004.
  • Quoted in "Singers sue city, say they're harassed," by Shelley Murphy, Boston Globe, July 24,2004, and in "Street performers sue, claiming harassment," by The Associated Press, Sarasota Herald-Tribune, Florida, July 24, 2004.
  • Quoted in "Suggestions to Overhaul U.S. Patent System Questioned," by Linda Goodspeed, Boston Business. Journal, June 4-10, 2004.
  • Quoted in "Lemelson Patents Ruled Invalid, Unenforceable and Not Infringed," by Daniel S. Burgess, Photonics Spectra, March 2004.
  • Quoted in "On the Docket: Digital Copyright Act, Pharmaceutical Disputes Will Define IP Battles," by Sheri Qualters, Boston Business Journal, September 5-11, 2003.
  • Mentioned in "At the Bar: Lawyering Can Turn Into a Real Lifesaver," by Maggie Mulvihill, Boston Herald, July 1, 2003.
  • Mentioned in "Hearsay" column, by Jeanne Greeley, Massachusetts Lawyer's Weekly, June 30, 2003.
  • Quoted in "Plug Pulled on File-Sharing Students," by Monty Phan, New York Newsday, April 27, 2003.
    Mentioned in "eBay's Behind the Scenes Move," by Victoria Slind-Flor, National Law Journal, August 7, 2000.
  • Quoted in Computer & Internet Lawcast, Vol. 11, No. 12, Week of July 10, 2000.
  • Quoted in "Bid for Fair Practice: Online auctioneer gains business from link site but doesn't want e-shoppers using the back door," by Debra Baker, ABA Journal, April 2000.
  • “Court decisions limit reach of certain method patents,” Boston Business Journal, September 2008
  • “The Inequitable Conduct Defense: Still a Real Issue,” The International Chamber of Commerce, United Kingdom Members Handbook, Cyworks, 2004.
  • “U.S. Patent Appeals Court Marks 20th Anniversary,” The Lawyers Weekly (Canada), November 29, 2002.
  • “New Protection for Databases - When?,” Intellectual Property Observer, Winter 2002.
  • “Unwanted Access: Online Trespass and Other Contact,” ABA’s National Cybercrime Conference Course Handbook, 2002.
  • “Avoid Negotiating Your Company Into an IP Lawsuit,” Intellectual Property Observer, Summer 2001.
  • “Using and Misusing Third Party Resources,” Practicing Law Institute’s Fifth Annual Internet Law Institute Course Handbook, 2001.
  • “Supreme Court Decides ‘On Sale’ Patent Case,” Venture Update, Summer 1999.
Trial Courts
  • Meddaugh v. WGBH Educational Foundation (Mass. Superior Ct. and Mass. App. Ct.). Tried case for defendant WGBH against claims that WGBH owed $19 million in allegedly unpaid royalties for the Martha Speaks animated public TV series based on books by author Susan Meddaugh. After trial, court entered judgment in 2018 of no actual damages and $100 in nominal damages.
  • CVS Pharmacy, Inc. v. John Lavin (D. R.I. and 1st Cir.). Representing former CVS executive John Lavin, who was hired by Amazon’s online retail pharmacy unit PillPack, LLC, in dispute over non-compete agreement.
  • Alnylam Pharmaceuticals, Inc. v. Silence Therapeutics plc (D. Mass.). Represented Alnylam in seeking declaratory judgment of non-infringement of five Silence Therapeutics patents by Alnylam’s RNAi therapeutic ONPATTRO™ (patisiran).
  • Walker v. AMVAC Chemical Company (M.D. Tenn. and C.D. Cal.). Defended AMVAC in inventorship and royalty dispute relating to AMVAC’s patent for an herbicide. Case settled after AMVAC obtained order transferring case to C.D. Cal.
  • Accusoft Corporation v. Quest Diagnostics, Inc. (D. Mass.). Defended Quest Diagnostics and its software subsidiary in software copyright and license royalty dispute. Case settled after obtaining partial summary judgment for Quest.
  • Source Search Technology v. KAYAK Software Corporation (D. N.J. and Fed. Cir.). Defended on line travel provider KAYAK in patent infringement suit involving travel services software systems. Obtained partial summary judgment of patent invalidity and non-infringement, final summary judgment of patent ineligibility, exceptional case order, and fee award. Affirmed on appeal.
  • Loken-Flack, LLC v. Novozymes Bioag, Inc. (D. Colo.). Obtained summary judgment of correct inventorship for defendant Novozymes regarding Novozymes’ patent for a crop treatment compound. Affirmed on appeal).
  • Gammino v. Sprint (E.D. Pa. and Fed. Cir.). Defended Sprint Nextel Corporation in patent Infringement case involving telephone switching systems. After partial summary judgment for Sprint and Nextel, and two day evidentiary Markman hearing and order, plaintiff agreed to final judgment of non-infringement by Sprint. Affirmed on appeal
  • Knopp Neurosciences Inc. v. Biogen Idec (D. Mass.) Represented Knopp in a patent license and breach of R&D contract action involving Knopp’s and Biogen’s joint development of dexpramipexole for treating ALS.
  • G. Pohl-Boskamp GmbH v. Akrimax (D. Mass.) and G. Pohl-Boskamp GmbH v. Perrigo (D. Mass.): Asserted German pharmaceutical maker Pohl-Boskamp’s Nitrolingual pumpspray trade dress and copyrights against competitor and generic manufacturer.
  • Instrumentation Laboratory v. Diamond Diagnostics (D. Mass.): Represented Instrumentation Laboratory in suit asserting infringement by Diamond Diagnostics’ own blood testing machine and infringement and counterfeiting by Diamond’s unauthorized refurbishment and resale of used Instrumentation Laboratory critical care machines.
  • PUMA AG and PUMA North America v. Payless Shoesource (D. Mass.) and PUMA AG and PUMA North America v. K-Swiss, Inc. (D.Mass. and C.D. Cal.). Asserted PUMA’s form stripe trade dress against infringers.
  • MOAEC, Inc. v. Napster, LLC (W.D. Wis.). Obtained summary judgment of patent non-infringement for digital music service Napster.
  • Technology Research Corporation v. Tower Manufacturing Corporation and Fedders Corporation (MD Fla.). Defended Tower Manufacturing and Fedders in patent infringement case involving fault tolerant circuits. Settled after two day hearing and Markman/summary judgment order.
  • Tower Manufacturing Company v. Shanghai ELE Mfg. Co. (D. R.I. and SDNY). Represented designer of safety circuits in patent infringement action against infringer.
  • Convera Corporation v. Autonomy (E.D. Va). Represented Convera in trade secret and breach of contract action.
  • Kozam and Datasci v. Phase Forward Incorporated (D. Md.). Defended leading maker of clinical trial software for collecting clinical trial data and FDA submission. Case settled after Markman and summary judgment hearing and orders.
  • eBay, Inc. v. Bidder’s Edge, Inc. (N.D. Cal.). Represented Bidder’s Edge in case involving issue of first impression regarding alleged trespass to chattels based on web crawling, and antitrust counterclaims against eBay.
  • Massachusetts Eye and Ear Infirmary v. QLT Phototherapeutics, Inc. and Novartis (D. Mass.). Represented Mass. Eye and Ear in patent portfolio development strategy for age related macular degeneration surgical procedure, and filed patent infringement action and license and royalty action that resulted in significant royalty payment to Mass. Eye and Ear.
  • Digital Privacy, Inc. v. RSA Security, Inc. (E.D. Va.). Obtained summary judgment of patent non-infringement for RSA Security.
  • Beam Laser Systems, Inc. v. Cox Communications and SeaChange International, Inc. (E.D. Va.) Obtained summary judgment of patent non-infringement for Cox and SeaChange.
  • Boston Scientific Corp. v. Circon Corp. (D.Mass. and E.D. Wis.). Represented Boston Scientific in patent infringement disputes involving patents on both sides.
  • Micron Separations, Inc. v. Pall Corporation (D.Mass. Bkrtcy.). Represented plaintiff Micron Separations, Inc.in adversary proceeding trial seeking recoupment of overpaid royalties on patent settlement agreement relating to polymeric filter technology. Court granted $3.7 million judgment for Micron Separations and injunction against collection by defendant Pall Corporation.
  • Micron Separations, Inc. v. Pall Corporation (D. Mass.) Represented Micron Separations at trial for alleged infringement by Micron’s design around filter product. Settled after trial but before judgment was entered.
  • Arrow Fastener v. The Stanley Works (D. Conn.). Represented plaintiff Arrow Fastener in trial for Stanley’s infringement of Arrow’s T-50 trademark for staple guns. Trial judgment for Arrow.
  • Parker Labs v. Pharmaceutical Innovations (SDNY). Represented Parker Labs in obtaining preliminary injunction in trade dress infringement case.
  • Du Pont and C.R. Bard v. Schneider-Shiley (D. Mass.). Represented Du Pont in patent infringement action against Schneider alleging infringement of Du Pont’s patent to a balloon for coronary catheters.
Notable Appeals
  • Source Search Technology v. KAYAK Software Company (Fed. Cir.). Argued for appellee KAYAK in appeal of patent case fee award to KAYAK. Affirmed.
  • Loken-Flack v. Novozymes Bioag (Fed. Cir.). Argued for appellee Novozymes on appeal of inventorship judgment for Novozymes. Affirmed.
  • Gammino v. Sprint (Fed. Cir.). Argued for appellee Sprint on appeal of non-infringement judgment for Sprint. Affirmed.
  • In re Biondi et al. (Fed. Cir.). Argued for appellant Biondi et al.in appeal of Board decision affirming rejection of Biondi’s patent application claims to networked medical device monitoring systems.
  • In re QLT Phototherapeutics, Inc. (vs. Massachusetts Eye and Ear Infirmary) (Fed. Cir.). Represented district court plaintiff Massachusetts Eye and Ear Infirmary in successful opposition to QLT’s Federal Circuit mandamus petition seeking to overturn order compelling production of allegedly privileged communications that established royalties owed to the Infirmary.
  • CVS Pharmacy, Inc. v. John Lavin (1st Cir.). Argued for appellant John Lavin in appeal of preliminary injunction enjoining him from employment at online retail pharmacy PillPack LLC.
  • Bidder’s Edge v. eBay, Inc. (9th Cir.). Represented appellant Bidder’s Edge in appeal from N.D. Cal. decision of first impression preliminarily enjoining web crawling based on trespass to chattels.
  • Citrix Systems, Inc. v. GraphOn Corporation (11th Cir.). Argued appellant Citrix’s appeal of dismissal of declaratory judgment action for lack of subject matter jurisdiction.
  • France Telecom v. RSA Security (International Chamber of Commerce, International Court of Arbitration). Represented RSA Security in arbitration for alleged patent infringement and unpaid license royalties on patent for encryption technology
  • Du Pont and C.R. Bard v. Cordis (AAA Arbitration) Represented patent owner Du Pont in patent infringement case arbitrated before Fed. Cir. Judge (ret.) Howard Baldwin involving balloon catheter technology.
PTO and PTAB Matters
  • Novozymes Bioag: Interference, counsel for senior party/patent owner. PTAB issued judgment for senior party that junior party had not established joint inventorship, leaving inventors as named by senior party.
  • KAYAK Software Corporation: Reexamination certificate issued 03/21/2013 cancelling numerous claims and narrowing scope of other claims.
  • Polyera Corp.: Interference, counsel for junior party in dispute involving electronics materials.
  • Instrumentation Laboratory: Interference, counsel for junior party in action involving blood testing technology. 
  • Japan Energy Corp.: Interference, counsel for junior party. Judgment for junior party on patents and application to protease inhibitor technology.
Pro Bono
  • Community Arts Advocates v. City of Boston (D. Mass.) Brought action seeking preliminary injunction on behalf of street performers and musicians group to invalidate City of Boston regulations restricting members’ first amendment rights to perform in public spaces. After hearing, the City rescinded its unconstitutional regulations and instituted constitutional regulations.
  • Matter of Joseph Anacassus (USDOJ Executive Office for Immigration Review, US Immigration Court). Brought administrative action, including trial and appeal, seeking political asylum for activist from Haiti.
  • Matter of Rashid Juma (USDOJ Executive Office for Immigration Review, US Immigration Court). Brought administrative action and obtained trial judgment of political asylum and citizenship for victim of political violence and torture in Tanzania.
  • In re Paul Overby (Mass. Probate Court) Obtained order of conservancy for widow of investigative reporter Paul Overby who went missing and was presumed abducted and killed in Pakistan or Afghanistan.
  • Other pro bono representations include matters for visual artists and for victims of cyberporn harassment.